├── README.md
├── Results_main.m
├── Sample Data
├── Language Task Additional 100 sub
│ ├── Analysis
│ │ └── EmptyFile.txt
│ ├── Data Pos
│ │ ├── 300618
│ │ │ └── EmptyFile.txt
│ │ └── 300719
│ │ │ └── EmptyFile.txt
│ ├── Preprocessed Data
│ │ └── EmptyFile.txt
│ ├── Raw Data
│ │ ├── 300618
│ │ │ └── EmptyFile.txt
│ │ └── 300719
│ │ │ └── EmptyFile.txt
│ ├── Spiral Detected
│ │ └── EmptyFile.txt
│ └── TaskLabel
│ │ └── EmptyFile.txt
├── Language Task Original 100 sub
│ ├── Analysis
│ │ └── EmptyFile.txt
│ ├── Data Pos
│ │ ├── 100206
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ │ └── 100610
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Preprocessed Data
│ │ └── EmptyFile.txt
│ ├── Raw Data
│ │ ├── 300618
│ │ │ └── EmptyFile.txt
│ │ └── 300719
│ │ │ └── EmptyFile.txt
│ ├── Spiral Detected
│ │ └── EmptyFile.txt
│ └── TaskLabel
│ │ └── EmptyFile.txt
├── Resting
│ ├── Analysis
│ │ └── EmptyFile.txt
│ ├── Data Pos
│ │ ├── 100206
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ │ └── 100610
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Preprocessed Data
│ │ └── EmptyFile.txt
│ ├── Raw Data
│ │ ├── 100206
│ │ │ └── EmptyFile.txt
│ │ └── 100610
│ │ │ └── EmptyFile.txt
│ └── Spiral Detected
│ │ └── EmptyFile.txt
├── Working Memory Task
│ ├── Analysis
│ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Data Pos
│ │ ├── 100206
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ │ └── 100610
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Preprocessed Data
│ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Raw Data
│ │ ├── 100206
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ │ └── 100610
│ │ │ └── L.flat.32k_fs_LR.surf.gii
│ ├── Spiral Detected
│ │ └── L.flat.32k_fs_LR.surf.gii
│ └── TaskLabel
│ │ └── L.flat.32k_fs_LR.surf.gii
├── parcellation_template.mat
└── parcellation_template7.mat
├── Sub-function
├── PCA.m
├── PhaseVectorAngle_local_classifier.m
├── Preprocessing_main.m
├── TaskLabel_Extract.m
├── anglesubtract.m
├── bandpa_fMRI.m
├── cifti-matlab-master
│ ├── @gifti
│ │ ├── Contents.m
│ │ ├── display.m
│ │ ├── export.m
│ │ ├── fieldnames.m
│ │ ├── gifti.m
│ │ ├── isfield.m
│ │ ├── plot.m
│ │ ├── private
│ │ │ ├── Makefile
│ │ │ ├── Makefile.var
│ │ │ ├── base64decode.m
│ │ │ ├── base64encode.m
│ │ │ ├── getdict.m
│ │ │ ├── isintent.m
│ │ │ ├── miniz.c
│ │ │ ├── mvtk_write.m
│ │ │ ├── read_freesurfer_file.m
│ │ │ ├── read_gifti_file_standalone.m
│ │ │ ├── xml_parser.m
│ │ │ ├── zstream.c
│ │ │ └── zstream.m
│ │ ├── save.m
│ │ ├── saveas.m
│ │ ├── struct.m
│ │ ├── subsasgn.m
│ │ └── subsref.m
│ ├── @xmltree
│ │ ├── Contents.m
│ │ ├── add.m
│ │ ├── attributes.m
│ │ ├── branch.m
│ │ ├── char.m
│ │ ├── children.m
│ │ ├── convert.m
│ │ ├── copy.m
│ │ ├── delete.m
│ │ ├── display.m
│ │ ├── editor.m
│ │ ├── find.m
│ │ ├── flush.m
│ │ ├── get.m
│ │ ├── getfilename.m
│ │ ├── isfield.m
│ │ ├── length.m
│ │ ├── move.m
│ │ ├── parent.m
│ │ ├── private
│ │ │ ├── xml_findstr.c
│ │ │ ├── xml_findstr.m
│ │ │ ├── xml_findstr.mexa64
│ │ │ ├── xml_findstr.mexglx
│ │ │ ├── xml_findstr.mexmaci
│ │ │ ├── xml_findstr.mexmaci64
│ │ │ ├── xml_findstr.mexw32
│ │ │ ├── xml_findstr.mexw64
│ │ │ └── xml_parser.m
│ │ ├── root.m
│ │ ├── save.m
│ │ ├── set.m
│ │ ├── setfilename.m
│ │ └── xmltree.m
│ ├── GPL
│ ├── LICENSE.fieldtrip
│ ├── LICENSE.gifti
│ ├── LICENSE.xmltree
│ ├── README.md
│ ├── VERSION
│ ├── documentation
│ │ ├── CIFTI-2_Appendix_FINAL_1March2014.pdf
│ │ └── CIFTI-2_Main_FINAL_1March2014.pdf
│ ├── emptyfile.txt
│ ├── ft_read_cifti.m
│ ├── ft_write_cifti.m
│ ├── package.sh
│ └── private
│ │ ├── copyfields.m
│ │ ├── fetch_url.m
│ │ ├── filetype_check_extension.m
│ │ ├── filetype_check_header.m
│ │ ├── filetype_check_uri.m
│ │ ├── find_outermost_boundary.m
│ │ ├── fixname.m
│ │ ├── fixpos.m
│ │ ├── ft_convert_units.m
│ │ ├── ft_datatype.m
│ │ ├── ft_datatype_sens.m
│ │ ├── ft_estimate_units.m
│ │ ├── ft_filetype.m
│ │ ├── ft_getopt.m
│ │ ├── ft_getopt.mexa64
│ │ ├── ft_getopt.mexglx
│ │ ├── ft_getopt.mexmaci
│ │ ├── ft_getopt.mexmaci64
│ │ ├── ft_getopt.mexw32
│ │ ├── ft_getopt.mexw64
│ │ ├── ft_hastoolbox.m
│ │ ├── ft_read_header.m
│ │ ├── ft_read_headshape.m
│ │ ├── ft_read_mri.m
│ │ ├── ft_read_sens.m
│ │ ├── ft_read_vol.m
│ │ ├── ft_scalingfactor.m
│ │ ├── ft_senstype.m
│ │ ├── ft_struct2double.m
│ │ ├── ft_voltype.m
│ │ ├── ft_warning.m
│ │ ├── ft_warp_apply.m
│ │ ├── ft_write_headshape.m
│ │ ├── getdimord.m
│ │ ├── getdimsiz.m
│ │ ├── hasyokogawa.m
│ │ ├── individual2sn.m
│ │ ├── inflate_file.m
│ │ ├── istrue.m
│ │ ├── keepfields.m
│ │ ├── ndgrid.m
│ │ ├── pos2transform.m
│ │ ├── read_asa.m
│ │ ├── read_besa_sfp.m
│ │ ├── read_bti_hs.m
│ │ ├── read_bv_srf.m
│ │ ├── read_caret_spec.m
│ │ ├── read_ctf_hc.m
│ │ ├── read_ctf_pos.m
│ │ ├── read_ctf_shape.m
│ │ ├── read_neuromag_hc.m
│ │ ├── read_nifti2_hdr.m
│ │ ├── read_off.m
│ │ ├── read_ply.m
│ │ ├── read_polhemus_fil.m
│ │ ├── read_stl.m
│ │ ├── read_vtk.m
│ │ ├── read_yokogawa_header.m
│ │ ├── read_yokogawa_header_new.m
│ │ ├── refine.m
│ │ ├── removefields.m
│ │ ├── renamefields.m
│ │ ├── sn2individual.m
│ │ ├── surf_to_tetgen.m
│ │ ├── tokenize.m
│ │ ├── write_nifti2_hdr.m
│ │ ├── write_off.m
│ │ ├── write_ply.m
│ │ ├── write_stl.m
│ │ └── write_vtk.m
├── emptyfile.txt
├── load_fMRI.m
├── nanconv
│ ├── license.txt
│ └── nanconv.m
├── parcellation_template.mat
├── parcellation_template22_RightBrain_subject1-100.mat
├── parcellation_template7.mat
├── pattDetection_v4.m
├── preproc_fRMI.m
├── region_of_coordination_ROC.m
├── spaceFreq_fMRI.m
├── spiral_classifer_language_task.m
├── spiral_contrast_significance.m
├── spiral_detection_surfilt.m
├── spiral_distribution_zscore_map_speed_duration_radius_count.m
├── spiral_interaction_statistics.m
├── task_evoked_unfiltered_fMRI_signal.m
└── task_specific_spiral_distribution.m
└── Videos
├── Supplementary_Video_S1.avi
├── Supplementary_Video_S2.avi
├── Supplementary_Video_S3.avi
├── Supplementary_Video_S4.avi
├── Supplementary_Video_S5.avi
├── Supplementary_Video_S6.avi
└── Video captions.docx
/README.md:
--------------------------------------------------------------------------------
1 | # BrainVortexToolbox
2 | MATLAB toolbox to automatically detect and analyse spiral wave patterns in the fMRI data, developed by Dr. Pulin Gong's group at University of Sydney.
3 |
4 | ## Instructions for use
5 | System dependencies: N/A
6 | Software version: MATLAB 2016b and above (has been tested on MATLAB 2016b and 2020a)
7 | Hardware requirement: N/A
8 |
9 | Data format: fMRI data in standard CIFTI grayordinate space, comprising 32K cortical vertices
10 | Data tested: 100 subjects from the Human Connectomb Project (HCP)
[https://db.humanconnectome.org/data/projects/HCP_1200]
11 |
12 | ### Launch:
13 | Sample data is not avaialble in GitHub due to size limitation, please download from the HCP site link above. No subject ID is provided as all subjects should be selected randomly from a corhort of 1200 subjects.
14 |
15 | Please download all folders from this repository and allocate the raw fMRI data files (i.e., 'tfMRI_LANGUAGE_LR_Atlas.dtseries.nii') and structural data files (i.e.,'L.flat.32k_fs_LR.surf.gii') downloaded from HCP database into subfolders named by the subject ID under 'Raw Data' and 'Data Pos' folders, repectively. For task state data, please also download the task label files for each subject (witihn the 'EVs' subfolder next to the raw fMRI data file).
16 |
17 | For example, the data under subject ID 100206 recorded during a language task should be allocated in the following folders:
18 | Raw fMRI data: '/main_folder/Sample Data/Language Task Original 100 sub/Raw Data/100206/tfMRI_LANGUAGE_LR_Atlas.dtseries.nii';
19 | Structural data: '/main_folder/Sample Data/Language Task Original 100 sub/Data Pos/100206/L.flat.32k_fs_LR.surf.gii';
20 | Task label files: '/main_folder/Sample Data/Language Task Original 100 sub/Raw Data/100206/EVs/present_math.txt';
21 |
22 | Run 'Results_main.m' in matlab to generate key results and figures.
23 |
24 |
25 |
26 | ### Main function:
27 |
28 | Results_main.m (directory to all subfunctions, from preprocessing to spiral detection to sprial-based analysis)
29 |
30 | ### Subfunctions:
31 |
32 | Preprocessing_main.m (pre-preocessing of raw fMRI data with/without spatiotemporal bandpassfilters)
33 | load_fMRI.m
34 | preproc_fRMI.m
35 | spaceFreq_fMRI.m
36 | bandpa_fMRI.m
37 | ft_read_cifti.m
38 | gifti.m
39 |
40 | spiral_detection_surfilt.m (spiral detection and filtering based on the statistical test against the null model)
41 | anglesubtract.m
42 | pattDetection_v4.m
43 |
44 | spiral_distribution_zscore_map_speed_duration_radius_count.m (spiral distribution z-score map, propagation speed, duration, radius and spiral count)
45 |
46 | distance_vs_amplitude.m (relationship between fMRI amplitude and its distance to spiral centres)
47 |
48 | spiral_interaction_statistics.m (% proportion of spiral-spiral interactions among three interaction types)
49 |
50 | TaskLabel_Extract.m (extract task labels of each subject)
51 |
52 | task_specific_spiral_distribution.m (trial-averaged spiral distribution maps across all subjects under each task condition)
53 |
54 | spiral_contrast_significance.m (spiral contrast significance maps between different task conditions and their density in 7 functional networks)
55 |
56 | spiral_classifer_language_task.m (spiral centre-based linear classifier)
57 |
58 | task_evoked_unfiltered_fMRI_signal.m (spiral detection based on task-evoked trial-averaged unfiltered fMRI signals)
59 |
60 | PCA.m (principle component analysis of the regional rotational dynamics in the task-evoked trial-averaged unfiltered fMRI signals)
61 |
62 | region_of_coordination_ROC.m (identification of the ROC)
63 |
64 | PhaseVectorAngle_local_classifier.m (local phase vector field-based linear classifier)
65 |
66 | ## Expected output
67 | Key figures in the paper "Interacting spiral wave patterns underlie complex brain dynamics and are related to cognitive processing" will be generated.
68 |
69 | figure 2d. Population-combined z-score maps of brain spiral density in the flattened left cortex
70 | spiral_distribution_zscore_map_speed_duration_radius_count.m
71 |
72 | figure 2e. fMRI amplitude vs. distance from singularity.
73 | distance_vs_amplitude.m
74 |
75 | figure 3e. spiral propagation speed distribution.
76 | spiral_distribution_zscore_map_speed_duration_radius_count.m
77 |
78 | figure 4a. spiral interaction type statistics.
79 | spiral_interaction_statistics.m
80 |
81 | figure 5 1st and 2nd columns. task-specific spiral distribution maps.
82 | task_specific_spiral_distribution.m
83 |
84 | figure 5 3rd column. spiral contrast significance maps.
85 | spiral_contrast_significance.m
86 |
87 | figure 6a. spiral contrast significance density across 7 functional networks.
88 | spiral_contrast_significance.m
89 |
90 | figure 6b-c. sprial centre-based linear classifer performances.
91 | spiral_classifer_language_task.m
92 |
93 | figure7a-c. sprial detected in task-evoked (trial-averaged) unfiltered fMRI signals.
94 | task_evoked_unfiltered_fMRI_signal.m
95 |
96 | figure7d. principle component analysis of the regional rotational dynamics in the task-evoked trial-averaged unfiltered fMRI signals.
97 | PCA.m
98 |
99 | figure8b & d. identification of the region of coordination (ROC).
100 | region_of_coordination_ROC.m
101 |
102 | figure8c. local phase vector field-based linear classifier.
103 | PhaseVectorAngle_local_classifier.m
104 |
105 |
106 |
107 | ## Authors
108 |
109 | * **Yiben Xu** - yixu4976@uni.sydney.edu.au
110 | * **Xian Long** - [Xian Long](https://github.com/longxian319)
111 | * **Pulin Gong** - pulin.gong@sydney.edu.au
112 |
113 |
114 |
115 |
116 |
117 |
118 |
119 |
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/Sample Data/parcellation_template.mat:
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/Sub-function/PCA.m:
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1 | function [score,latent] = PCA(flagSur,hemisphere,main_folder,No_of_Subject,flagTask,listen_or_answer,motor_or_PCC);
2 |
3 | %% PCA analysis of raw amplitude map, mathlisten 1-20
4 |
5 | % load task-evoked unfiltered trial averaged fMRI signal file
6 | foldername = [main_folder,'/Sample Data/Language Task Original 100 sub/Analysis'];
7 | cd(foldername)
8 | filename = ['task_evoked_unfiltered_fMRI_signal.mat'];
9 | load(filename)
10 |
11 | % min-max normalization
12 |
13 | data_math_listen_avg_max = nanmax(data_math_listen_avg,[],3);
14 | data_math_listen_avg_min = nanmin(data_math_listen_avg,[],3);
15 | data_math_listen_avg_minmaxnorm = (data_math_listen_avg-data_math_listen_avg_min)./(data_math_listen_avg_max-data_math_listen_avg_min);
16 |
17 | data_math_answer_avg_max = nanmax(data_math_answer_avg,[],3);
18 | data_math_answer_avg_min = nanmin(data_math_answer_avg,[],3);
19 | data_math_answer_avg_minmaxnorm = (data_math_answer_avg-data_math_answer_avg_min)./(data_math_answer_avg_max-data_math_answer_avg_min);
20 |
21 |
22 | %%
23 | if hemisphere == 1
24 | if listen_or_answer == 1
25 | if motor_or_PCC == 1
26 | temp1 = permute(data_math_listen_avg_minmaxnorm(90:120,110:140,:),[3,1,2]); % left-motor/premotor
27 | elseif motor_or_PCC == 2
28 | temp1 = permute(data_math_listen_avg_minmaxnorm(128:158,175:205,:),[3,1,2]); % left-PCC-listen
29 | end
30 | elseif listen_or_answer == 2
31 | temp1 = permute(data_math_answer_avg_minmaxnorm(90:120,110:140,:),[3,1,2]); % left-motor/premotor
32 | end
33 | elseif hemisphere == 2
34 | if listen_or_answer == 1
35 | if motor_or_PCC == 1
36 | temp1 = permute(data_math_listen_avg_minmaxnorm(105:135,120:150,:),[3,1,2]); % right-listen Mor
37 | elseif motor_or_PCC == 2
38 | temp1 = permute(data_math_listen_avg_minmaxnorm(128:158,65:95,:),[3,1,2]); % right-listen_PCC
39 | end
40 | elseif listen_or_answer == 2
41 | temp1 = permute(data_math_answer_avg_minmaxnorm(95:125,120:150,:),[3,1,2]); % right-listen PCC
42 | end
43 | end
44 | temp2 = reshape(temp1,20,[]);
45 |
46 | [coeff,score,latent,tsquared,explained,mu] = pca(temp2);
47 |
48 | figure();
49 | hold on
50 | for iTime = 1:1 %size(score,1)
51 | if hemisphere == 1
52 | if listen_or_answer == 1
53 | p = plot3(score(iTime:iTime+19,2),score(iTime:iTime+19,1),score(iTime:iTime+19,3),'b')
54 | p.LineWidth = 2;
55 | scatter3(score(1,2),score(1,1),score(1,3),35,'b','filled')
56 | elseif listen_or_answer == 2
57 | p = plot3(score(iTime:iTime+19,2),score(iTime:iTime+19,1),score(iTime:iTime+19,3),'b-')
58 | p.LineWidth = 2;
59 | scatter3(score(1,2),score(1,1),score(1,3),35,'b','filled')
60 | end
61 | elseif hemisphere == 2
62 | if listen_or_answer == 1
63 | p = plot3(score(iTime:iTime+19,2),score(iTime:iTime+19,1),score(iTime:iTime+19,3),'r')
64 | scatter3(score(1,2),score(1,1),score(1,3),35,'r','filled')
65 | p.LineWidth = 2;
66 | elseif listen_or_answer == 2
67 | p = plot3(score(iTime:iTime+19,2),score(iTime:iTime+19,1),score(iTime:iTime+19,3),'r-')
68 | p.LineWidth = 2;
69 | scatter3(score(1,2),score(1,1),score(1,3),35,'r','filled')
70 | end
71 | end
72 | xlim([-15,15])
73 | ylim([-15,15])
74 | % title(['task-evoked raw amplitude, listen 1-20, RIGHT PCC, PCA, PC1=',num2str(latent(1)),'% variance, PC2=',num2str(latent(2)),'%'])
75 | title(['task-evoked raw amplitude, math listen 1-20, LEFT M1-PMd, PCA, PC1=',num2str(latent(1)),'% variance, PC2=',num2str(latent(2)),'%'])
76 | end
77 |
78 |
79 | end
--------------------------------------------------------------------------------
/Sub-function/anglesubtract.m:
--------------------------------------------------------------------------------
1 | function xydiff = anglesubtract(x, y, angleFlag)
2 | % ANGLESUBTRACT Subtracts the matrix y from the equally sized matrix x and
3 | % returns a value between -pi and +pi. This is valid if x and y both
4 | % contain angular data in radians. If angleFlag is false, returns a
5 | % non-angular subtraction.
6 | %
7 | % Rory Townsend, Oct 2017
8 | % rory.townsend@sydney.edu.au
9 |
10 | % Assume input is angular if unspecified
11 | if nargin < 3
12 | angleFlag = 1;
13 | end
14 |
15 | if angleFlag == 1
16 | % METHOD 1: Modulo method
17 | xydiff = mod(x - y + pi, 2*pi) - pi;
18 |
19 | % METHOD 2: Trig method, works but is slower
20 | % xydiff2 = atan2(sin(x-y), cos(x-y));
21 |
22 | else
23 | xydiff = x - y;
24 | end
25 |
26 | end
--------------------------------------------------------------------------------
/Sub-function/bandpa_fMRI.m:
--------------------------------------------------------------------------------
1 | function [bandpasSig, hilbertSig, ampSig, phaseSig] = bandpa_fMRI(sigValid,fs,fLow,fHigh) ;
2 | % bandpass the fMRI data
3 | % output: bandpassSig, hilbertSig, ampSig, phaseSig
4 |
5 | % % Design Butterworth band-pass filter
6 | % h = fdesign.bandpass('N,F3dB1,F3dB2',6,fLow,fHigh,fs);
7 | % Hd = design(h, 'butter');
8 | % set(Hd, 'Arithmetic', 'double');
9 | %
10 | % SOS = Hd.sosMatrix;
11 | % G = Hd.ScaleValues;
12 |
13 | [z,p,k]=butter(4,[fLow fHigh]/(fs/2),'bandpass');
14 | % [z,p,k]=butter(4,[fLow]/(fs/2),'low');
15 | [sos,g]=zp2sos(z,p,k);
16 | [b, a]=butter(4,[fLow fHigh]/(fs/2),'bandpass');
17 | % [b, a]=butter(4,[fLow]/(fs/2),'low');
18 |
19 | badChannels = find(isnan(sigValid(:,1))==1) ;
20 | bandpasSig = nan(size(sigValid)) ;
21 | hilbertSig = nan(size(sigValid)) ;
22 | phaseSig = nan(size(sigValid)) ;
23 | ampSig = nan(size(sigValid)) ;
24 |
25 | % which filtfilt
26 | disp('start fitlering...');
27 | tic
28 | for iNode = setdiff(1:size(sigValid,1),badChannels)
29 | sigOriDemean = (sigValid(iNode,:)-mean(sigValid(iNode,:))) ;
30 | % bandpasSig(iNode,:) = filter(b,a,sigValid(iNode,:));
31 | bandpasSig(iNode,:) = filtfilt(sos,g,sigOriDemean); % may be corrupted by
32 | % fieldtrip toolbox
33 | hilbertSig(iNode,:) = hilbert(bandpasSig(iNode,:)) ;
34 | phaseSig(iNode,:) = angle(hilbertSig(iNode,:)) ;
35 | ampSig(iNode,:) = abs(hilbertSig(iNode,:)) ;
36 | end
37 | toc
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/Contents.m:
--------------------------------------------------------------------------------
1 | % GIfTI Class for MATLAB
2 | %
3 | % Geometry format under the Neuroimaging Informatics Technology Initiative
4 | % (NIfTI):
5 | % http://www.nitrc.org/projects/gifti/
6 | % http://nifti.nimh.nih.gov/
7 | %
8 | % This MATLAB class is part of SPM:
9 | % http://www.fil.ion.ucl.ac.uk/spm/
10 | %
11 | % It relies on external libraries:
12 | % Base64, by Peter J. Acklam:
13 | % http://home.online.no/~pjacklam/
14 | % miniz, by Rich Geldreich:
15 | % http://code.google.com/p/miniz/
16 | % XMLTree, by Guillaume Flandin:
17 | % http://www.artefact.tk/software/matlab/xml/
18 | %__________________________________________________________________________
19 | % Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
20 |
21 | % Guillaume Flandin
22 | % $Id: Contents.m 6404 2015-04-13 14:29:53Z guillaume $
23 |
24 | % GIfTI file format for MATLAB (The Mathworks, Inc.).
25 | % Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
26 | %
27 | % This program is free software; you can redistribute it and/or
28 | % modify it under the terms of the GNU General Public License
29 | % as published by the Free Software Foundation; either version 2
30 | % of the License, or any later version.
31 | %
32 | % This program is distributed in the hope that it will be useful,
33 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
34 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 | % GNU General Public License for more details.
36 | %
37 | % You should have received a copy of the GNU General Public License
38 | % along with this program; if not, write to the Free Software
39 | % Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/display.m:
--------------------------------------------------------------------------------
1 | function display(this)
2 | % Display method for GIfTI objects
3 | % FORMAT display(this)
4 | % this - GIfTI object
5 | %__________________________________________________________________________
6 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
7 |
8 | % Guillaume Flandin
9 | % $Id: display.m 4182 2011-02-01 12:29:09Z guillaume $
10 |
11 | display_name = inputname(1);
12 | if isempty(display_name)
13 | display_name = 'ans';
14 | end
15 |
16 | if length(this) == 1 && ~isempty(this.data)
17 | eval([display_name ' = struct(this);']);
18 | eval(['display(' display_name ');']);
19 | else
20 | disp(' ')
21 | disp([display_name ' =']);
22 | disp(' ');
23 | eval([display_name ' = this;']);
24 | eval(['disp(' display_name ');']);
25 | end
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/export.m:
--------------------------------------------------------------------------------
1 | function s = export(this,target)
2 | % Export a GIfTI object into specific MATLAB struct
3 | % FORMAT s = export(this,target)
4 | % this - GIfTI object
5 | % target - string describing target output [default: MATLAB]
6 | % s - a structure containing public fields of the object
7 | %__________________________________________________________________________
8 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
9 |
10 | % Guillaume Flandin
11 | % $Id: export.m 6401 2015-04-09 17:21:33Z guillaume $
12 |
13 | if numel(this) > 1, warning('Only handle scalar objects yet.'); end
14 |
15 | if nargin <= 1, target = 'MATLAB'; end
16 |
17 | switch lower(target)
18 | case 'matlab'
19 | s = struct(this);
20 |
21 | case 'patch'
22 | if isfield(this,'vertices')
23 | s.vertices = double(subsref(this, substruct('.', 'vertices')));
24 | end
25 | if isfield(this,'faces')
26 | s.faces = subsref(this, substruct('.', 'faces'));
27 | end
28 | if isfield(this,'cdata')
29 | s.facevertexcdata = double(subsref(this, substruct('.', 'cdata')));
30 | end
31 | try, s; catch, s = struct([]); end
32 |
33 | case {'fieldtrip', 'ft'}
34 | s = struct('tri',[], 'pnt',[]);
35 | if isfield(this,'vertices')
36 | s.pnt = double(subsref(this, substruct('.', 'vertices')));
37 | end
38 | if isfield(this,'faces')
39 | s.tri = double(subsref(this, substruct('.', 'faces')));
40 | end
41 |
42 | case {'spm'}
43 | s = struct('face',[], 'vert',[]);
44 | if isfield(this,'vertices')
45 | s.vert = double(subsref(this, substruct('.', 'vertices')));
46 | end
47 | if isfield(this,'faces')
48 | s.face = uint32(subsref(this, substruct('.', 'faces')));
49 | end
50 |
51 | otherwise
52 | error('Unknown target ''%s''.', target);
53 | end
54 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/fieldnames.m:
--------------------------------------------------------------------------------
1 | function names = fieldnames(this)
2 | % Fieldnames method for GIfTI objects
3 | % FORMAT names = fieldnames(this)
4 | % this - GIfTI object
5 | % names - field names
6 | %__________________________________________________________________________
7 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
8 |
9 | % Guillaume Flandin
10 | % $Id: fieldnames.m 6507 2015-07-24 16:48:02Z guillaume $
11 |
12 | if numel(this) > 1, warning('Only handle scalar objects yet.'); end
13 |
14 | pfn = {'vertices','faces','normals','cdata','mat','labels','indices'};
15 |
16 | names = unique(pfn(isintent(this,pfn)));
17 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/gifti.m:
--------------------------------------------------------------------------------
1 | function this = gifti(varargin)
2 | % GIfTI Geometry file format class
3 | % Geometry format under the Neuroimaging Informatics Technology Initiative
4 | % (NIfTI):
5 | % http://www.nitrc.org/projects/gifti/
6 | % http://nifti.nimh.nih.gov/
7 | %__________________________________________________________________________
8 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
9 |
10 | % Guillaume Flandin
11 | % $Id: gifti.m 6347 2015-02-24 17:59:16Z guillaume $
12 |
13 | switch nargin
14 |
15 | case 0
16 | this = giftistruct;
17 | this = class(this,'gifti');
18 |
19 | case 1
20 | if isa(varargin{1},'gifti')
21 | this = varargin{1};
22 |
23 | elseif isstruct(varargin{1})
24 | f = {'faces', 'face', 'tri' 'vertices', 'vert', 'pnt', 'cdata', 'indices'};
25 | ff = {'faces', 'faces', 'faces', 'vertices', 'vertices', 'vertices', 'cdata', 'indices'};
26 | [c, ia] = intersect(f,fieldnames(varargin{1}));
27 | if ~isempty(c)
28 | this = gifti;
29 | for i=1:length(c)
30 | this = subsasgn(this,...
31 | struct('type','.','subs',ff{ia(i)}),...
32 | varargin{1}.(c{i}));
33 | end
34 | elseif isempty(setxor(fieldnames(varargin{1}),...
35 | {'metadata','label','data'}))
36 | this = class(varargin{1},'gifti');
37 | else
38 | error('[GIFTI] Invalid structure.');
39 | end
40 |
41 | elseif ishandle(varargin{1})
42 | this = struct('vertices',get(varargin{1},'Vertices'), ...
43 | 'faces', get(varargin{1},'Faces'));
44 | if ~isempty(get(varargin{1},'FaceVertexCData'));
45 | this.cdata = get(varargin{1},'FaceVertexCData');
46 | end
47 | this = gifti(this);
48 |
49 | elseif isnumeric(varargin{1})
50 | this = gifti;
51 | this = subsasgn(this,...
52 | struct('type','.','subs','cdata'),...
53 | varargin{1});
54 |
55 | elseif ischar(varargin{1})
56 | if size(varargin{1},1)>1
57 | this = gifti(cellstr(varargin{1}));
58 | return;
59 | end
60 | [p,n,e] = fileparts(varargin{1});
61 | if strcmpi(e,'.mat')
62 | try
63 | this = gifti(load(varargin{1}));
64 | catch
65 | error('[GIFTI] Loading of file %s failed.', varargin{1});
66 | end
67 | elseif strcmpi(e,'.asc') || strcmpi(e,'.srf')
68 | this = read_freesurfer_file(varargin{1});
69 | this = gifti(this);
70 | else
71 | this = read_gifti_file_standalone(varargin{1},giftistruct);
72 | this = class(this,'gifti');
73 | end
74 |
75 | elseif iscellstr(varargin{1})
76 | fnames = varargin{1};
77 | this(numel(fnames)) = giftistruct;
78 | this = class(this,'gifti');
79 | for i=1:numel(fnames)
80 | this(i) = gifti(fnames{i});
81 | end
82 |
83 | else
84 | error('[GIFTI] Invalid object construction.');
85 | end
86 |
87 | otherwise
88 | error('[GIFTI] Invalid object construction.');
89 | end
90 |
91 | %==========================================================================
92 | function s = giftistruct
93 | s = struct(...
94 | 'metadata', ...
95 | struct(...
96 | 'name', {}, ...
97 | 'value', {} ...
98 | ), ...
99 | 'label', ...
100 | struct(...
101 | 'name', {}, ...
102 | 'index', {} ...
103 | ), ...
104 | 'data', ...
105 | struct(...
106 | 'attributes', {}, ...
107 | 'metadata', struct('name',{}, 'value',{}), ...
108 | 'space', {}, ...
109 | 'data', {} ...
110 | ) ...
111 | );
112 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/isfield.m:
--------------------------------------------------------------------------------
1 | function tf = isfield(this,field)
2 | % Isfield method for GIfTI objects
3 | % FORMAT tf = isfield(this,field)
4 | % this - GIfTI object
5 | % field - string of cell array
6 | % tf - logical array
7 | %__________________________________________________________________________
8 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
9 |
10 | % Guillaume Flandin
11 | % $Id: isfield.m 6507 2015-07-24 16:48:02Z guillaume $
12 |
13 | tf = ismember(field, fieldnames(this));
14 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/plot.m:
--------------------------------------------------------------------------------
1 | function varargout = plot(varargin)
2 | % plot method for GIfTI objects
3 | %__________________________________________________________________________
4 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
5 |
6 | % Guillaume Flandin
7 | % $Id: plot.m 5888 2014-02-19 19:54:12Z guillaume $
8 |
9 | % if ishandle(varargin{1})
10 | % h = figure(varargin{1});
11 | % else
12 | % h = figure;
13 | % %axis equal;
14 | % %axis off;
15 | % %camlight;
16 | % %camlight(-80,-10);
17 | % %lighting phong;
18 | % end
19 | % cameramenu;
20 |
21 |
22 | cdata = [];
23 | ax = [];
24 | if nargin == 1
25 | this = varargin{1};
26 | h = gcf;
27 | else
28 | if ishandle(varargin{1})
29 | ax = varargin{1};
30 | h = figure(get(ax,'parent'));
31 | this = varargin{2};
32 | else
33 | this = varargin{1};
34 | h = gcf;
35 | cdata = subsref(varargin{2},struct('type','.','subs','cdata'));
36 | end
37 | if nargin > 2
38 | indc = varargin{3};
39 | else
40 | indc = 1;
41 | end
42 | end
43 |
44 | if isempty(ax), ax = axes('Parent',h); end
45 | axis(ax,'equal');
46 | axis(ax,'off');
47 | hp = patch(struct(...
48 | 'vertices', subsref(this,struct('type','.','subs','vertices')),...
49 | 'faces', subsref(this,struct('type','.','subs','faces'))),...
50 | 'FaceColor', 'b',...
51 | 'EdgeColor', 'none',...
52 | 'Parent',ax);
53 |
54 | if ~isempty(cdata)
55 | set(hp,'FaceVertexCData',cdata(:,indc), 'FaceColor','interp')
56 | end
57 |
58 | axes(ax);
59 | camlight;
60 | camlight(-80,-10);
61 | lighting phong;
62 | axes(ax);
63 | cameramenu;
64 |
65 | if nargout
66 | varargout{1} = hp;
67 | end
68 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/Makefile:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env make -f
2 | # GIfTI Makefile
3 | #
4 | # Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
5 | #
6 | # $Id: Makefile 6402 2015-04-09 18:11:06Z guillaume $
7 |
8 | include Makefile.var
9 |
10 | SPMMEX = zstream.$(SUF)
11 |
12 | ifeq (mex,$(SUF))
13 | export CFLAGS = $(shell $(MEX) -p CFLAGS) -std=c99
14 | else
15 | MEXOPTS += CFLAGS='$$CFLAGS -std=c99'
16 | endif
17 |
18 | all: $(SPMMEX)
19 | @:
20 |
21 | clean:
22 | @:
23 |
24 | distclean: clean
25 | $(DEL) $(SPMMEX)
26 |
27 | install:
28 | @:
29 |
30 | tarball: all
31 | $(TAR) cf spm_mex.tar $(SPMMEX)
32 |
33 | %.$(SUF) : %.c
34 | $(MEX) $< $(MEXEND)
35 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/Makefile.var:
--------------------------------------------------------------------------------
1 | # Makefile default variables
2 | #
3 | # Copyright (C) 1991-2014 Wellcome Trust Centre for Neuroimaging
4 | #
5 | # $Id: Makefile.var 6099 2014-07-11 12:21:35Z guillaume $
6 | #
7 | ###############################################################################
8 | #
9 | # This file defines variables used in Makefile and has been tested under
10 | # Linux, Windows and MacOS.
11 | #
12 | # If you have to tweak this file to compile the SPM MEX-files for your
13 | # platform, please send the details to so they can be
14 | # included here.
15 | #
16 | # You can find some more help online on the SPM wikibook:
17 | # * Linux:
18 | # http://en.wikibooks.org/wiki/SPM/Installation_on_Linux
19 | # http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux
20 | # * Windows:
21 | # http://en.wikibooks.org/wiki/SPM/Installation_on_Windows
22 | # http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Windows
23 | # MinGW: http://www.mingw.org/
24 | # * MacOS:
25 | # http://en.wikibooks.org/wiki/SPM/Installation_on_Mac_OS_(Intel)
26 | # http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)
27 | #
28 | ###############################################################################
29 |
30 | SHELL = /bin/sh
31 | MAKE = make
32 | MEXBIN = mex
33 | MEXOPTS = -O -largeArrayDims
34 | MEXEND =
35 | MOSUF = o # mex output object suffix
36 | UNAME = uname
37 | AR = ar rcs
38 | COPY = cp -f
39 | DEL = rm -f
40 | MOVE = mv -f
41 | TAR = tar
42 | ZIP = gzip -f
43 |
44 | ifndef SUF
45 | ifndef PLATFORM
46 | PLATFORM = $(shell $(UNAME))
47 | endif
48 | ##### Linux #####
49 | ifeq (Linux,$(PLATFORM))
50 | HARDWARE = $(shell $(UNAME) -m)
51 | ifeq (i386,$(HARDWARE))
52 | SUF = mexglx
53 | endif
54 | ifeq (i686,$(HARDWARE))
55 | SUF = mexglx
56 | endif
57 | ifeq (x86_64,$(HARDWARE))
58 | SUF = mexa64
59 | endif
60 | ifndef SUF
61 | $(error Unknowm platform $(PLATFORM)-$(HARDWARE))
62 | endif
63 | endif
64 | ##### MacOS #####
65 | ifeq (Darwin,$(PLATFORM))
66 | HARDWARE = $(shell $(UNAME) -p)
67 | ifeq (i386,$(HARDWARE))
68 | SUF = mexmaci64
69 | endif
70 | ifndef SUF
71 | $(error Unknowm platform $(PLATFORM)-$(HARDWARE))
72 | endif
73 | endif
74 | ##### Windows #####
75 | ifeq (MINGW32,$(word 1,$(subst _, ,$(PLATFORM))))
76 | override PLATFORM = windows
77 | endif
78 | ifeq (windows,$(PLATFORM))
79 | ifeq (x86,$(PROCESSOR_ARCHITECTURE))
80 | SUF = mexw32
81 | else
82 | SUF = mexw64
83 | endif
84 | MEXBIN = cmd /c "mex.bat
85 | MEXOPTS += -DSPM_WIN32
86 | MEXEND = "
87 | MOSUF = obj
88 | AR = lib.exe /out:
89 | endif
90 | #### Octave ####
91 | ifeq (octave,$(PLATFORM))
92 | MEXBIN = mkoctfile
93 | MEXOPTS = --mex
94 | SUF = mex
95 | override PLATFORM = $(shell $(UNAME))
96 | endif
97 | ifndef SUF
98 | $(error Unknowm platform $(PLATFORM))
99 | endif
100 | endif
101 |
102 | MEX = $(MEXBIN) $(MEXOPTS)
103 |
104 | MATLABROOT = $(realpath $(shell which $(firstword $(MEXBIN))))
105 |
106 | define verb
107 | @ echo "_____________________________________________________________"
108 | @ echo ""
109 | @ echo " " $(1)
110 | @ echo "_____________________________________________________________"
111 | @ echo ""
112 | endef
113 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/base64decode.m:
--------------------------------------------------------------------------------
1 | function y = base64decode(x)
2 | %BASE64DECODE Perform base64 decoding on a string.
3 | %
4 | % BASE64DECODE(STR) decodes the given base64 string STR.
5 | %
6 | % Any character not part of the 65-character base64 subset set is silently
7 | % ignored.
8 | %
9 | % This function is used to decode strings from the Base64 encoding specified
10 | % in RFC 2045 - MIME (Multipurpose Internet Mail Extensions). The Base64
11 | % encoding is designed to represent arbitrary sequences of octets in a form
12 | % that need not be humanly readable. A 65-character subset ([A-Za-z0-9+/=])
13 | % of US-ASCII is used, enabling 6 bits to be represented per printable
14 | % character.
15 | %
16 | % See also BASE64ENCODE.
17 |
18 | % Author: Peter J. Acklam
19 | % Time-stamp: 2004-09-20 08:20:50 +0200
20 | % E-mail: pjacklam@online.no
21 | % URL: http://home.online.no/~pjacklam
22 |
23 | % Modified by Guillaume Flandin, May 2008
24 |
25 |
26 | % Perform the following mapping
27 | %--------------------------------------------------------------------------
28 | % A-Z -> 0 - 25 a-z -> 26 - 51 0-9 -> 52 - 61
29 | % + -> 62 / -> 63 = -> 64
30 | % anything else -> NaN
31 |
32 | base64chars = NaN(1,256);
33 | base64chars('ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/=') = 0:64;
34 | x = base64chars(x);
35 |
36 | % Remove/ignore any characters not in the base64 characters list or '='
37 | %--------------------------------------------------------------------------
38 |
39 | x = x(~isnan(x));
40 |
41 | % Replace any incoming padding ('=' -> 64) with a zero pad
42 | %--------------------------------------------------------------------------
43 |
44 | if x(end-1) == 64, p = 2; x(end-1:end) = 0;
45 | elseif x(end) == 64, p = 1; x(end) = 0;
46 | else p = 0;
47 | end
48 |
49 | % Allocate decoded data array
50 | %--------------------------------------------------------------------------
51 |
52 | n = length(x) / 4; % number of groups
53 | x = reshape(uint8(x), 4, n); % input data
54 | y = zeros(3, n, 'uint8'); % decoded data
55 |
56 | % Rearrange every 4 bytes into 3 bytes
57 | %--------------------------------------------------------------------------
58 | % 00aaaaaa 00bbbbbb 00cccccc 00dddddd
59 | %
60 | % to form
61 | %
62 | % aaaaaabb bbbbcccc ccdddddd
63 |
64 | y(1,:) = bitshift(x(1,:), 2); % 6 highest bits of y(1,:)
65 | y(1,:) = bitor(y(1,:), bitshift(x(2,:), -4)); % 2 lowest bits of y(1,:)
66 |
67 | y(2,:) = bitshift(x(2,:), 4); % 4 highest bits of y(2,:)
68 | y(2,:) = bitor(y(2,:), bitshift(x(3,:), -2)); % 4 lowest bits of y(2,:)
69 |
70 | y(3,:) = bitshift(x(3,:), 6); % 2 highest bits of y(3,:)
71 | y(3,:) = bitor(y(3,:), x(4,:)); % 6 lowest bits of y(3,:)
72 |
73 | % Remove any zero pad that was added to make this a multiple of 24 bits
74 | %--------------------------------------------------------------------------
75 |
76 | if p, y(end-p+1:end) = []; end
77 |
78 | % Reshape to a row vector
79 | %--------------------------------------------------------------------------
80 |
81 | y = reshape(y, 1, []);
82 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/getdict.m:
--------------------------------------------------------------------------------
1 | function d = getdict
2 | % Dictionary of GIfTI/NIfTI stuff
3 | %__________________________________________________________________________
4 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
5 |
6 | % Guillaume Flandin
7 | % $Id: getdict.m 4505 2011-09-30 11:45:58Z guillaume $
8 |
9 | persistent dict;
10 | if ~isempty(dict)
11 | d = dict;
12 | return;
13 | end
14 |
15 | table = {...
16 | 'NIFTI_TYPE_UINT8', 'uint8', '%d', @uint8, 'uint8'
17 | 'NIFTI_TYPE_INT32', 'int32', '%d', @int32, 'int32'
18 | 'NIFTI_TYPE_FLOAT32', 'float32', '%f', @single, 'single'
19 | 'NIFTI_TYPE_FLOAT64', 'float64', '%f', @double, 'double'};
20 |
21 | for i=1:size(table,1)
22 | dict.(table{i,1}) = cell2struct({table{i,2:end}},...
23 | {'class', 'format', 'conv', 'cast'}, 2);
24 | end
25 |
26 | d = dict;
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/isintent.m:
--------------------------------------------------------------------------------
1 | function [a, b] = isintent(this,intent)
2 | % Correspondance between fieldnames and NIfTI intent codes
3 | % FORMAT ind = isintent(this,intent)
4 | % this - GIfTI object
5 | % intent - fieldnames
6 | % a - indices of found intent(s)
7 | % b - indices of dataarrays of found intent(s)
8 | %__________________________________________________________________________
9 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
10 |
11 | % Guillaume Flandin
12 | % $Id: isintent.m 6345 2015-02-20 12:25:50Z guillaume $
13 |
14 | a = [];
15 | b = [];
16 | if ischar(intent), intent = cellstr(intent); end
17 | for i=1:length(this(1).data)
18 | switch this(1).data{i}.attributes.Intent(14:end)
19 | case 'POINTSET'
20 | [tf, loc] = ismember('vertices',intent);
21 | if tf
22 | a(end+1) = loc;
23 | b(end+1) = i;
24 | end
25 | [tf, loc] = ismember('mat',intent);
26 | if tf
27 | a(end+1) = loc;
28 | b(end+1) = i;
29 | end
30 | case 'TRIANGLE'
31 | [tf, loc] = ismember('faces',intent);
32 | if tf
33 | a(end+1) = loc;
34 | b(end+1) = i;
35 | end
36 | case 'VECTOR'
37 | [tf, loc] = ismember('normals',intent);
38 | if tf
39 | a(end+1) = loc;
40 | b(end+1) = i;
41 | end
42 | case 'NODE_INDEX'
43 | [tf, loc] = ismember('indices',intent);
44 | if tf
45 | a(end+1) = loc;
46 | b(end+1) = i;
47 | end
48 | case cdata
49 | [tf, loc] = ismember('cdata',intent);
50 | if tf
51 | a(end+1) = loc;
52 | b(end+1) = i;
53 | end
54 | if strcmp(this(1).data{i}.attributes.Intent(14:end),'LABEL')
55 | [tf, loc] = ismember('labels',intent);
56 | if tf
57 | a(end+1) = loc;
58 | b(end+1) = i;
59 | end
60 | end
61 | otherwise
62 | fprintf('Intent %s is ignored.\n',this.data{i}.attributes.Intent);
63 | end
64 | end
65 | %[d,i] = unique(a);
66 | %if length(d) < length(a)
67 | % warning('Several fields match intent type. Using first.');
68 | % a = a(i);
69 | % b = b(i);
70 | %end
71 |
72 | function c = cdata
73 |
74 | c = {
75 | 'NONE'
76 | 'CORREL'
77 | 'TTEST'
78 | 'FTEST'
79 | 'ZSCORE'
80 | 'CHISQ'
81 | 'BETA'
82 | 'BINOM'
83 | 'GAMMA'
84 | 'POISSON'
85 | 'NORMAL'
86 | 'FTEST_NONC'
87 | 'CHISQ_NONC'
88 | 'LOGISTIC'
89 | 'LAPLACE'
90 | 'UNIFORM'
91 | 'TTEST_NONC'
92 | 'WEIBULL'
93 | 'CHI'
94 | 'INVGAUSS'
95 | 'EXTVAL'
96 | 'PVAL'
97 | 'LOGPVAL'
98 | 'LOG10PVAL'
99 | 'ESTIMATE'
100 | 'LABEL'
101 | 'NEURONAMES'
102 | 'GENMATRIX'
103 | 'SYMMATRIX'
104 | 'DISPVECT'
105 | 'QUATERNION'
106 | 'DIMLESS'
107 | 'TIME_SERIES'
108 | 'RGB_VECTOR'
109 | 'RGBA_VECTOR'
110 | 'SHAPE'
111 | 'CONNECTIVITY_DENSE'
112 | 'CONNECTIVITY_DENSE_TIME'
113 | 'CONNECTIVITY_PARCELLATED'
114 | 'CONNECTIVITY_PARCELLATED_TIME'
115 | 'CONNECTIVITY_CONNECTIVITY_TRAJECTORY'
116 | };
117 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/read_freesurfer_file.m:
--------------------------------------------------------------------------------
1 | function this = read_freesurfer_file(filename)
2 | % Low level reader of FreeSurfer files (ASCII triangle surface file)
3 | % FORMAT this = read_freesurfer_file(filename)
4 | % filename - FreeSurfer file
5 | %
6 | % See http://wideman-one.com/gw/brain/fs/surfacefileformats.htm
7 | %__________________________________________________________________________
8 | % Copyright (C) 2013 Wellcome Trust Centre for Neuroimaging
9 |
10 | % Guillaume Flandin
11 | % $Id: read_freesurfer_file.m 5322 2013-03-13 15:04:14Z guillaume $
12 |
13 |
14 | fid = fopen(filename,'rt');
15 | if fid == -1, error('Cannot open "%s".',filename); end
16 |
17 | fgetl(fid); % #!ascii
18 | N = fscanf(fid,'%d',2);
19 | this.vertices = fscanf(fid,'%f %f %f %d',[4 N(1)])';
20 | this.faces = fscanf(fid,'%d %d %d %d',[4 N(2)])';
21 |
22 | fclose(fid);
23 |
24 | this.vertices = this.vertices(:,1:3);
25 | this.faces = this.faces(:,1:3) + 1;
26 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/zstream.c:
--------------------------------------------------------------------------------
1 | /*
2 | * $Id: zstream.c 6417 2015-04-21 16:03:44Z guillaume $
3 | * Guillaume Flandin
4 | */
5 |
6 | /* mex -O CFLAGS='$CFLAGS -std=c99' -largeArrayDims zstream.c */
7 |
8 | /* setenv CFLAGS "`mkoctfile -p CFLAGS` -std=c99" */
9 | /* mkoctfile --mex zstream.c */
10 |
11 | /* miniz: http://code.google.com/p/miniz/ */
12 | #define MINIZ_NO_STDIO
13 | #define MINIZ_NO_ARCHIVE_APIS
14 | #define MINIZ_NO_TIME
15 | #define MINIZ_NO_ZLIB_APIS
16 | #include "miniz.c"
17 |
18 | #include "mex.h"
19 |
20 | /* --- GATEWAY FUNCTION --- */
21 | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
22 | {
23 |
24 | char *action;
25 | unsigned char *IN = NULL, *OUT = NULL;
26 | size_t INlen, OUTlen;
27 |
28 | /* Check for proper number of arguments */
29 | if (nrhs < 2)
30 | mexErrMsgTxt("Not enough input arguments.");
31 | else if (nrhs > 2)
32 | mexErrMsgTxt("Too many input arguments.");
33 | else if (nlhs > 1)
34 | mexErrMsgTxt("Too many output arguments.");
35 |
36 | /* The input ACTION must be a string */
37 | if (!mxIsChar(prhs[0]))
38 | mexErrMsgTxt("Input ACTION must be a string.");
39 | action = mxArrayToString(prhs[0]);
40 |
41 | /* The input IN must be a real uint8 array */
42 | if (!mxIsUint8(prhs[1]) || mxIsComplex(prhs[1]))
43 | mexErrMsgTxt("Input IN must be a real uint8 array.");
44 |
45 | INlen = mxGetNumberOfElements(prhs[1]);
46 | IN = mxGetData(prhs[1]);
47 |
48 | if (!strcmp(action,"D")) {
49 |
50 | /* Decompress data */
51 | OUT = tinfl_decompress_mem_to_heap(IN, INlen, &OUTlen, TINFL_FLAG_PARSE_ZLIB_HEADER);
52 |
53 | if (OUT == NULL)
54 | mexErrMsgTxt("Error when decompressing data.");
55 | }
56 | else if (!strcmp(action,"C")) {
57 | /* Compress data */
58 | OUT = tdefl_compress_mem_to_heap(IN, INlen, &OUTlen, TDEFL_WRITE_ZLIB_HEADER);
59 |
60 | if (OUT == NULL)
61 | mexErrMsgTxt("Error when compressing data.");
62 | }
63 | else {
64 | mexErrMsgTxt("Unknown ACTION type.");
65 | }
66 |
67 | /* */
68 | plhs[0] = mxCreateNumericMatrix(OUTlen,1,mxUINT8_CLASS,mxREAL);
69 | if (plhs[0] == NULL)
70 | mexErrMsgTxt("Error when creating output variable.");
71 |
72 | memcpy(mxGetData(plhs[0]), OUT, OUTlen);
73 |
74 | mxFree(action);
75 | mz_free(OUT);
76 |
77 | }
78 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/private/zstream.m:
--------------------------------------------------------------------------------
1 | function Z = zstream(action,D)
2 | % Compress/decompress stream of bytes using Deflate/Inflate
3 | % FORMAT Z = zstream('C',D)
4 | % D - data stream to compress (converted to uint8 if needed)
5 | % Z - compressed data stream (uint8 vector)
6 | % FORMAT D = zstream('D',Z)
7 | % Z - data stream to decompress (uint8 vector)
8 | % D - decompressed data stream (uint8 vector)
9 | %__________________________________________________________________________
10 | %
11 | % This C-MEX file relies on:
12 | % * miniz, by Rich Geldreich
13 | % http://code.google.com/p/miniz/
14 | % Fallback Java implementation is adapted from:
15 | % * dzip/dunzip, by Michael Kleder
16 | % http://www.mathworks.com/matlabcentral/fileexchange/8899
17 | %__________________________________________________________________________
18 | % Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
19 |
20 | % Guillaume Flandin
21 | % $Id: zstream.m 6417 2015-04-21 16:03:44Z guillaume $
22 |
23 |
24 | if exist('OCTAVE_VERSION','builtin')
25 | error('zstream.c not compiled - see Makefile');
26 | end
27 |
28 | switch upper(action)
29 | case 'C'
30 | D = typecast(D(:),'uint8');
31 | f = java.io.ByteArrayOutputStream();
32 | g = java.util.zip.DeflaterOutputStream(f);
33 | g.write(D);
34 | g.close;
35 | Z = typecast(f.toByteArray,'uint8');
36 | f.close;
37 |
38 | case 'D'
39 | import com.mathworks.mlwidgets.io.InterruptibleStreamCopier
40 | a = java.io.ByteArrayInputStream(D);
41 | b = java.util.zip.InflaterInputStream(a);
42 | isc = InterruptibleStreamCopier.getInterruptibleStreamCopier;
43 | c = java.io.ByteArrayOutputStream;
44 | isc.copyStream(b,c);
45 | Z = c.toByteArray;
46 |
47 | otherwise
48 | error('Unknown action "%s".',action);
49 | end
50 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/struct.m:
--------------------------------------------------------------------------------
1 | function s = struct(this)
2 | % Struct method for GIfTI objects
3 | % FORMAT s = struct(this)
4 | % this - GIfTI object
5 | % s - a structure containing public fields of the object
6 | %__________________________________________________________________________
7 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
8 |
9 | % Guillaume Flandin
10 | % $Id: struct.m 6507 2015-07-24 16:48:02Z guillaume $
11 |
12 | names = fieldnames(this);
13 | values = cell(length(names), length(this(:)));
14 |
15 | for i=1:length(names)
16 | [values{i,:}] = subsref(this(:), substruct('.',names{i}));
17 | end
18 | s = reshape(cell2struct(values,names,1),size(this));
19 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@gifti/subsref.m:
--------------------------------------------------------------------------------
1 | function varargout = subsref(this,subs)
2 | % Subscript referencing for GIfTI objects
3 | %__________________________________________________________________________
4 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
5 |
6 | % Guillaume Flandin
7 | % $Id: subsref.m 6345 2015-02-20 12:25:50Z guillaume $
8 |
9 | if length(this) > 1 && ~strcmp(subs(1).type,'()')
10 | warning('Not implemented.');
11 | for i=1:numel(this)
12 | varargout{i} = subsref(this(i),subs);
13 | end
14 | return;
15 | end
16 |
17 | switch subs(1).type
18 | case '.'
19 | [i,j] = isintent(this,subs(1).subs);
20 | if isempty(i)
21 | if strcmp(subs(1).subs,'private')
22 | varargout{1} = builtin('struct',this);
23 | else
24 | error('Reference to non-existent field ''%s''.',subs(1).subs);
25 | end
26 | else
27 | if strcmp(subs(1).subs,'mat')
28 | varargout{1} = this.data{j}.space.MatrixData;
29 | elseif strcmp(subs(1).subs,'labels')
30 | varargout{1} = this.label;
31 | else
32 | if length(j) == 1
33 | varargout{1} = this.data{j}.data;
34 | else
35 | a = [this.data{j}];
36 | try
37 | varargout{1} = [a.data];
38 | catch
39 | error('Data arrays are of different sizes.');
40 | end
41 | end
42 | end
43 | end
44 | if strcmp(subs(1).subs,'faces') || strcmp(subs(1).subs,'indices')
45 | varargout{1} = varargout{1} + 1; % indices start at 1
46 | end
47 | if length(subs) > 1
48 | varargout{1} = subsref(varargout{1},subs(2:end));
49 | end
50 | case '{}'
51 | error('Cell contents reference from a non-cell array object.');
52 | case '()'
53 | if length(subs) == 1
54 | varargout{1} = builtin('subsref',this,subs(1));
55 | else
56 | varargout{1} = subsref(builtin('subsref',this,subs(1)),subs(2:end));
57 | end
58 | otherwise
59 | error('This should not happen.');
60 | end
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/Contents.m:
--------------------------------------------------------------------------------
1 | % XMLTree: XML Toolbox for MATLAB and GNU Octave
2 | % Version 2.0 14-Aug-2015
3 | %
4 | % XML file I/O.
5 | % xmltree - Constructor (XML parser).
6 | % save - Save an XMLTree in a file.
7 | %
8 | % XML Tree manipulation methods.
9 | % add - Add a node in a tree.
10 | % attributes - Handle attributes of a node.
11 | % branch - Extract a subtree from a tree.
12 | % children - Return children of a node.
13 | % convert - Convert a tree in a MATLAB structure.
14 | % copy - Copy nodes within a tree.
15 | % delete - Delete a node in a tree.
16 | % find - Find nodes in a tree.
17 | % flush - Clear a subtree.
18 | % get - get node properties.
19 | % getfilename - Get filename.
20 | % isfield - Return true if a field is present in a node.
21 | % length - Return the length of a tree.
22 | % move - Move a node within a tree.
23 | % parent - Return parents of a node.
24 | % root - Return the root element of a tree.
25 | % set - Set node properties.
26 | % setfilename - Set filename.
27 | %
28 | % Graphical user interface methods (basic).
29 | % editor - Graphical display of a tree.
30 | %
31 | % Low level class methods.
32 | % char - Convert a tree into a string (for display).
33 | % display - Display a tree in the workspace.
34 | %
35 | % Private methods.
36 | % xml_parser - XML parser.
37 | % xml_findstr - Find one string within another (C-MEX file).
38 | %
39 | % Conversions struct <=> XML.
40 | % loadxml -
41 | % savexml -
42 | % mat2xml -
43 | % xml2mat -
44 | % struct2xml -
45 | %
46 | % Demos.
47 | % xmldemo1 - Create an XML tree from scratch and save it.
48 | % xmldemo2 - Read an XML file and access fields.
49 | % xmldemo3 - Read an XML file, modify some fields and save it.
50 |
51 | % Copyright 2002-2015 http://www.artefact.tk/
52 |
53 | % Guillaume Flandin
54 | % $Id: Contents.m 6480 2015-06-13 01:08:30Z guillaume $
55 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/add.m:
--------------------------------------------------------------------------------
1 | function varargout = add(tree,uid,type,parameter)
2 | % XMLTREE/ADD Method (add childs to elements of an XML Tree)
3 | % FORMAT vararout = add(tree,uid,type,parameter)
4 | %
5 | % tree - XMLTree object
6 | % uid - array of uid's
7 | % type - 'element', 'chardata', 'cdata', 'pi' or 'comment'
8 | % parameter - property name (a character array unless type='pi' for
9 | % which parameter=struct('target','','value',''))
10 | %
11 | % new_uid - UID's of the newly created nodes
12 | %
13 | % tree = add(tree,uid,type,parameter);
14 | % [tree, new_uid] = add(tree,uid,type,parameter);
15 | %__________________________________________________________________________
16 | %
17 | % Add a node (element, chardata, cdata, pi or comment) in the XML Tree.
18 | % It adds a child to the element whose UID is iud.
19 | % Use attributes({'set','get','add','del','length'},...) function to
20 | % deal with the attributes of an element node (initialized empty).
21 | % The tree parameter must be in input AND in output.
22 | %__________________________________________________________________________
23 | % Copyright (C) 2002-2011 http://www.artefact.tk/
24 |
25 | % Guillaume Flandin
26 | % $Id: add.m 4460 2011-09-05 14:52:16Z guillaume $
27 |
28 |
29 | if ~isa(uid,'double')
30 | error('[XMLTree] UID must be a double array.');
31 | end
32 | if ~ischar(type)
33 | error('[XMLTree] TYPE must be a valid item type.');
34 | end
35 | if strcmp(type,'pi')
36 | if ~isfield(parameter,'target') || ~isfield(parameter,'value') || ...
37 | ~ischar(parameter.target) || ~ischar(parameter.value)
38 | error(['[XMLTree] For a Processing Instruction, ',...
39 | 'PARAMETER must be a struct.']);
40 | end
41 | elseif ~ischar(parameter)
42 | error('[XMLTree] PARAMETER must be a string.');
43 | end
44 |
45 | if nargout == 2
46 | l = length(tree.tree);
47 | varargout{2} = (l+1):(l+numel(uid));
48 | end
49 |
50 | for i=1:numel(uid)
51 | if uid(i)<1 || uid(i)>length(tree.tree)
52 | error('[XMLTree] Invalid UID.');
53 | end
54 | if ~strcmp(tree.tree{uid(i)}.type,'element')
55 | error('[XMLTree] Cannot add a child to a non-element node.');
56 | end
57 | l = length(tree.tree);
58 | switch type
59 | case 'element'
60 | tree.tree{l+1} = struct('type','element',...
61 | 'name',parameter,...
62 | 'attributes',[],...
63 | 'contents',[],...
64 | 'parent',[],...
65 | 'uid',l+1);
66 | case 'chardata'
67 | tree.tree{l+1} = struct('type','chardata',...
68 | 'value',parameter,...
69 | 'parent',[],...
70 | 'uid',l+1);
71 | case 'cdata'
72 | tree.tree{l+1} = struct('type','cdata',...
73 | 'value',parameter,...
74 | 'parent',[],...
75 | 'uid',l+1);
76 | case 'pi'
77 | tree.tree{l+1} = struct('type','pi',...
78 | 'target',parameter.target,...
79 | 'value',parameter.value,...
80 | 'parent',[],...
81 | 'uid',l+1);
82 | case 'comment'
83 | tree.tree{l+1} = struct('type','comment',...
84 | 'value',parameter,...
85 | 'parent',[],...
86 | 'uid',l+1);
87 | otherwise
88 | error(sprintf('[XMLTree] %s: unknown item type.',type));
89 | end
90 | tree.tree{uid(i)}.contents = [tree.tree{uid(i)}.contents l+1];
91 | tree.tree{l+1}.parent = uid(i);
92 | end
93 |
94 | varargout{1} = tree;
95 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/attributes.m:
--------------------------------------------------------------------------------
1 | function varargout = attributes(varargin)
2 | % XMLTREE/ATTRIBUTES Method (handle attributes of an element node)
3 | % FORMAT varargout = attributes(varargin)
4 | %
5 | % tree - XMLTree object
6 | % method - 'set','get','add','del' or 'length'
7 | % uid - the UID of an element node
8 | % n - indice of the attribute
9 | % key - string key="..."
10 | % val - string ...="val"
11 | % attr - cell array of struct(key,val) or just struct(key,val)
12 | % l - number of attributes of the element node uid
13 | %
14 | % tree = attributes(tree,'set',uid,n,key,val)
15 | % attr = attributes(tree,'get',uid[,n])
16 | % tree = attributes(tree,'add',uid,key,val)
17 | % tree = attributes(tree,'del',uid[,n])
18 | % l = attributes(tree,'length',uid)
19 | %__________________________________________________________________________
20 | %
21 | % Handle attributes of an element node.
22 | % The tree parameter must be in input AND in output for 'set', 'add' and
23 | % 'del' methods.
24 | %__________________________________________________________________________
25 | % Copyright (C) 2002-2011 http://www.artefact.tk/
26 |
27 | % Guillaume Flandin
28 | % $Id: attributes.m 4460 2011-09-05 14:52:16Z guillaume $
29 |
30 |
31 | %error(nargchk(3,6,nargin));
32 |
33 | tree = varargin{1};
34 | if ~ischar(varargin{2}) || ...
35 | ~any(strcmp(varargin{2},{'set','get','add','del','length'}))
36 | error('[XMLTree] Unknown method.');
37 | end
38 | uid = varargin{3};
39 | if ~isa(uid,'double') || any(uid>length(tree)) || any(uid<1)
40 | error('[XMLTree] UID must be a positive integer scalar.');
41 | end
42 |
43 | if ~strcmp(tree.tree{uid}.type,'element')
44 | error('[XMLTree] This node has no attributes.');
45 | end
46 |
47 | switch varargin{2}
48 | case 'set'
49 | %error(nargchk(6,6,nargin));
50 | if ~isa(varargin{4},'double') || ...
51 | any(varargin{4}>length(tree.tree{uid}.attributes)) || ...
52 | any(varargin{4}<1)
53 | error('[XMLTree] Invalid attribute indice.');
54 | end
55 | ind = varargin{4};
56 | tree.tree{uid}.attributes{ind} = struct('key',varargin{5},'val',varargin{6});
57 | varargout{1} = tree;
58 | case 'get'
59 | %error(nargchk(3,4,nargin));
60 | if nargin == 4
61 | if ischar(varargin{4})
62 | for i=1:length(tree.tree{uid}.attributes)
63 | if strcmp(varargin{4},tree.tree{uid}.attributes{i}.key)
64 | varargout{1} = tree.tree{uid}.attributes{i}.val;
65 | return;
66 | end
67 | end
68 | varargout{1} = [];
69 | elseif ~isa(varargin{4},'double') || ...
70 | any(varargin{4}>length(tree.tree{uid}.attributes)) || ...
71 | any(varargin{4}<1)
72 | error('[XMLTree] Invalid attribute indice.');
73 | else
74 | if length(varargin{4}) == 1
75 | varargout{1} = tree.tree{uid}.attributes{varargin{4}(1)};
76 | else
77 | varargout{1} = {};
78 | for i=1:length(varargin{4})
79 | varargout{1}{i} = tree.tree{uid}.attributes{varargin{4}(i)};
80 | end
81 | end
82 | end
83 | else
84 | if length(tree.tree{uid}.attributes) == 1
85 | varargout{1} = tree.tree{uid}.attributes{1};
86 | else
87 | varargout{1} = {};
88 | for i=1:length(tree.tree{uid}.attributes)
89 | varargout{1}{i} = tree.tree{uid}.attributes{i};
90 | end
91 | end
92 | end
93 | case 'add'
94 | %error(nargchk(5,5,nargin));
95 | ind = length(tree.tree{uid}.attributes) + 1;
96 | tree.tree{uid}.attributes{ind} = struct('key',varargin{4},'val',varargin{5});
97 | varargout{1} = tree;
98 | case 'del'
99 | %error(nargchk(3,4,nargin));
100 | if nargin == 4
101 | if ~isa(varargin{4},'double') || ...
102 | any(varargin{4}>length(tree.tree{uid}.attributes)) || ...
103 | any(varargin{4}<1)
104 | error('[XMLTree] Invalid attribute indice.');
105 | end
106 | ind = varargin{4};
107 | tree.tree{uid}.attributes(ind) = [];
108 | else
109 | tree.tree{uid}.attributes = [];
110 | end
111 | varargout{1} = tree;
112 | case 'length'
113 | %error(nargchk(3,3,nargin));
114 | varargout{1} = length(tree.tree{uid}.attributes);
115 | otherwise
116 | error('[XMLTree] Unknown method.');
117 | end
118 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/branch.m:
--------------------------------------------------------------------------------
1 | function subtree = branch(tree,uid)
2 | % XMLTREE/BRANCH Branch Method
3 | % FORMAT uid = parent(tree,uid)
4 | %
5 | % tree - XMLTree object
6 | % uid - UID of the root element of the subtree
7 | % subtree - XMLTree object (a subtree from tree)
8 | %__________________________________________________________________________
9 | %
10 | % Return a subtree from a tree.
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: branch.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 |
18 | %error(nargchk(2,2,nargin));
19 |
20 | if uid > length(tree) || ...
21 | numel(uid)~=1 || ...
22 | ~strcmp(tree.tree{uid}.type,'element')
23 | error('[XMLTree] Invalid UID.');
24 | end
25 |
26 | subtree = xmltree;
27 | subtree = set(subtree,root(subtree),'name',tree.tree{uid}.name);
28 | %- fix by Piotr Dollar to copy attributes for the root node:
29 | subtree = set(subtree,root(subtree),'attributes',tree.tree{uid}.attributes);
30 |
31 | child = children(tree,uid);
32 |
33 | for i=1:length(child)
34 | l = length(subtree);
35 | subtree = sub_branch(tree,subtree,child(i),root(subtree));
36 | subtree.tree{root(subtree)}.contents = [subtree.tree{root(subtree)}.contents l+1];
37 | end
38 |
39 | %==========================================================================
40 | function tree = sub_branch(t,tree,uid,p)
41 |
42 | l = length(tree);
43 | tree.tree{l+1} = t.tree{uid};
44 | tree.tree{l+1}.uid = l + 1;
45 | tree.tree{l+1}.parent = p;
46 | tree.tree{l+1}.contents = [];
47 | if isfield(t.tree{uid},'contents')
48 | contents = get(t,uid,'contents');
49 | m = length(tree);
50 | for i=1:length(contents)
51 | tree.tree{l+1}.contents = [tree.tree{l+1}.contents m+1];
52 | tree = sub_branch(t,tree,contents(i),l+1);
53 | m = length(tree);
54 | end
55 | end
56 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/char.m:
--------------------------------------------------------------------------------
1 | function s = char(tree)
2 | % XMLTREE/CHAR Converter function from XMLTree to a description string
3 | % FORMAT s = char(tree)
4 | %
5 | % tree - XMLTree object
6 | % s - a description string of an XMLTree
7 | %__________________________________________________________________________
8 | %
9 | % Return a string describing the XMLTree:
10 | % 'XMLTree object (x nodes) [filename]'
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: char.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 |
18 | s = strcat('XMLTree object (',num2str(length(tree)),' nodes) [',getfilename(tree),']');
19 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/children.m:
--------------------------------------------------------------------------------
1 | function child = children(tree,uid)
2 | % XMLTREE/CHILDREN Return children's UIDs of node uid
3 | % FORMAT child = children(tree,uid)
4 | %
5 | % tree - a tree
6 | % uid - uid of the element
7 | % child - array of the UIDs of children of node uid
8 | %__________________________________________________________________________
9 | %
10 | % Return UID's of children of node uid
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: children.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 | %error(nargchk(2,2,nargin));
18 |
19 | child = [];
20 | uid = uid(:);
21 | l = length(tree);
22 | for i=1:length(uid)
23 | if uid(i) > 0 && uid(i) <= l
24 | if strcmp(tree.tree{uid(i)}.type,'element')
25 | child = [child tree.tree{uid(i)}.contents];
26 | end
27 | else
28 | error('[XMLTree] Invalid UID.');
29 | end
30 | end
31 | if isempty(child), child = []; end
32 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/copy.m:
--------------------------------------------------------------------------------
1 | function tree = copy(tree,subuid,uid)
2 | % XMLTREE/COPY Copy Method (copy a subtree in another branch)
3 | % FORMAT tree = copy(tree,subuid,uid)
4 | %
5 | % tree - XMLTree object
6 | % subuid - UID of the subtree to copy
7 | % uid - UID of the element where the subtree must be duplicated
8 | %__________________________________________________________________________
9 | %
10 | % Copy a subtree to another branch.
11 | % The tree parameter must be in input AND in output.
12 | %__________________________________________________________________________
13 | % Copyright (C) 2002-2015 http://www.artefact.tk/
14 |
15 | % Guillaume Flandin
16 | % $Id: copy.m 6480 2015-06-13 01:08:30Z guillaume $
17 |
18 |
19 | %error(nargchk(2,3,nargin));
20 |
21 | if nargin == 2
22 | uid = parent(tree,subuid);
23 | end
24 |
25 | l = length(tree);
26 | tree = sub_copy(tree,subuid,uid);
27 | tree.tree{uid}.contents = [tree.tree{uid}.contents l+1];
28 |
29 | % to have the copy next to the original and not at the end?
30 | % contents = get(tree,parent,'contents');
31 | % i = find(contents==uid);
32 | % tree = set(tree,parent,'contents',[contents(1:i) l+1 contents(i+1:end)]);
33 |
34 | %==========================================================================
35 | function tree = sub_copy(tree,uid,p)
36 |
37 | l = length(tree);
38 | tree.tree{l+1} = tree.tree{uid};
39 | tree.tree{l+1}.uid = l+1;
40 | tree.tree{l+1}.parent = p;
41 | tree.tree{l+1}.contents = [];
42 | if isfield(tree.tree{uid},'contents')
43 | contents = get(tree,uid,'contents');
44 | m = length(tree);
45 | for i=1:length(contents)
46 | tree.tree{l+1}.contents = [tree.tree{l+1}.contents m+1];
47 | tree = sub_copy(tree,contents(i),l+1);
48 | m = length(tree);
49 | end
50 | end
51 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/delete.m:
--------------------------------------------------------------------------------
1 | function tree = delete(tree,uid)
2 | % XMLTREE/DELETE Delete (delete a subtree given its UID)
3 | %
4 | % tree - XMLTree object
5 | % uid - array of UID's of subtrees to be deleted
6 | %__________________________________________________________________________
7 | %
8 | % Delete a subtree given its UID
9 | % The tree parameter must be in input AND in output
10 | %__________________________________________________________________________
11 | % Copyright (C) 2002-2011 http://www.artefact.tk/
12 |
13 | % Guillaume Flandin
14 | % $Id: delete.m 4460 2011-09-05 14:52:16Z guillaume $
15 |
16 | %error(nargchk(2,2,nargin));
17 |
18 | uid = uid(:);
19 | for i=1:length(uid)
20 | if uid(i)==1
21 | warning('[XMLTree] Cannot delete root element.');
22 | else
23 | p = tree.tree{uid(i)}.parent;
24 | tree = sub_delete(tree,uid(i));
25 | tree.tree{p}.contents(find(tree.tree{p}.contents==uid(i))) = [];
26 | end
27 | end
28 |
29 | %==========================================================================
30 | function tree = sub_delete(tree,uid)
31 | if isfield(tree.tree{uid},'contents')
32 | for i=1:length(tree.tree{uid}.contents)
33 | tree = sub_delete(tree,tree.tree{uid}.contents(i));
34 | end
35 | end
36 | tree.tree{uid} = struct('type','deleted');
37 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/display.m:
--------------------------------------------------------------------------------
1 | function display(tree)
2 | % XMLTREE/DISPLAY Command window display of an XMLTree
3 | % FORMAT display(tree)
4 | %
5 | % tree - XMLTree object
6 | %__________________________________________________________________________
7 | %
8 | % This method is called when the semicolon is not used to terminate a
9 | % statement which returns an XMLTree.
10 | %__________________________________________________________________________
11 | % Copyright (C) 2002-2011 http://www.artefact.tk/
12 |
13 | % Guillaume Flandin
14 | % $Id: display.m 4460 2011-09-05 14:52:16Z guillaume $
15 |
16 | disp(' ');
17 | disp([inputname(1),' = ']);
18 | disp(' ');
19 | for i=1:numel(tree)
20 | disp([blanks(length(inputname(1))+3) char(tree(i))]);
21 | end
22 | disp(' ');
23 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/flush.m:
--------------------------------------------------------------------------------
1 | function tree = flush(tree,uid)
2 | % XMLTREE/FLUSH Flush (Clear a subtree given its UID)
3 | %
4 | % tree - XMLTree object
5 | % uid - array of UID's of subtrees to be cleared
6 | % Default is root
7 | %__________________________________________________________________________
8 | %
9 | % Clear a subtree given its UID (remove all the leaves of the tree)
10 | % The tree parameter must be in input AND in output
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: flush.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 |
18 | %error(nargchk(1,2,nargin));
19 |
20 | if nargin == 1,
21 | uid = root(tree);
22 | end
23 |
24 | uid = uid(:);
25 | for i=1:length(uid)
26 | tree = sub_flush(tree,uid(i));
27 | end
28 |
29 | %==========================================================================
30 | function tree = sub_flush(tree,uid)
31 | if isfield(tree.tree{uid},'contents')
32 | % contents is parsed in reverse order because each child is
33 | % deleted and the contents vector is then eventually reduced
34 | for i=length(tree.tree{uid}.contents):-1:1
35 | tree = sub_flush(tree,tree.tree{uid}.contents(i));
36 | end
37 | end
38 | if strcmp(tree.tree{uid}.type,'chardata') ||...
39 | strcmp(tree.tree{uid}.type,'pi') ||...
40 | strcmp(tree.tree{uid}.type,'cdata') ||...
41 | strcmp(tree.tree{uid}.type,'comment')
42 | tree = delete(tree,uid);
43 | end
44 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/get.m:
--------------------------------------------------------------------------------
1 | function value = get(tree,uid,parameter)
2 | % XMLTREE/GET Get Method (get object properties)
3 | % FORMAT value = get(tree,uid,parameter)
4 | %
5 | % tree - XMLTree object
6 | % uid - array of uid's
7 | % parameter - property name
8 | % value - property value
9 | %__________________________________________________________________________
10 | %
11 | % Get object properties of a tree given their UIDs.
12 | %__________________________________________________________________________
13 | % Copyright (C) 2002-2011 http://www.artefact.tk/
14 |
15 | % Guillaume Flandin
16 | % $Id: get.m 4460 2011-09-05 14:52:16Z guillaume $
17 |
18 |
19 | %error(nargchk(2,3,nargin));
20 |
21 | value = cell(size(uid));
22 | uid = uid(:);
23 | if nargin==2
24 | for i=1:length(uid)
25 | if uid(i)<1 || uid(i)>length(tree.tree)
26 | error('[XMLTree] Invalid UID.');
27 | end
28 | % According to the type of the node, return only some parameters
29 | % Need changes...
30 | value{i} = tree.tree{uid(i)};
31 | end
32 | else
33 | for i=1:length(uid)
34 | try
35 | value{i} = subsref(tree.tree{uid(i)}, struct('type','.','subs',parameter));
36 | catch
37 | error(sprintf('[XMLTree] Parameter %s not found.',parameter));
38 | end
39 | end
40 | end
41 | if length(value)==1
42 | value = value{1};
43 | end
44 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/getfilename.m:
--------------------------------------------------------------------------------
1 | function filename = getfilename(tree)
2 | % XMLTREE/GETFILENAME Get filename method
3 | % FORMAT filename = getfilename(tree)
4 | %
5 | % tree - XMLTree object
6 | % filename - XML filename
7 | %__________________________________________________________________________
8 | %
9 | % Return the filename of the XML tree if loaded from disk and an empty
10 | % string otherwise.
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: getfilename.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 | filename = tree.filename;
18 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/isfield.m:
--------------------------------------------------------------------------------
1 | function F = isfield(tree,uid,parameter)
2 | % XMLTREE/ISFIELD Is parameter a field of tree{uid} ?
3 | % FORMAT F = isfield(tree,uid,parameter)
4 | %
5 | % tree - a tree
6 | % uid - uid of the element
7 | % parameter - a field of the root tree
8 | % F - 1 if present, 0 otherwise
9 | %__________________________________________________________________________
10 | %
11 | % Is parameter a field of tree{uid} ?
12 | %__________________________________________________________________________
13 | % Copyright (C) 2002-2011 http://www.artefact.tk/
14 |
15 | % Guillaume Flandin
16 | % $Id: isfield.m 4460 2011-09-05 14:52:16Z guillaume $
17 |
18 |
19 | %error(nargchk(3,3,nargin));
20 |
21 | F = zeros(1,length(uid));
22 | for i=1:length(uid)
23 | if isfield(tree.tree{uid(i)},parameter)
24 | F(i) = 1;
25 | end
26 | end
27 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/length.m:
--------------------------------------------------------------------------------
1 | function l = length(tree,r)
2 | % XMLTREE/LENGTH Length Method
3 | % FORMAT l = length(tree,r)
4 | %
5 | % tree - XMLTree object
6 | % r - 'real' if present, returns the real number of nodes in the
7 | % tree (deleted nodes aren't populated)
8 | % l - length of the XML tree (number of nodes)
9 | %__________________________________________________________________________
10 | %
11 | % Return the number of nodes of an XMLTree object.
12 | %__________________________________________________________________________
13 | % Copyright (C) 2002-2011 http://www.artefact.tk/
14 |
15 | % Guillaume Flandin
16 | % $Id: length.m 4460 2011-09-05 14:52:16Z guillaume $
17 |
18 |
19 | %error(nargchk(1,2,nargin));
20 |
21 | % Return the full number of nodes once allocated
22 | l = length(tree.tree);
23 |
24 | % Substract the number of deleted nodes to the previous length
25 | if nargin == 2
26 | if strcmp(r,'real')
27 | ll = 0;
28 | for i=1:l
29 | if ~strcmp(tree.tree{i}.type,'deleted')
30 | ll = ll + 1;
31 | end
32 | end
33 | l = ll;
34 | else
35 | error('[XMLTree] Bad input argument.');
36 | end
37 | end
38 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/move.m:
--------------------------------------------------------------------------------
1 | function tree = move(tree,uida, uidb)
2 | % XMLTREE/MOVE Move (move a subtree inside a tree from A to B)
3 | %
4 | % tree - XMLTree object
5 | % uida - initial position of the subtree
6 | % uidb - parent of the final position of the subtree
7 | %__________________________________________________________________________
8 | %
9 | % Move a subtree inside a tree from A to B.
10 | % The tree parameter must be in input AND in output.
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2015 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: move.m 6480 2015-06-13 01:08:30Z guillaume $
16 |
17 |
18 | %error(nargchk(3,3,nargin));
19 |
20 | p = tree.tree{uida}.parent;
21 | tree.tree{p}.contents(find(tree.tree{p}.contents==uida)) = [];
22 | tree.tree(uidb).contents = [tree.tree(uidb).contents uida];
23 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/parent.m:
--------------------------------------------------------------------------------
1 | function p = parent(tree,uid)
2 | % XMLTREE/PARENT Parent Method
3 | % FORMAT uid = parent(tree,uid)
4 | %
5 | % tree - XMLTree object
6 | % uid - UID of the lonely child
7 | % p - UID of the parent ([] if root is the child)
8 | %__________________________________________________________________________
9 | %
10 | % Return the uid of the parent of a node.
11 | %__________________________________________________________________________
12 | % Copyright (C) 2002-2011 http://www.artefact.tk/
13 |
14 | % Guillaume Flandin
15 | % $Id: parent.m 4460 2011-09-05 14:52:16Z guillaume $
16 |
17 | p = tree.tree{uid}.parent;
18 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/private/xml_findstr.c:
--------------------------------------------------------------------------------
1 | #include "mex.h"
2 |
3 | /*
4 | * $Id: xml_findstr.c 6480 2015-06-13 01:08:30Z guillaume $
5 | * Guillaume Flandin
6 | */
7 |
8 | /*
9 | Differences with built-in findstr:
10 | - allows to search only the n first occurences of a pattern
11 | - allows to search only in a substring (given an index of the beginning)
12 |
13 | MATLAB hack:
14 | - doesn't use mxGetString to prevent a copy of the string.
15 | - assumes MATLAB stores strings as unsigned short (Unicode 16 bits)
16 | matrix.h: typedef uint16_T mxChar;
17 | (that's the case for MATLAB 5.*, 6.* and 7.* but MATLAB 4.* stores
18 | strings as double and GNU Octave as char, see src/mxarray.h)
19 | */
20 |
21 | /* Comment the following line to use standard mxGetString (slower) */
22 | #if !defined (HAVE_OCTAVE)
23 | #define __HACK_MXCHAR__
24 | #endif
25 |
26 | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
27 |
28 | unsigned int i, j, stext, spattern, nbmatch = 0, ind = 1, occur = 0, nboccur = 0;
29 | #ifdef __HACK_MXCHAR__
30 | unsigned short int *text = NULL, *pattern = NULL;
31 | #else
32 | char *text = NULL, *pattern = NULL;
33 | #endif
34 | unsigned int *k = NULL;
35 | mxArray *out = NULL;
36 |
37 | /* Check for proper number of arguments. */
38 | if ((nrhs == 0) || (nrhs == 1))
39 | mexErrMsgTxt("Not enough input arguments.");
40 | else if (nrhs > 4)
41 | mexErrMsgTxt("Too many input arguments.");
42 | else if (nlhs > 1)
43 | mexErrMsgTxt("Too many output arguments.");
44 |
45 | /* The input TEXT must be a string */
46 | if (!mxIsChar(prhs[0]))
47 | mexErrMsgTxt("Inputs must be character arrays.");
48 | stext = mxGetM(prhs[0]) * mxGetN(prhs[0]);
49 | #ifdef __HACK_MXCHAR__
50 | text = mxGetData(prhs[0]);
51 | #else
52 | text = mxCalloc(stext+1, sizeof(char));
53 | mxGetString(prhs[0], text, stext+1);
54 | #endif
55 |
56 | /* The input PATTERN must be a string */
57 | if (!mxIsChar(prhs[1]))
58 | mexErrMsgTxt("Inputs must be character arrays.");
59 | spattern = mxGetM(prhs[1]) * mxGetN(prhs[1]);
60 | #ifdef __HACK_MXCHAR__
61 | pattern = mxGetData(prhs[1]);
62 | #else
63 | pattern = mxCalloc(spattern+1, sizeof(char));
64 | mxGetString(prhs[1], pattern, spattern+1);
65 | #endif
66 |
67 | /* The input INDEX must be an integer */
68 | if (nrhs > 2) {
69 | if ((!mxIsNumeric(prhs[2]) || (mxGetM(prhs[2]) * mxGetN(prhs[2]) != 1)))
70 | mexErrMsgTxt("Index input must be an integer.");
71 | ind = (unsigned int)mxGetScalar(prhs[2]);
72 | if (ind < 1)
73 | mexErrMsgTxt("Index must be greater than 1.");
74 | }
75 |
76 | /* The input OCCUR must be an integer */
77 | if (nrhs == 4) {
78 | if ((!mxIsNumeric(prhs[3]) || (mxGetM(prhs[3]) * mxGetN(prhs[3]) != 1)))
79 | mexErrMsgTxt("Index input must be an integer.");
80 | nboccur = (unsigned int)mxGetScalar(prhs[3]);
81 | }
82 |
83 | /* Find pattern in text */
84 | for (i=ind-1;i=i);
42 | if ~isempty(k), k = k(1:min(n,length(k))); end
43 |
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/Sub-function/cifti-matlab-master/@xmltree/root.m:
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1 | function uid = root(tree)
2 | % XMLTREE/ROOT Root Method
3 | % FORMAT uid = root(tree)
4 | %
5 | % tree - XMLTree object
6 | % uid - UID of the root element of tree
7 | %__________________________________________________________________________
8 | %
9 | % Return the uid of the root element of the tree.
10 | %__________________________________________________________________________
11 | % Copyright (C) 2002-2008 http://www.artefact.tk/
12 |
13 | % Guillaume Flandin
14 | % $Id: root.m 4460 2011-09-05 14:52:16Z guillaume $
15 |
16 | % Actually root is necessarily the element whos UID is 1, by
17 | % construction. However, xml_parser should return a tree with a ROOT
18 | % element with as many children as needed but only ONE *element* child
19 | % who would be the real root (and this method should return the UID of
20 | % this element).
21 |
22 | uid = 1;
23 |
24 | % Update:
25 | % xml_parser has been modified (not as explained above) to handle the
26 | % case when several nodes are at the top level of the XML.
27 | % Example: blah blah
28 | % Now root is the first element node of the tree.
29 |
30 | % Look for the first element in the XML Tree
31 | for i=1:length(tree)
32 | if strcmp(get(tree,i,'type'),'element')
33 | uid = i;
34 | break
35 | end
36 | end
37 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/save.m:
--------------------------------------------------------------------------------
1 | function varargout = save(tree, filename)
2 | % XMLTREE/SAVE Save an XML tree in an XML file
3 | % FORMAT varargout = save(tree,filename)
4 | %
5 | % tree - XMLTree
6 | % filename - XML output filename
7 | % varargout - XML string
8 | %__________________________________________________________________________
9 | %
10 | % Convert an XML tree into a well-formed XML string and write it into
11 | % a file or return it as a string if no filename is provided.
12 | %__________________________________________________________________________
13 | % Copyright (C) 2002-2011 http://www.artefact.tk/
14 |
15 | % Guillaume Flandin
16 | % $Id: save.m 4460 2011-09-05 14:52:16Z guillaume $
17 |
18 |
19 | %error(nargchk(1,2,nargin));
20 |
21 | prolog = '\n';
22 |
23 | %- Return the XML tree as a string
24 | if nargin == 1
25 | varargout{1} = [sprintf(prolog) ...
26 | print_subtree(tree,'',root(tree))];
27 | %- Output specified
28 | else
29 | %- Filename provided
30 | if ischar(filename)
31 | [fid, msg] = fopen(filename,'w');
32 | if fid==-1, error(msg); end
33 | if isempty(tree.filename), tree.filename = filename; end
34 | %- File identifier provided
35 | elseif isnumeric(filename) && numel(filename) == 1
36 | fid = filename;
37 | prolog = ''; %- With this option, do not write any prolog
38 | else
39 | error('[XMLTree] Invalid argument.');
40 | end
41 | fprintf(fid,prolog);
42 | save_subtree(tree,fid,root(tree));
43 | if ischar(filename), fclose(fid); end
44 | if nargout == 1
45 | varargout{1} = print_subtree(tree,'',root(tree));
46 | end
47 | end
48 |
49 | %==========================================================================
50 | function xmlstr = print_subtree(tree,xmlstr,uid,order)
51 | if nargin < 4, order = 0; end
52 | xmlstr = [xmlstr blanks(3*order)];
53 | switch tree.tree{uid}.type
54 | case 'element'
55 | xmlstr = sprintf('%s<%s',xmlstr,tree.tree{uid}.name);
56 | for i=1:length(tree.tree{uid}.attributes)
57 | xmlstr = sprintf('%s %s="%s"', xmlstr, ...
58 | tree.tree{uid}.attributes{i}.key,...
59 | tree.tree{uid}.attributes{i}.val);
60 | end
61 | if isempty(tree.tree{uid}.contents)
62 | xmlstr = sprintf('%s/>\n',xmlstr);
63 | else
64 | xmlstr = sprintf('%s>\n',xmlstr);
65 | for i=1:length(tree.tree{uid}.contents)
66 | xmlstr = print_subtree(tree,xmlstr, ...
67 | tree.tree{uid}.contents(i),order+1);
68 | end
69 | xmlstr = [xmlstr blanks(3*order)];
70 | xmlstr = sprintf('%s\n',xmlstr,...
71 | tree.tree{uid}.name);
72 | end
73 | case 'chardata'
74 | xmlstr = sprintf('%s%s\n',xmlstr, ...
75 | entity(tree.tree{uid}.value));
76 | case 'cdata'
77 | xmlstr = sprintf('%s\n',xmlstr, ...
78 | tree.tree{uid}.value);
79 | case 'pi'
80 | xmlstr = sprintf('%s\n',xmlstr, ...
81 | tree.tree{uid}.target, tree.tree{uid}.value);
82 | case 'comment'
83 | xmlstr = sprintf('%s\n',xmlstr,...
84 | tree.tree{uid}.value);
85 | otherwise
86 | warning(sprintf('Type %s unknown: not saved', ...
87 | tree.tree{uid}.type));
88 | end
89 |
90 | %==========================================================================
91 | function save_subtree(tree,fid,uid,order)
92 | if nargin < 4, order = 0; end
93 | fprintf(fid,blanks(3*order));
94 | switch tree.tree{uid}.type
95 | case 'element'
96 | fprintf(fid,'<%s',tree.tree{uid}.name);
97 | for i=1:length(tree.tree{uid}.attributes)
98 | fprintf(fid,' %s="%s"',...
99 | tree.tree{uid}.attributes{i}.key, ...
100 | tree.tree{uid}.attributes{i}.val);
101 | end
102 | if isempty(tree.tree{uid}.contents)
103 | fprintf(fid,'/>\n');
104 | else
105 | fprintf(fid,'>\n');
106 | for i=1:length(tree.tree{uid}.contents)
107 | save_subtree(tree,fid,...
108 | tree.tree{uid}.contents(i),order+1)
109 | end
110 | fprintf(fid,blanks(3*order));
111 | fprintf(fid,'\n',tree.tree{uid}.name);
112 | end
113 | case 'chardata'
114 | fprintf(fid,'%s\n',entity(tree.tree{uid}.value));
115 | case 'cdata'
116 | fprintf(fid,'\n',tree.tree{uid}.value);
117 | case 'pi'
118 | fprintf(fid,'\n',tree.tree{uid}.target, ...
119 | tree.tree{uid}.value);
120 | case 'comment'
121 | fprintf(fid,'\n',tree.tree{uid}.value);
122 | otherwise
123 | warning(sprintf('[XMLTree] Type %s unknown: not saved', ...
124 | tree.tree{uid}.type));
125 | end
126 |
127 |
128 | %==========================================================================
129 | function str = entity(str)
130 | % This has the side effect of strtrim'ming the char array.
131 | str = char(strrep(cellstr(str), '&', '&' ));
132 | str = char(strrep(cellstr(str), '<', '<' ));
133 | str = char(strrep(cellstr(str), '>', '>' ));
134 | str = char(strrep(cellstr(str), '"', '"'));
135 | str = char(strrep(cellstr(str), '''', '''));
136 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/set.m:
--------------------------------------------------------------------------------
1 | function tree = set(tree,uid, parameter, value)
2 | % XMLTREE/SET Method (set object properties)
3 | % FORMAT tree = set(tree,uid,parameter,value)
4 | %
5 | % tree - XMLTree object
6 | % uid - array (or cell) of uid's
7 | % parameter - property name
8 | % value - property value
9 | %__________________________________________________________________________
10 | %
11 | % Set object properties given its uid and pairs parameter/value
12 | % The tree parameter must be in input AND in output
13 | %__________________________________________________________________________
14 | % Copyright (C) 2002-2011 http://www.artefact.tk/
15 |
16 | % Guillaume Flandin
17 | % $Id: set.m 4460 2011-09-05 14:52:16Z guillaume $
18 |
19 |
20 | %error(nargchk(4,4,nargin));
21 |
22 | if iscell(uid), uid = [uid{:}]; else uid = uid(:); end
23 |
24 | for i=1:length(uid)
25 | tree.tree{uid(i)} = builtin('subsasgn', tree.tree{uid(i)}, struct('type','.','subs',parameter), value);
26 | %tree.tree{uid(i)} = setfield(tree.tree{uid(i)},parameter,value);
27 | end
28 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/setfilename.m:
--------------------------------------------------------------------------------
1 | function tree = setfilename(tree,filename)
2 | % XMLTREE/SETFILENAME Set filename method
3 | % FORMAT tree = setfilename(tree,filename)
4 | %
5 | % tree - XMLTree object
6 | % filename - XML filename
7 | %__________________________________________________________________________
8 | %
9 | % Set the filename linked to the XML tree as filename.
10 | %__________________________________________________________________________
11 | % Copyright (C) 2002-2011 http://www.artefact.tk/
12 |
13 | % Guillaume Flandin
14 | % $Id: setfilename.m 4460 2011-09-05 14:52:16Z guillaume $
15 |
16 | tree.filename = filename;
17 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/@xmltree/xmltree.m:
--------------------------------------------------------------------------------
1 | function tree = xmltree(varargin)
2 | % XMLTREE/XMLTREE Constructor of the XMLTree class
3 | % FORMAT tree = xmltree(varargin)
4 | %
5 | % varargin - XML filename or XML string
6 | % tree - XMLTree Object
7 | %
8 | % tree = xmltree; % creates a minimal XML tree: ''
9 | % tree = xmltree('foo.xml'); % creates a tree from XML file 'foo.xml'
10 | % tree = xmltree('content') % creates a tree from string
11 | %__________________________________________________________________________
12 | %
13 | % This is the constructor of the XMLTree class.
14 | % It creates a tree of an XML 1.0 file (after parsing) that is stored
15 | % using a Document Object Model (DOM) representation.
16 | % See http://www.w3.org/TR/REC-xml for details about XML 1.0.
17 | % See http://www.w3.org/DOM/ for details about DOM platform.
18 | %__________________________________________________________________________
19 | % Copyright (C) 2002-2011 http://www.artefact.tk/
20 |
21 | % Guillaume Flandin
22 | % $Id: xmltree.m 4460 2011-09-05 14:52:16Z guillaume $
23 |
24 | switch(nargin)
25 | case 0
26 | tree.tree{1} = struct('type','element',...
27 | 'name','tag',...
28 | 'attributes',[],...
29 | 'contents',[],...
30 | 'parent',[],...
31 | 'uid',1);
32 | tree.filename = '';
33 | tree = class(tree,'xmltree');
34 | case 1
35 | if isa(varargin{1},'xmltree')
36 | tree = varargin{1};
37 | elseif ischar(varargin{1})
38 | % Input argument is an XML string
39 | if (~exist(varargin{1},'file') && ...
40 | ~isempty(xml_findstr(varargin{1},'<',1,1)))
41 | tree.tree = xml_parser(varargin{1});
42 | tree.filename = '';
43 | % Input argument is an XML filename
44 | else
45 | fid = fopen(varargin{1},'rt');
46 | if (fid == -1)
47 | error(['[XMLTree] Cannot open ' varargin{1}]);
48 | end
49 | xmlstr = fread(fid,'*char')';
50 | %xmlstr = fscanf(fid,'%c');
51 | fclose(fid);
52 | tree.tree = xml_parser(xmlstr);
53 | tree.filename = varargin{1};
54 | end
55 | tree = class(tree,'xmltree');
56 | else
57 | error('[XMLTree] Bad input argument');
58 | end
59 | otherwise
60 | error('[XMLTree] Too many input arguments');
61 | end
62 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/LICENSE.fieldtrip:
--------------------------------------------------------------------------------
1 | FieldTrip - the MATLAB toolbox for MEG and EEG analysis
2 | Copyright (C) 2002-2014 by the members of the FieldTrip team
3 |
4 | This program is free software; you can redistribute it and/or
5 | modify it under the terms of the GNU General Public License
6 | as published by the Free Software Foundation; either version 2
7 | of the License, or any later version.
8 |
9 | This program is distributed in the hope that it will be useful,
10 | but WITHOUT ANY WARRANTY; without even the implied warranty of
11 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 | GNU General Public License for more details.
13 |
14 | You should have received a copy of the GNU General Public License
15 | along with this program; if not, write to the Free Software
16 | Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
17 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/LICENSE.gifti:
--------------------------------------------------------------------------------
1 | GIfTI - a MATLAB GIfTI Library
2 | Copyright (C) 2008-2015 Guillaume Flandin
3 |
4 | This program is free software; you can redistribute it and/or
5 | modify it under the terms of the GNU General Public License
6 | as published by the Free Software Foundation; either version 2
7 | of the License, or any later version.
8 |
9 | This program is distributed in the hope that it will be useful,
10 | but WITHOUT ANY WARRANTY; without even the implied warranty of
11 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 | GNU General Public License for more details.
13 |
14 | You should have received a copy of the GNU General Public License
15 | along with this program; if not, write to the Free Software
16 | Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
17 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/LICENSE.xmltree:
--------------------------------------------------------------------------------
1 | XMLTree - an XML toolbox for MATLAB
2 | Copyright (C) 2008 Guillaume Flandin
3 |
4 | This program is free software; you can redistribute it and/or
5 | modify it under the terms of the GNU General Public License
6 | as published by the Free Software Foundation; either version 2
7 | of the License, or any later version.
8 |
9 | This program is distributed in the hope that it will be useful,
10 | but WITHOUT ANY WARRANTY; without even the implied warranty of
11 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 | GNU General Public License for more details.
13 |
14 | You should have received a copy of the GNU General Public License
15 | along with this program; if not, write to the Free Software
16 | Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
17 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/README.md:
--------------------------------------------------------------------------------
1 | MATLAB code for reading and writing CIFTI files
2 | ===============================================
3 |
4 | NOTE: The code available in this repository has known behaviors that are problematic when using fMRI CIFTI data processed with HCP templates. For fMRI CIFTI data, we recommend and provide support for using ciftiopen/ciftisave/ciftisavereset, available at https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ, FAQ #2, option B.
5 |
6 | This repository contains a subset of the MATLAB code from the FieldTrip and
7 | the SPM toolboxes. It should allow MATLAB users and developers to integrate
8 | the CIFTI file format in their analysis pipelines, using the data and tools
9 | of the Human Connectome Project (HCP).
10 |
11 | See http://www.humanconnectome.org for details on the HCP.
12 |
13 | See http://www.nitrc.org/forum/forum.php?forum_id=1955 for details on CIFTI.
14 |
15 | See http://www.fieldtriptoolbox.org for details on FieldTrip.
16 |
17 | See http://www.fil.ion.ucl.ac.uk/spm/ for details on SPM.
18 |
19 | See the LICENSE and GPL files for copyright information.
20 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/VERSION:
--------------------------------------------------------------------------------
1 | Sat Apr 16 08:08:11 UTC 2016
2 | https://github.com/fieldtrip/fieldtrip/commits/d6ada706fdb09f824c38e4de7655757076be4a21
3 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/documentation/CIFTI-2_Appendix_FINAL_1March2014.pdf:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/BrainDynamicsUSYD/BrainVortexToolbox/69d681fde5c3f3cf6508c6aeba5d7fab64373588/Sub-function/cifti-matlab-master/documentation/CIFTI-2_Appendix_FINAL_1March2014.pdf
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/Sub-function/cifti-matlab-master/documentation/CIFTI-2_Main_FINAL_1March2014.pdf:
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https://raw.githubusercontent.com/BrainDynamicsUSYD/BrainVortexToolbox/69d681fde5c3f3cf6508c6aeba5d7fab64373588/Sub-function/cifti-matlab-master/documentation/CIFTI-2_Main_FINAL_1March2014.pdf
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/emptyfile.txt:
--------------------------------------------------------------------------------
1 |
2 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/copyfields.m:
--------------------------------------------------------------------------------
1 | function b = copyfields(a, b, fields)
2 |
3 | % COPYFIELDS copies a selection of the fields from one structure to another
4 | %
5 | % Use as
6 | % b = copyfields(a, b, fields);
7 | % which copies the specified fields over from structure a to structure b. Fields that
8 | % are specified but not present will be silently ignored.
9 | %
10 | % See also KEEPFIELDS, REMOVEFIELDS, RENAMEFIELDS
11 |
12 | % Copyright (C) 2014, Robert Oostenveld
13 | %
14 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
15 | % for the documentation and details.
16 | %
17 | % FieldTrip is free software: you can redistribute it and/or modify
18 | % it under the terms of the GNU General Public License as published by
19 | % the Free Software Foundation, either version 3 of the License, or
20 | % (at your option) any later version.
21 | %
22 | % FieldTrip is distributed in the hope that it will be useful,
23 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
24 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 | % GNU General Public License for more details.
26 | %
27 | % You should have received a copy of the GNU General Public License
28 | % along with FieldTrip. If not, see .
29 | %
30 | % $Id$
31 |
32 | if isempty(a)
33 | % this prevents problems if a is an empty double, i.e. []
34 | return
35 | end
36 |
37 | if isempty(b)
38 | % this prevents problems if a is an empty double, i.e. []
39 | b = keepfields(a, fields);
40 | return
41 | end
42 |
43 | if ischar(fields)
44 | fields = {fields};
45 | elseif ~iscell(fields)
46 | error('fields input argument must be a cell array of strings or a single string');
47 | end
48 |
49 | fields = intersect(fieldnames(a), fields);
50 | for i=1:numel(fields)
51 | b.(fields{i}) = a.(fields{i});
52 | end
53 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/fetch_url.m:
--------------------------------------------------------------------------------
1 | function filename = fetch_url(filename)
2 |
3 | % FETCH_URL checks the filename and downloads the file to a local copy in
4 | % case it is specified as an Universal Resource Locator. It returns the
5 | % name of the temporary file on the local filesystem.
6 | %
7 | % Use as
8 | % filename = fetch_url(filename)
9 | %
10 | % In case the filename does not specify an URL, it just returns the original
11 | % filename.
12 |
13 | % Copyright (C) 2012 Robert Oostenveld
14 | %
15 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
16 | % for the documentation and details.
17 | %
18 | % FieldTrip is free software: you can redistribute it and/or modify
19 | % it under the terms of the GNU General Public License as published by
20 | % the Free Software Foundation, either version 3 of the License, or
21 | % (at your option) any later version.
22 | %
23 | % FieldTrip is distributed in the hope that it will be useful,
24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 | % GNU General Public License for more details.
27 | %
28 | % You should have received a copy of the GNU General Public License
29 | % along with FieldTrip. If not, see .
30 | %
31 | % $Id$
32 |
33 | if filetype_check_uri(filename, 'sftp')
34 | [user, host, filename] = filetype_check_uri(filename);
35 | [p, f, x] = fileparts(filename);
36 | p = tempdir;
37 | try
38 | mkdir(p);
39 | cmd = sprintf('sftp %s@%s:%s %s', user, host, filename, fullfile(p, [f x]));
40 | system(cmd);
41 | filename = fullfile(p, [f x]);
42 | end
43 | % elseif filetype_check_uri(filename, 'http')
44 | % FIXME the http scheme should be supported using default MATLAB
45 | % elseif filetype_check_uri(filename, 'ftp')
46 | % FIXME the http scheme should be supported using default MATLAB
47 | % elseif filetype_check_uri(filename, 'smb')
48 | % FIXME the smb scheme can be supported using smbclient
49 | end
50 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/filetype_check_extension.m:
--------------------------------------------------------------------------------
1 | function [val] = filetype_check_extension(filename, ext)
2 |
3 | % FILETYPE_CHECK_EXTENSION helper function to determine the file type
4 | % by performing a case insensitive string comparison of the extension.
5 |
6 | % Copyright (C) 2003-2012 Robert Oostenveld
7 | %
8 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
9 | % for the documentation and details.
10 | %
11 | % FieldTrip is free software: you can redistribute it and/or modify
12 | % it under the terms of the GNU General Public License as published by
13 | % the Free Software Foundation, either version 3 of the License, or
14 | % (at your option) any later version.
15 | %
16 | % FieldTrip is distributed in the hope that it will be useful,
17 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
18 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 | % GNU General Public License for more details.
20 | %
21 | % You should have received a copy of the GNU General Public License
22 | % along with FieldTrip. If not, see .
23 | %
24 | % $Id$
25 |
26 | % these are for remembering the type on subsequent calls with the same input arguments
27 | persistent previous_argin previous_argout
28 |
29 | current_argin = {filename, ext};
30 | if isequal(current_argin, previous_argin)
31 | % don't do the detection again, but return the previous value from cache
32 | val = previous_argout;
33 | return
34 | end
35 |
36 | if iscell(filename)
37 | % compare the extension of multiple files
38 | val = zeros(size(filename));
39 | for i=1:length(filename)
40 | val(i) = filetype_check_extension(filename{i}, ext);
41 | end
42 | elseif iscell(ext)
43 | val = zeros(size(ext));
44 | for i=1:length(ext)
45 | val(i) = filetype_check_extension(filename, ext{i});
46 | end
47 | else
48 | % compare the extension of a single file
49 | if numel(filename).
24 | %
25 | % $Id$
26 |
27 | % these are for remembering the type on subsequent calls with the same input arguments
28 | persistent previous_argin previous_argout cache
29 |
30 | if nargin<3
31 | offset = 0;
32 | end
33 |
34 | if isempty(cache)
35 | cache = false;
36 | end
37 |
38 | current_argin = {filename, head, offset};
39 | if isequal(current_argin, previous_argin) && cache
40 | % don't do the detection again, but return the previous value from cache
41 | val = previous_argout;
42 | return
43 | end
44 |
45 | % from here on it should use the persistent variables as cache to speed up repeated calls
46 | cache = true;
47 |
48 | if iscell(filename)
49 | % compare the header of multiple files
50 | val = zeros(size(filename));
51 | for i=1:length(filename)
52 | val(i) = filetype_check_header(filename{i}, head, offset);
53 | end
54 | elseif isdir(filename)
55 | % a directory cannot have a header
56 | val = false;
57 | elseif ~exist(filename, 'file')
58 | val = false;
59 | cache = false; % the file does not exist now, but can exist later
60 | else
61 | % read the first few bytes from the file and compare them to the desired header
62 | fid = fopen(filename, 'rb');
63 | if fid<0
64 | ft_warning(sprintf('could not open %s', filename));
65 | val = false;
66 | else
67 | fseek(fid, offset, 'cof');
68 | if iscell(head)
69 | for i=1:length(head)
70 | len(i) = length(head{i});
71 | end
72 | [str, siz] = fread(fid, max(len), 'uint8');
73 | fclose(fid);
74 | for i=1:length(head)
75 | val = all(str(1:len(i))==head{i}(:));
76 | if val
77 | break
78 | end
79 | end
80 | else
81 | [str, siz] = fread(fid, length(head), 'uint8=>char');
82 | fclose(fid);
83 | if siz~=length(head)
84 | ft_warning(sprintf('could not read the header from %s', filename));
85 | val = false;
86 | else
87 | val = all(str(:)==head(:));
88 | end
89 | end
90 | end
91 | end
92 |
93 | % remember the current input and output arguments, so that they can be
94 | % reused on a subsequent call in case the same input argument is given
95 | current_argout = val;
96 | previous_argin = current_argin;
97 | previous_argout = current_argout;
98 |
99 | return % main()
100 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/find_outermost_boundary.m:
--------------------------------------------------------------------------------
1 | function [outermost, inside] = find_outermost_boundary(bnd)
2 |
3 | % FIND_OUTERMOST_BOUNDARY locates outermost compartment of a BEM model
4 | % by looking at the containment of the triangular meshes describing
5 | % the surface boundaries
6 | %
7 | % [outermost] = find_innermost_boundary(bnd)
8 | %
9 | % with the boundaries described by a struct array bnd with
10 | % bnd(i).pnt vertices of boundary i (matrix of size Nx3)
11 | % bnd(i).tri triangles of boundary i (matrix of size Mx3)
12 |
13 | % Copyright (C) 2003, Robert Oostenveld
14 | %
15 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
16 | % for the documentation and details.
17 | %
18 | % FieldTrip is free software: you can redistribute it and/or modify
19 | % it under the terms of the GNU General Public License as published by
20 | % the Free Software Foundation, either version 3 of the License, or
21 | % (at your option) any later version.
22 | %
23 | % FieldTrip is distributed in the hope that it will be useful,
24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 | % GNU General Public License for more details.
27 | %
28 | % You should have received a copy of the GNU General Public License
29 | % along with FieldTrip. If not, see .
30 | %
31 | % $Id$
32 |
33 | ncmp = length(bnd);
34 |
35 | % try to locate the outermost compartment
36 | for i=1:ncmp
37 | for j=1:ncmp
38 | % determine for a single vertex on each surface if it is inside or outside the other surfaces
39 | curpos1 = bnd(i).pos(1,:); % any point on the boundary is ok
40 | curpos = bnd(j).pos;
41 | curtri = bnd(j).tri;
42 | if i==j
43 | inside(i,j) = 0;
44 | else
45 | inside(i,j) = bounding_mesh(curpos1, curpos, curtri);
46 | end
47 | end
48 | end
49 | % assume that the sources are in the innermost compartment
50 | tmp = sum(inside, 2);
51 | [i, outermost] = min(tmp);
52 |
53 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/fixname.m:
--------------------------------------------------------------------------------
1 | function str = fixname(str)
2 |
3 | % FIXNAME changes all inappropriate characters in a sting into '_'
4 | % such that it can be used as a filename or as a structure field name. If
5 | % the string begins with a numeric digit, an 'x' is prepended.
6 | %
7 | % Use as
8 | % str = fixname(str)
9 | %
10 | % MATLAB 2014a introduces the matlab.lang.makeValidName and
11 | % matlab.lang.makeUniqueStrings functions for constructing unique MATLAB identifiers,
12 | % but this particular implementation also works with older MATLAB versions.
13 | %
14 | % See also DEBLANK
15 |
16 | % Copyright (C) 2012-2016, Robert Oostenveld
17 | %
18 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
19 | % for the documentation and details.
20 | %
21 | % FieldTrip is free software: you can redistribute it and/or modify
22 | % it under the terms of the GNU General Public License as published by
23 | % the Free Software Foundation, either version 3 of the License, or
24 | % (at your option) any later version.
25 | %
26 | % FieldTrip is distributed in the hope that it will be useful,
27 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
28 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 | % GNU General Public License for more details.
30 | %
31 | % You should have received a copy of the GNU General Public License
32 | % along with FieldTrip. If not, see .
33 | %
34 | % $Id$
35 |
36 | str = lower(str);
37 | str(regexp(str,'\W')) = '_';
38 |
39 | while(str(1) == '_'), str = str(2:end); end; % remove all underscore at the begin of the string
40 | while(str(end) == '_'), str = str(1:end-1); end; % remove all underscore at the end of the string
41 |
42 | if int8(str(1))<58 && int8(str(1))>47
43 | % the string begins with a digit, prepend an 'x'
44 | str = ['x' str];
45 | end
46 |
47 | % truncate the string if it's too long: MATLAB maximizes the string length to 63 characters (and throws a warning when truncating)
48 | if numel(str)>63
49 | str = str(1:63);
50 | ft_warning(sprintf('%s exceeds MATLAB''s maximum name length of 63 characters and has been truncated to %s', str, str(1:63)));
51 | end
52 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/fixpos.m:
--------------------------------------------------------------------------------
1 | function mesh = fixpos(mesh, recurse)
2 |
3 | % FIXPOS helper function to ensure that meshes are described properly
4 |
5 | if nargin==1
6 | recurse = 1;
7 | end
8 |
9 | if isa(mesh, 'delaunayTriangulation')
10 | % convert to structure, otherwise the code below won't work properly
11 | ws = warning('off', 'MATLAB:structOnObject');
12 | mesh = struct(mesh);
13 | warning(ws);
14 | end
15 |
16 | if ~isa(mesh, 'struct')
17 | return;
18 | end
19 |
20 | if numel(mesh)>1
21 | % loop over all individual elements
22 | clear tmp
23 | for i=1:numel(mesh)
24 | % this is to prevent an "Subscripted assignment between dissimilar structures" error
25 | tmp(i) = fixpos(mesh(i));
26 | end
27 | mesh = tmp;
28 | clear tmp
29 | return
30 | end
31 |
32 | % convert from MATLAB delaunayTriangulation output to FieldTrip convention
33 | if isfield(mesh, 'Points') && isfield(mesh, 'ConnectivityList')
34 | mesh.pos = mesh.Points;
35 | switch size(mesh.ConnectivityList,2)
36 | case 2
37 | mesh.edge = mesh.ConnectivityList;
38 | case 3
39 | mesh.tri = mesh.ConnectivityList;
40 | case 4
41 | mesh.tet = mesh.ConnectivityList;
42 | case 8
43 | mesh.hex = mesh.ConnectivityList;
44 | otherwise
45 | error('unsupported ConnectivityList')
46 | end % switch
47 | mesh = rmfield(mesh, {'Points', 'ConnectivityList', 'Constraints'});
48 | end
49 |
50 | % convert from BrainStorm/MNE to FieldTrip convention
51 | if isfield(mesh, 'vertices') && isfield(mesh, 'faces')
52 | mesh.pos = mesh.vertices;
53 | mesh.tri = mesh.faces;
54 | mesh = rmfield(mesh, {'faces', 'vertices'});
55 | elseif isfield(mesh, 'Vertices') && isfield(mesh, 'Faces')
56 | mesh.pos = mesh.Vertices;
57 | mesh.tri = mesh.Faces;
58 | mesh = rmfield(mesh, {'Faces', 'Vertices'});
59 | end
60 |
61 | % replace pnt by pos
62 | if isfield(mesh, 'pnt')
63 | mesh.pos = mesh.pnt;
64 | mesh = rmfield(mesh, 'pnt');
65 | end
66 |
67 | if recurse<3
68 | % recurse into substructures, not too deep
69 | fn = fieldnames(mesh);
70 | fn = setdiff(fn, {'cfg'}); % don't recurse into the cfg structure
71 | for i=1:length(fn)
72 | if isstruct(mesh.(fn{i}))
73 | mesh.(fn{i}) = fixpos(mesh.(fn{i}), recurse+1);
74 | end
75 | end
76 | end
77 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/ft_estimate_units.m:
--------------------------------------------------------------------------------
1 | function unit = ft_estimate_units(size)
2 |
3 | % FT_ESTIMATE_UNITS tries to determine the units of a geometrical object by
4 | % looking at its size and by relating this to the approximate size of the
5 | % human head according to the following table:
6 | % from 0.050 to 0.500 -> meter
7 | % from 0.500 to 5.000 -> decimeter
8 | % from 5.000 to 50.000 -> centimeter
9 | % from 50.000 to 500.000 -> millimeter
10 | %
11 | % Use as
12 | % unit = ft_estimate_units(size)
13 | %
14 | % This function will return one of the following strings
15 | % 'm'
16 | % 'dm'
17 | % 'cm'
18 | % 'mm'
19 | %
20 | % See also FT_CONVERT_UNITS
21 |
22 | % Copyright (C) 2009-2013, Robert Oostenveld
23 | %
24 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
25 | % for the documentation and details.
26 | %
27 | % FieldTrip is free software: you can redistribute it and/or modify
28 | % it under the terms of the GNU General Public License as published by
29 | % the Free Software Foundation, either version 3 of the License, or
30 | % (at your option) any later version.
31 | %
32 | % FieldTrip is distributed in the hope that it will be useful,
33 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
34 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 | % GNU General Public License for more details.
36 | %
37 | % You should have received a copy of the GNU General Public License
38 | % along with FieldTrip. If not, see .
39 | %
40 | % $Id$
41 |
42 | % do some magic based on the size
43 | unit = {'m', 'dm', 'cm', 'mm'};
44 | est = log10(size)+1.8;
45 | indx = round(est);
46 |
47 | if indx>length(unit)
48 | indx = length(unit);
49 | warning('assuming that the units are "%s"', unit{indx});
50 | elseif indx<1
51 | indx = 1;
52 | warning('assuming that the units are "%s"', unit{indx});
53 | elseif abs((est-floor(est)) - 0.5)<0.1
54 | % the size estimate falls within the expected range, but is not very decisive
55 | % for example round(1.49) results in meter, but round(1.51) results in decimeter
56 | warning('the estimated units are not very decisive, assuming that the units are "%s"', unit{indx});
57 | end
58 |
59 | unit = unit{indx};
60 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/ft_getopt.m:
--------------------------------------------------------------------------------
1 | function val = ft_getopt(opt, key, default, emptymeaningful)
2 |
3 | % FT_GETOPT gets the value of a specified option from a configuration structure
4 | % or from a cell-array with key-value pairs.
5 | %
6 | % Use as
7 | % val = ft_getopt(s, key, default, emptymeaningful)
8 | % where the input values are
9 | % s = structure or cell-array
10 | % key = string
11 | % default = any valid MATLAB data type
12 | % emptymeaningful = boolean value (optional, default = 0)
13 | %
14 | % If the key is present as field in the structure, or as key-value
15 | % pair in the cell-array, the corresponding value will be returned.
16 | %
17 | % If the key is not present, ft_getopt will return an empty array.
18 | %
19 | % If the key is present but has an empty value, then the emptymeaningful
20 | % flag specifies whether the empty value or the default value should
21 | % be returned. If emptymeaningful==true, then an empty array will be
22 | % returned. If emptymeaningful==false, then the specified default will
23 | % be returned.
24 | %
25 | % See also FT_SETOPT, FT_CHECKOPT
26 |
27 | % Copyright (C) 2011-2012, Robert Oostenveld
28 | %
29 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
30 | % for the documentation and details.
31 | %
32 | % FieldTrip is free software: you can redistribute it and/or modify
33 | % it under the terms of the GNU General Public License as published by
34 | % the Free Software Foundation, either version 3 of the License, or
35 | % (at your option) any later version.
36 | %
37 | % FieldTrip is distributed in the hope that it will be useful,
38 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
39 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
40 | % GNU General Public License for more details.
41 | %
42 | % You should have received a copy of the GNU General Public License
43 | % along with FieldTrip. If not, see .
44 | %
45 | % $Id$
46 |
47 | if nargin<3
48 | default = [];
49 | end
50 |
51 | if nargin < 4
52 | emptymeaningful = 0;
53 | end
54 |
55 | if isa(opt, 'struct') || isa(opt, 'config')
56 | % get the key-value from the structure
57 | fn = fieldnames(opt);
58 | if ~any(strcmp(key, fn))
59 | val = default;
60 | else
61 | val = opt.(key);
62 | end
63 |
64 | elseif isa(opt, 'cell')
65 | % get the key-value from the cell-array
66 | if mod(length(opt),2)
67 | error('optional input arguments should come in key-value pairs, i.e. there should be an even number');
68 | end
69 |
70 | % the 1st, 3rd, etc. contain the keys, the 2nd, 4th, etc. contain the values
71 | keys = opt(1:2:end);
72 | vals = opt(2:2:end);
73 |
74 | % the following may be faster than cellfun(@ischar, keys)
75 | valid = false(size(keys));
76 | for i=1:numel(keys)
77 | valid(i) = ischar(keys{i});
78 | end
79 |
80 | if ~all(valid)
81 | error('optional input arguments should come in key-value pairs, the optional input argument %d is invalid (should be a string)', i);
82 | end
83 |
84 | hit = find(strcmpi(key, keys));
85 | if isempty(hit)
86 | % the requested key was not found
87 | val = default;
88 | elseif length(hit)==1
89 | % the requested key was found
90 | val = vals{hit};
91 | else
92 | error('multiple input arguments with the same name');
93 | end
94 |
95 | elseif isempty(opt)
96 | % no options are specified, return default
97 | val = default;
98 | end % isstruct or iscell or isempty
99 |
100 | if isempty(val) && ~isempty(default) && ~emptymeaningful
101 | % use the default value instead of the empty input that was specified:
102 | % this applies for example if you do functionname('key', []), where
103 | % the empty is meant to indicate that the user does not know or care
104 | % what the value is
105 | val = default;
106 | end
107 |
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/Sub-function/cifti-matlab-master/private/ft_read_vol.m:
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1 | function [headmodel] = ft_read_vol(filename, varargin)
2 |
3 | % FT_READ_VOL reads a volume conduction model from various manufacturer
4 | % specific files. Currently supported are ASA, CTF, Neuromag, MBFYS
5 | % and Matlab.
6 | %
7 | % Use as
8 | % headmodel = ft_read_vol(filename, ...)
9 | %
10 | % Additional options should be specified in key-value pairs and can be
11 | % 'fileformat' string
12 | %
13 | % The volume conduction model is represented as a structure with fields
14 | % that depend on the type of model.
15 | %
16 | % See also FT_TRANSFORM_VOL, FT_PREPARE_VOL_SENS, FT_COMPUTE_LEADFIELD
17 |
18 | % Copyright (C) 2008-2013 Robert Oostenveld
19 | %
20 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
21 | % for the documentation and details.
22 | %
23 | % FieldTrip is free software: you can redistribute it and/or modify
24 | % it under the terms of the GNU General Public License as published by
25 | % the Free Software Foundation, either version 3 of the License, or
26 | % (at your option) any later version.
27 | %
28 | % FieldTrip is distributed in the hope that it will be useful,
29 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
30 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31 | % GNU General Public License for more details.
32 | %
33 | % You should have received a copy of the GNU General Public License
34 | % along with FieldTrip. If not, see .
35 | %
36 | % $Id$
37 |
38 | % optionally get the data from the URL and make a temporary local copy
39 | filename = fetch_url(filename);
40 |
41 | % test whether the file exists
42 | if ~exist(filename)
43 | error(sprintf('file ''%s'' does not exist', filename));
44 | end
45 |
46 | % get the options
47 | fileformat = ft_getopt(varargin, 'fileformat', ft_filetype(filename));
48 |
49 | switch fileformat
50 | case 'matlab'
51 | % FIXME in the future the file should contain the variable 'headmodel' instead of vol
52 | headmodel = loadvar(filename, 'vol');
53 |
54 | case 'ctf_hdm'
55 | headmodel = read_ctf_hdm(filename);
56 |
57 | case 'asa_vol'
58 | headmodel = read_asa_vol(filename);
59 | headmodel.type = 'asa';
60 |
61 | case 'mbfys_ama'
62 | ama = loadama(filename);
63 | headmodel = ama2vol(ama);
64 |
65 | otherwise
66 | error('unknown fileformat for volume conductor model');
67 | end
68 |
69 | % this will ensure that the structure is up to date, e.g. that the type is correct and that it has units
70 | headmodel = ft_datatype_headmodel(headmodel);
71 |
72 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/ft_struct2double.m:
--------------------------------------------------------------------------------
1 | function [x] = ft_struct2double(x, maxdepth)
2 |
3 | % FT_STRUCT2DOUBLE converts all single precision numeric data in a structure
4 | % into double precision. It will also convert plain matrices and
5 | % cell-arrays.
6 | %
7 | % Use as
8 | % x = ft_struct2double(x)
9 | %
10 | % Starting from MATLAB 7.0, you can use single precision data in your
11 | % computations, i.e. you do not have to convert back to double precision.
12 | %
13 | % MATLAB version 6.5 and older only support single precision for storing
14 | % data in memory or on disk, but do not allow computations on single
15 | % precision data. Therefore you should converted your data from single to
16 | % double precision after reading from file.
17 | %
18 | % See also FT_STRUCT2SINGLE
19 |
20 | % Copyright (C) 2005-2014, Robert Oostenveld
21 | %
22 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
23 | % for the documentation and details.
24 | %
25 | % FieldTrip is free software: you can redistribute it and/or modify
26 | % it under the terms of the GNU General Public License as published by
27 | % the Free Software Foundation, either version 3 of the License, or
28 | % (at your option) any later version.
29 | %
30 | % FieldTrip is distributed in the hope that it will be useful,
31 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
32 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
33 | % GNU General Public License for more details.
34 | %
35 | % You should have received a copy of the GNU General Public License
36 | % along with FieldTrip. If not, see .
37 | %
38 | % $Id$
39 |
40 | if nargin<2
41 | maxdepth = inf;
42 | end
43 |
44 | % convert the data, work recursively through the complete structure
45 | x = convert(x, 0, maxdepth);
46 |
47 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
48 | % this subfunction does the actual work
49 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
50 | function [a] = convert(a, depth, maxdepth)
51 |
52 | if depth>maxdepth
53 | error('recursive depth exceeded');
54 | end
55 |
56 | switch class(a)
57 | case 'struct'
58 | % process all fields of the structure recursively
59 | fna = fieldnames(a);
60 | % process all elements of the array
61 | for j=1:length(a(:))
62 | % warning, this is a recursive call to traverse nested structures
63 | for i=1:length(fna)
64 | fn = fna{i};
65 | ra = getfield(a(j), fn);
66 | ra = convert(ra, depth+1, maxdepth);
67 | a(j) = setfield(a(j), fn, ra);
68 | end
69 | end
70 |
71 | case 'cell'
72 | % process all elements of the cell-array recursively
73 | % warning, this is a recursive call to traverse nested structures
74 | for i=1:length(a(:))
75 | a{i} = convert(a{i}, depth+1, maxdepth);
76 | end
77 |
78 | case {'single' 'int64' 'uint64' 'int32' 'uint32' 'int16' 'uint16' 'int8' 'uint8'}
79 | % convert the values to double precision
80 | a = double(a);
81 |
82 | case 'double'
83 | % keep as it is
84 |
85 | otherwise
86 | % do nothing
87 | end
88 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/getdimsiz.m:
--------------------------------------------------------------------------------
1 | function dimsiz = getdimsiz(data, field)
2 |
3 | % GETDIMSIZ
4 | %
5 | % Use as
6 | % dimsiz = getdimsiz(data, field)
7 | %
8 | % If the length of the vector that is returned is smaller than the
9 | % number of dimensions that you would expect from GETDIMORD, you
10 | % should assume that it has trailing singleton dimensions.
11 | %
12 | % Example use
13 | % dimord = getdimord(datastructure, fieldname);
14 | % dimtok = tokenize(dimord, '_');
15 | % dimsiz = getdimsiz(datastructure, fieldname);
16 | % dimsiz(end+1:length(dimtok)) = 1; % there can be additional trailing singleton dimensions
17 | %
18 | % See also GETDIMORD, GETDATFIELD
19 |
20 | if ~isfield(data, field) && isfield(data, 'avg') && isfield(data.avg, field)
21 | field = ['avg.' field];
22 | elseif ~isfield(data, field) && isfield(data, 'trial') && isfield(data.trial, field)
23 | field = ['trial.' field];
24 | elseif ~isfield(data, field)
25 | error('field "%s" not present in data', field);
26 | end
27 |
28 | if strncmp(field, 'avg.', 4)
29 | prefix = [];
30 | field = field(5:end); % strip the avg
31 | data.(field) = data.avg.(field); % move the avg into the main structure
32 | data = rmfield(data, 'avg');
33 | elseif strncmp(field, 'trial.', 6)
34 | prefix = numel(data.trial);
35 | field = field(7:end); % strip the trial
36 | data.(field) = data.trial(1).(field); % move the first trial into the main structure
37 | data = rmfield(data, 'trial');
38 | else
39 | prefix = [];
40 | end
41 |
42 | dimsiz = cellmatsize(data.(field));
43 |
44 | % add nrpt in case of source.trial
45 | dimsiz = [prefix dimsiz];
46 |
47 | end % main function
48 |
49 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
50 | % SUBFUNCTION to determine the size of data representations like {pos}_ori_time
51 | % FIXME this will fail for {xxx_yyy}_zzz
52 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
53 | function siz = cellmatsize(x)
54 | if iscell(x)
55 | if isempty(x)
56 | siz = 0;
57 | return % nothing else to do
58 | elseif isvector(x)
59 | cellsize = numel(x); % the number of elements in the cell-array
60 | else
61 | cellsize = size(x);
62 | x = x(:); % convert to vector for further size detection
63 | end
64 | [dum, indx] = max(cellfun(@numel, x));
65 | matsize = size(x{indx}); % the size of the content of the cell-array
66 | siz = [cellsize matsize]; % concatenate the two
67 | else
68 | siz = size(x);
69 | end
70 | end % function cellmatsize
71 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/hasyokogawa.m:
--------------------------------------------------------------------------------
1 | function [version] = hasyokogawa(desired)
2 |
3 | % HASYOKOGAWA tests whether the data input toolbox for MEG systems by
4 | % Yokogawa (www.yokogawa.com, designed by KIT/EagleTechnology) is
5 | % installed. Only the newest version of the toolbox is accepted.
6 | %
7 | % Use as
8 | % string = hasyokogawa;
9 | % which returns a string describing the toolbox version, e.g. "12bitBeta3",
10 | % "16bitBeta3", or "16bitBeta6" for preliminary versions, or '1.4' for the
11 | % official Yokogawa MEG Reader Toolbox. An empty string is returned if the toolbox
12 | % is not installed. The string "unknown" is returned if it is installed but
13 | % the version is unknown.
14 | %
15 | % Alternatively you can use it as
16 | % [boolean] = hasyokogawa(desired);
17 | % where desired is a string with the desired version.
18 | %
19 | % See also READ_YOKOGAWA_HEADER, READ_YOKOGAWA_DATA, READ_YOKOGAWA_EVENT,
20 | % YOKOGAWA2GRAD
21 |
22 | % Copyright (C) 2010, Tilmann Sander-Thoemmes
23 | %
24 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
25 | % for the documentation and details.
26 | %
27 | % FieldTrip is free software: you can redistribute it and/or modify
28 | % it under the terms of the GNU General Public License as published by
29 | % the Free Software Foundation, either version 3 of the License, or
30 | % (at your option) any later version.
31 | %
32 | % FieldTrip is distributed in the hope that it will be useful,
33 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
34 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 | % GNU General Public License for more details.
36 | %
37 | % You should have received a copy of the GNU General Public License
38 | % along with FieldTrip. If not, see .
39 | %
40 | % $Id$
41 |
42 | ws = warning('off', 'MATLAB:pfileOlderThanMfile');
43 |
44 | % there are a few versions of the old preliminary implementation, such as
45 | % 12bitBeta3, 16bitBeta3 and 16bitBeta6. In 2011 a completely new
46 | % implementation was officially released, which contains functions with
47 | % other names. At the time of writing this, the new implementation is
48 | % version 1.4.
49 |
50 | if exist('getYkgwVersion')
51 | res = getYkgwVersion();
52 | version = res.version;
53 |
54 | elseif exist('GetMeg160ADbitInfoM') || exist('GetMeg160ChannelInfoM') || exist('GetMeg160ContinuousRawDataM')
55 | % start with unknown, try to refine the version
56 | version = 'unknown';
57 |
58 | try
59 | % Call some functions with input argument "Inf": If
60 | % the functions are present they return their revision number.
61 | % Call first GetMeg160ADbitInfoM as this is not present in
62 | % the 12bit library, in case of error the "catch" part will take over.
63 | % The code below is intentionally very literal for easy of reading.
64 | res = textscan(evalc('GetMeg160ADbitInfoM(Inf);'),'%s %s %c %s %s %d');
65 | rev_ADbitInfoM = res{6};
66 | res = textscan(evalc('GetMeg160ChannelInfoM(Inf);'),'%s %s %c %s %s %d');
67 | rev_ChannelInfoM = res{6};
68 | res = textscan(evalc('GetMeg160AmpGainM(Inf);'),'%s %s %c %s %s %d');
69 | rev_AmpGainM = res{6};
70 | res = textscan(evalc('GetMeg160MatchingInfoM(Inf);'),'%s %s %c %s %s %d');
71 | rev_MatchingInfoM = res{6};
72 | if [0 2 1 5] == [rev_ADbitInfoM rev_ChannelInfoM rev_AmpGainM rev_MatchingInfoM]
73 | version='16bitBeta3';
74 | elseif [0 2 2 5] == [rev_ADbitInfoM rev_ChannelInfoM rev_AmpGainM rev_MatchingInfoM]
75 | version='16bitBeta6';
76 | else
77 | warning('The version of the installed Yokogawa toolbox cannot be determined.');
78 | end
79 | catch
80 | m = lasterror;
81 | m.identifier;
82 | if strcmp(m.identifier, 'MATLAB:UndefinedFunction') || strcmp(m.identifier, 'MATLAB:FileIO:InvalidFid')
83 | if (exist('GetMeg160ChannelInfoM') && exist('GetMeg160ContinuousRawDataM'));
84 | version = '12bitBeta3';
85 | end
86 | end
87 | end
88 |
89 | else
90 | % return empty if none of them is present
91 | version = [];
92 | end
93 |
94 | if nargin>0
95 | % return a true/false value
96 | if isempty(version)
97 | version = false;
98 | else
99 | version = strcmpi(version, desired);
100 | end
101 | end
102 |
103 | % revert to the original warning state
104 | warning(ws);
105 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/individual2sn.m:
--------------------------------------------------------------------------------
1 | function [warped]= individual2sn(P, input)
2 |
3 | % INDIVIDUAL2SN warps the input coordinates (defined as Nx3 matrix) from
4 | % individual headspace coordinates into normalised MNI coordinates, using the
5 | % (inverse of the) warp parameters defined in the structure spmparams.
6 | %
7 | % this is code inspired by nutmeg and spm: nut_mri2mni, nut_spm_sn2def and
8 | % nut_spm_invdef which were themselves modified from code originally written
9 | % by John Ashburner:
10 | % http://www.sph.umich.edu/~nichols/JohnsGems2.html
11 | %
12 | % Use as
13 | % [warped] = individual2sn(P, input)
14 | %
15 | % Input parameters:
16 | % P = structure that contains the contents of an spm generated _sn.mat
17 | % file
18 | % input = Nx3 array containing the input positions
19 |
20 | % Copyright (C) 2013, Jan-Mathijs Schoffelen
21 | %
22 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
23 | % for the documentation and details.
24 | %
25 | % FieldTrip is free software: you can redistribute it and/or modify
26 | % it under the terms of the GNU General Public License as published by
27 | % the Free Software Foundation, either version 3 of the License, or
28 | % (at your option) any later version.
29 | %
30 | % FieldTrip is distributed in the hope that it will be useful,
31 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
32 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
33 | % GNU General Public License for more details.
34 | %
35 | % You should have received a copy of the GNU General Public License
36 | % along with FieldTrip. If not, see .
37 | %
38 | % $Id$
39 |
40 | ft_hastoolbox('spm8up', 1);
41 |
42 | % The following is a three-step procedure
43 |
44 | % 1: create the spatial deformation field from the sn parameters
45 | [Def, M] = get_sn2def(P);
46 |
47 | % 2a: invert the spatial deformation field
48 | [p,f,e] = fileparts(which('spm_invdef'));
49 | templatedirname = fullfile(p,'templates');
50 | d = dir([templatedirname,'/T1*']);
51 | VT = spm_vol(fullfile(templatedirname,d(1).name));
52 | [iy1,iy2,iy3] = spm_invdef(Def{1},Def{2},Def{3},VT.dim(1:3),inv(VT.mat),M);
53 |
54 | % 2b: write the deformation fields in x/y/z direction to temporary files
55 | V1.fname = [tempname '.img'];
56 | V1.dim(1:3) = VT.dim(1:3);
57 | V1.pinfo = [1 0 0]';
58 | V1.mat = VT.mat;
59 | V1.dt = [64 0];
60 | V1.descrip = 'Inverse deformation field';
61 | spm_write_vol(V1,iy1);
62 |
63 | V2.fname = [tempname '.img'];
64 | V2.dim(1:3) = VT.dim(1:3);
65 | V2.pinfo = [1 0 0]';
66 | V2.mat = VT.mat;
67 | V2.dt = [64 0];
68 | V2.descrip = 'Inverse deformation field';
69 | spm_write_vol(V2,iy2);
70 |
71 | V3.fname = [tempname '.img'];
72 | V3.dim(1:3) = VT.dim(1:3);
73 | V3.pinfo = [1 0 0]';
74 | V3.mat = VT.mat;
75 | V3.dt = [64 0];
76 | V3.descrip = 'Inverse deformation field';
77 | spm_write_vol(V3,iy3);
78 |
79 | % 3: extract the coordinates
80 | warped = ft_warp_apply(inv(V1.mat), input); % Express as voxel indices
81 | warped = cat(2, spm_sample_vol(V1,warped(:,1),warped(:,2),warped(:,3),1), ...
82 | spm_sample_vol(V2,warped(:,1),warped(:,2),warped(:,3),1), ...
83 | spm_sample_vol(V3,warped(:,1),warped(:,2),warped(:,3),1));
84 |
85 | %_______________________________________________________________________
86 | function [Def,mat] = get_sn2def(sn)
87 | % Convert a SPM _sn.mat file into a deformation field, and return it.
88 | % This is code that was taken from SPM8.
89 |
90 | dim = sn.VG(1).dim;
91 | x = 1:dim(1);
92 | y = 1:dim(2);
93 | z = 1:dim(3);
94 | mat = sn.VG(1).mat;
95 |
96 | [X,Y] = ndgrid(x,y);
97 |
98 | st = size(sn.Tr);
99 |
100 | if (prod(st) == 0),
101 | affine_only = true;
102 | basX = 0;
103 | basY = 0;
104 | basZ = 0;
105 | else
106 | affine_only = false;
107 | basX = spm_dctmtx(sn.VG(1).dim(1),st(1),x-1);
108 | basY = spm_dctmtx(sn.VG(1).dim(2),st(2),y-1);
109 | basZ = spm_dctmtx(sn.VG(1).dim(3),st(3),z-1);
110 | end,
111 |
112 | Def = single(0);
113 | Def(numel(x),numel(y),numel(z)) = 0;
114 | Def = {Def; Def; Def};
115 |
116 | for j=1:length(z)
117 | if (~affine_only)
118 | tx = reshape( reshape(sn.Tr(:,:,:,1),st(1)*st(2),st(3)) *basZ(j,:)', st(1), st(2) );
119 | ty = reshape( reshape(sn.Tr(:,:,:,2),st(1)*st(2),st(3)) *basZ(j,:)', st(1), st(2) );
120 | tz = reshape( reshape(sn.Tr(:,:,:,3),st(1)*st(2),st(3)) *basZ(j,:)', st(1), st(2) );
121 |
122 | X1 = X + basX*tx*basY';
123 | Y1 = Y + basX*ty*basY';
124 | Z1 = z(j) + basX*tz*basY';
125 | end
126 |
127 | Mult = sn.VF.mat*sn.Affine;
128 | if (~affine_only)
129 | X2= Mult(1,1)*X1 + Mult(1,2)*Y1 + Mult(1,3)*Z1 + Mult(1,4);
130 | Y2= Mult(2,1)*X1 + Mult(2,2)*Y1 + Mult(2,3)*Z1 + Mult(2,4);
131 | Z2= Mult(3,1)*X1 + Mult(3,2)*Y1 + Mult(3,3)*Z1 + Mult(3,4);
132 | else
133 | X2= Mult(1,1)*X + Mult(1,2)*Y + (Mult(1,3)*z(j) + Mult(1,4));
134 | Y2= Mult(2,1)*X + Mult(2,2)*Y + (Mult(2,3)*z(j) + Mult(2,4));
135 | Z2= Mult(3,1)*X + Mult(3,2)*Y + (Mult(3,3)*z(j) + Mult(3,4));
136 | end
137 |
138 | Def{1}(:,:,j) = single(X2);
139 | Def{2}(:,:,j) = single(Y2);
140 | Def{3}(:,:,j) = single(Z2);
141 | end;
142 | %_______________________________________________________________________
143 |
144 |
145 |
146 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/inflate_file.m:
--------------------------------------------------------------------------------
1 | function outputfile = inflate_file(inputfile)
2 |
3 | % INFLATE_FILE helper function to uncompress a compressed file of arbitrary
4 | % compression type. Returns the full path to the extracted file or
5 | % directory, which will be located in a temporary location.
6 |
7 | % Copyright (C) 2012 Eelke Spaak
8 | %
9 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
10 | % for the documentation and details.
11 | %
12 | % FieldTrip is free software: you can redistribute it and/or modify
13 | % it under the terms of the GNU General Public License as published by
14 | % the Free Software Foundation, either version 3 of the License, or
15 | % (at your option) any later version.
16 | %
17 | % FieldTrip is distributed in the hope that it will be useful,
18 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
19 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 | % GNU General Public License for more details.
21 | %
22 | % You should have received a copy of the GNU General Public License
23 | % along with FieldTrip. If not, see .
24 | %
25 | % $Id$
26 |
27 | % use a cache to prevent extracting the same file multiple times
28 | persistent extractcache;
29 | inputfilemd5 = fixname(CalcMD5(inputfile));
30 | if isfield(extractcache, inputfilemd5)
31 | outputfile = extractcache.(inputfilemd5);
32 | if exist(outputfile, 'file') % checks for files or folders
33 | fprintf('compressed dataset has already been extracted to %s\n', outputfile);
34 | return;
35 | else
36 | % apparently the file is gone
37 | extractcache = rmfield(extractcache, inputfilemd5);
38 | end
39 | end
40 |
41 | % determine compression type
42 | if filetype_check_extension(inputfile, 'zip')
43 | type = 'zip';
44 | elseif filetype_check_extension(inputfile, 'tar')...
45 | || filetype_check_extension(inputfile, '.tar.gz')...
46 | || filetype_check_extension(inputfile, 'tgz')
47 | type = 'tar';
48 | elseif filetype_check_extension(inputfile, 'gz')
49 | type = 'gzip';
50 | else
51 | error('unsupported compression type, only zip/tar(gz)/gz are supported');
52 | end
53 |
54 | % determine temporary output folder
55 | outputdir = [tempdir() inputfilemd5];
56 |
57 | % give some feedback
58 | fprintf('extracting compressed dataset to %s...\n', outputdir);
59 |
60 | % do appropriate inflation
61 | switch (type)
62 | case 'zip'
63 | unzip(inputfile, outputdir);
64 | case 'tar'
65 | untar(inputfile, outputdir);
66 | case 'gzip'
67 | gunzip(inputfile, outputdir);
68 | end
69 |
70 | % if we extracted only a single file (or directory), return path to that file, if it was a
71 | % set of files, return path to the biggeset file
72 | outfiles = dir(outputdir);
73 | if numel(outfiles) == 3 % first two will always be . and ..
74 | outputfile = [outputdir '/' outfiles(3).name];
75 | else
76 | siz = [outfiles.bytes];
77 | maxind = find(siz == max(siz),1); % use find() because we want at most 1
78 | outputfile = [outputdir '/' outfiles(maxind).name];
79 | end
80 |
81 | fprintf('extracted dataset is located at %s\n', outputfile);
82 | extractcache.(inputfilemd5) = outputfile;
83 |
84 | end
85 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/istrue.m:
--------------------------------------------------------------------------------
1 | function y = istrue(x)
2 |
3 | % ISTRUE ensures that a true/false input argument like "yes", "true"
4 | % or "on" is converted into a boolean
5 |
6 | % Copyright (C) 2009-2012, Robert Oostenveld
7 | %
8 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
9 | % for the documentation and details.
10 | %
11 | % FieldTrip is free software: you can redistribute it and/or modify
12 | % it under the terms of the GNU General Public License as published by
13 | % the Free Software Foundation, either version 3 of the License, or
14 | % (at your option) any later version.
15 | %
16 | % FieldTrip is distributed in the hope that it will be useful,
17 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
18 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 | % GNU General Public License for more details.
20 | %
21 | % You should have received a copy of the GNU General Public License
22 | % along with FieldTrip. If not, see .
23 | %
24 | % $Id$
25 |
26 | true_list = {'yes' 'true' 'on' 'y' };
27 | false_list = {'no' 'false' 'off' 'n' 'none'};
28 |
29 | if ischar(x)
30 | % convert string to boolean value
31 | if any(strcmpi(x, true_list))
32 | y = true;
33 | elseif any(strcmpi(x, false_list))
34 | y = false;
35 | else
36 | error('cannot determine whether "%s" should be interpreted as true or false', x);
37 | end
38 | else
39 | % convert numerical value to boolean
40 | y = logical(x);
41 | end
42 |
43 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/keepfields.m:
--------------------------------------------------------------------------------
1 | function [s] = keepfields(s, fields)
2 |
3 | % KEEPFIELDS makes a selection of the fields in a structure
4 | %
5 | % Use as
6 | % s = keepfields(s, fields);
7 | %
8 | % See also REMOVEFIELDS, COPYFIELDS
9 |
10 | % Copyright (C) 2014, Robert Oostenveld
11 | %
12 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
13 | % for the documentation and details.
14 | %
15 | % FieldTrip is free software: you can redistribute it and/or modify
16 | % it under the terms of the GNU General Public License as published by
17 | % the Free Software Foundation, either version 3 of the License, or
18 | % (at your option) any later version.
19 | %
20 | % FieldTrip is distributed in the hope that it will be useful,
21 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
22 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 | % GNU General Public License for more details.
24 | %
25 | % You should have received a copy of the GNU General Public License
26 | % along with FieldTrip. If not, see .
27 | %
28 | % $Id$
29 |
30 | if isempty(s)
31 | % this prevents problems if s is an empty double, i.e. []
32 | return
33 | end
34 |
35 | if ischar(fields)
36 | fields = {fields};
37 | elseif ~iscell(fields)
38 | error('fields input argument must be a cell array of strings or a single string');
39 | end
40 |
41 | fields = setdiff(fieldnames(s), fields);
42 | for i=1:numel(fields)
43 | s = rmfield(s, fields{i});
44 | end
45 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/ndgrid.m:
--------------------------------------------------------------------------------
1 | function [varargout] = ndgrid(varargin)
2 |
3 | % NDGRID Generation of arrays for N-D functions and interpolation.
4 | % [X1,X2,X3,...] = NDGRID(x1,x2,x3,...) transforms the domain
5 | % specified by vectors x1,x2,x3, etc. into arrays X1,X2,X3, etc. that
6 | % can be used for the evaluation of functions of N variables and N-D
7 | % interpolation. The i-th dimension of the output array Xi are copies
8 | % of elements of the vector xi.
9 | %
10 | % [X1,X2,...] = NDGRID(x) is the same as [X1,X2,...] = NDGRID(x,x,...).
11 | %
12 | % For example, to evaluate the function x2*exp(-x1^2-x2^2-x^3) over the
13 | % range -2 < x1 < 2, -2 < x2 < 2, -2 < x3 < 2,
14 | %
15 | % [x1,x2,x3] = ndgrid(-2:.2:2, -2:.25:2, -2:.16:2);
16 | % z = x2 .* exp(-x1.^2 - x2.^2 - x3.^2);
17 | % slice(x2,x1,x3,z,[-1.2 .8 2],2,[-2 -.2])
18 | %
19 | % NDGRID is like MESHGRID except that the order of the first two input
20 | % arguments are switched (i.e., [X1,X2,X3] = NDGRID(x1,x2,x3) produces
21 | % the same result as [X2,X1,X3] = MESHGRID(x2,x1,x3)). Because of
22 | % this, NDGRID is better suited to N-D problems that aren't spatially
23 | % based, while MESHGRID is better suited to problems in cartesian
24 | % space (2-D or 3-D).
25 | %
26 | % This is a drop-in replacement for the MATLAB version in elmat, which is
27 | % relatively slow for big grids. Note that this function only works up
28 | % to 5 dimensions
29 | %
30 | % See also MESHGRID, INTERPN.
31 |
32 | % Copyright(C) 2010, Jan-Mathijs Schoffelen, DCCN
33 | %
34 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
35 | % for the documentation and details.
36 | %
37 | % FieldTrip is free software: you can redistribute it and/or modify
38 | % it under the terms of the GNU General Public License as published by
39 | % the Free Software Foundation, either version 3 of the License, or
40 | % (at your option) any later version.
41 | %
42 | % FieldTrip is distributed in the hope that it will be useful,
43 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
44 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
45 | % GNU General Public License for more details.
46 | %
47 | % You should have received a copy of the GNU General Public License
48 | % along with FieldTrip. If not, see .
49 | %
50 | % $Id$
51 |
52 | if nargin==0
53 | error('MATLAB:ndgrid:NotEnoughInputs', 'Not enough input arguments.');
54 | end
55 | if nargin==1, varargin = repmat(varargin,[1 max(nargout,2)]); end
56 |
57 | ndims = numel(varargin);
58 | switch ndims
59 | case 2
60 | ones1 = ones(1,numel(varargin{1}));
61 | ones2 = ones(1,numel(varargin{2}));
62 |
63 | x = varargin{1}(:);
64 | y = varargin{2}(:)';
65 |
66 | varargout{1} = x(:, ones2);
67 | varargout{2} = y(ones1, :);
68 | case 3
69 | ones1 = ones(1,numel(varargin{1}));
70 | ones2 = ones(1,numel(varargin{2}));
71 | ones3 = ones(1,numel(varargin{3}));
72 |
73 | x = varargin{1}(:);
74 | y = varargin{2}(:)';
75 | z = zeros(1,1,numel(varargin{3}));
76 | z(:) = varargin{3};
77 |
78 | varargout{1} = x(:, ones2, ones3);
79 | varargout{2} = y(ones1, :, ones3);
80 | varargout{3} = z(ones1, ones2, :);
81 | case 4
82 | ones1 = ones(1,numel(varargin{1}));
83 | ones2 = ones(1,numel(varargin{2}));
84 | ones3 = ones(1,numel(varargin{3}));
85 | ones4 = ones(1,numel(varargin{4}));
86 |
87 | x = varargin{1}(:);
88 | y = varargin{2}(:)';
89 | z = zeros(1,1,numel(varargin{3}));
90 | z(:) = varargin{3};
91 | xx = zeros(1,1,1,numel(varargin{4}));
92 | xx(:) = varargin{4};
93 |
94 | varargout{1} = x(:, ones2, ones3, ones4);
95 | varargout{2} = y(ones1, :, ones3, ones4);
96 | varargout{3} = z(ones1, ones2, :, ones4);
97 | varargout{4} = xx(ones1, ones2, ones3, :);
98 | case 5
99 | ones1 = ones(1,numel(varargin{1}));
100 | ones2 = ones(1,numel(varargin{2}));
101 | ones3 = ones(1,numel(varargin{3}));
102 | ones4 = ones(1,numel(varargin{4}));
103 | ones5 = ones(1,numel(varargin{5}));
104 |
105 | x = varargin{1}(:);
106 | y = varargin{2}(:)';
107 | z = zeros(1,1,numel(varargin{3}));
108 | z(:) = varargin{3};
109 | xx = zeros(1,1,1,numel(varargin{4}));
110 | xx(:) = varargin{4};
111 | yy = zeros(1,1,1,1,numel(varargin{5}));
112 | yy(:) = varargin{5};
113 |
114 | varargout{1} = x(:, ones2, ones3, ones4, ones5);
115 | varargout{2} = y(ones1, :, ones3, ones4, ones5);
116 | varargout{3} = z(ones1, ones2, :, ones4, ones5);
117 | varargout{4} = xx(ones1, ones2, ones3, :,ones5);
118 | varargout{5} = yy(ones1, ones2, ones3, :,ones5);
119 | otherwise
120 | error('this version of ndgrid supports inputs up to 5 dimensions');
121 | %call the ndgrid from elmat
122 | %FIXME this has to be done
123 | end
124 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/pos2transform.m:
--------------------------------------------------------------------------------
1 | function [transform] = pos2transform(pos, dim)
2 |
3 | % POS2TRANSFORM reconstructs a transformation matrix from an ordered list
4 | % of positions.
5 | %
6 | % Use as
7 | % [transform] = pos2transform(pos, dim) where pos is an ordered list of positions
8 | % and should specify a full 3D volume
9 | %
10 | % The output transform is a 4x4 homogenous transformation matrix which transforms
11 | % from 'voxelspace' into the positions provided in the input
12 | %
13 | % See also POS2DIM
14 |
15 | % Copyright (C) 2009, Jan-Mathijs Schoffelen
16 |
17 | if nargin>1,
18 | % do nothing
19 | else
20 | dim = pos2dim(pos);
21 | end
22 | x = 1:dim(1);
23 | y = 1:dim(2);
24 | z = 1:dim(3);
25 | [X,Y,Z] = ndgrid(x, y, z);
26 | ind = [X(:) Y(:) Z(:)];
27 | ind = ind';ind(4,:) = 1;
28 | pos = pos';pos(4,:) = 1;
29 |
30 | % build in some robustness against nans
31 | sel = sum(isfinite(pos))==4;
32 |
33 | transform = pos(:,sel)/ind(:,sel);
34 |
35 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_asa.m:
--------------------------------------------------------------------------------
1 | function [val] = read_asa(filename, elem, format, number, token)
2 |
3 | % READ_ASA reads a specified element from an ASA file
4 | %
5 | % val = read_asa(filename, element, type, number)
6 | %
7 | % where the element is a string such as
8 | % NumberSlices
9 | % NumberPositions
10 | % Rows
11 | % Columns
12 | % etc.
13 | %
14 | % and format specifies the datatype according to
15 | % %d (integer value)
16 | % %f (floating point value)
17 | % %s (string)
18 | %
19 | % number is optional to specify how many lines of data should be read
20 | % The default is 1 for strings and Inf for numbers.
21 | %
22 | % token is optional to specifiy a character that separates the values from
23 | % anything not wanted.
24 |
25 | % Copyright (C) 2002-2012, Robert Oostenveld
26 | %
27 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
28 | % for the documentation and details.
29 | %
30 | % FieldTrip is free software: you can redistribute it and/or modify
31 | % it under the terms of the GNU General Public License as published by
32 | % the Free Software Foundation, either version 3 of the License, or
33 | % (at your option) any later version.
34 | %
35 | % FieldTrip is distributed in the hope that it will be useful,
36 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
37 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
38 | % GNU General Public License for more details.
39 | %
40 | % You should have received a copy of the GNU General Public License
41 | % along with FieldTrip. If not, see .
42 | %
43 | % $Id$
44 |
45 | fid = fopen(filename, 'rt');
46 | if fid==-1
47 | error(sprintf('could not open file %s', filename));
48 | end
49 |
50 | if nargin<4
51 | if strcmp(format, '%s')
52 | number = 1;
53 | else
54 | number = Inf;
55 | end
56 | end
57 |
58 | if nargin<5
59 | token = '';
60 | end
61 |
62 |
63 | val = [];
64 | elem = strtrim(lower(elem));
65 |
66 | while (1)
67 | line = fgetl(fid);
68 | if ~isempty(line) && isequal(line, -1)
69 | % prematurely reached end of file
70 | fclose(fid);
71 | return
72 | end
73 | line = strtrim(line);
74 | lower_line = lower(line);
75 | if strmatch(elem, lower_line)
76 | data = line((length(elem)+1):end);
77 | break
78 | end
79 | end
80 |
81 | while isempty(data)
82 | line = fgetl(fid);
83 | if isequal(line, -1)
84 | % prematurely reached end of file
85 | fclose(fid);
86 | return
87 | end
88 | data = strtrim(line);
89 | end
90 |
91 | if strcmp(format, '%s')
92 | if number==1
93 | % interpret the data as a single string, create char-array
94 | val = detoken(strtrim(data), token);
95 | if val(1)=='='
96 | val = val(2:end); % remove the trailing =
97 | end
98 | fclose(fid);
99 | return
100 | end
101 | % interpret the data as a single string, create cell-array
102 | val{1} = detoken(strtrim(data), token);
103 | count = 1;
104 | % read the remaining strings
105 | while count.
25 | %
26 | % $Id$
27 |
28 | if nargin == 1
29 | outfile = [];
30 | end %if
31 |
32 | fid = fopen(filename, 'r', 'b');
33 | version = fread(fid, 1, '*uint32');
34 | timestamp = fread(fid, 1, '*int32');
35 | checksum = fread(fid, 1, '*int32');
36 | nPoints = fread(fid, 1, '*int32');
37 |
38 | firstIndexPoint = fread(fid, [3, 5], 'double')';
39 |
40 | points = fread(fid, [3, double(nPoints)], 'double');
41 |
42 | fclose(fid);
43 |
44 | if(nargout > 0)
45 | output = points';
46 | end %if
47 |
48 | if(nargin == 2)
49 | fid = fopen(outfile, 'wt');
50 | fprintf(fid, '%d\n', nPoints);
51 | for i = 1:size(points, 2)
52 | fprintf(fid, '%.3f\t%.3f\t%.3f\n', points(1, i), points(2, i), points(3, i));
53 | end %for
54 | fclose(fid);
55 |
56 | end %if
57 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_caret_spec.m:
--------------------------------------------------------------------------------
1 | function [spec, headerinfo] = read_caret_spec(specfile)
2 |
3 | % READ_CARET_SPEC reads in a caret .spec file.
4 | %
5 | % Use as
6 | % [spec, headerinfo] = read_caret_spec(specfile)
7 | %
8 | % Output arguments:
9 | % spec = structure containing per file type the files listed
10 | % headerinfo = structure containing the specfile header
11 | %
12 | % The file can be an xml-file or an ascii formatted file
13 |
14 | % Copyright (C) 2013, Jan-Mathijs Schoffelen
15 |
16 | try,
17 | % read xml-file that contains a description to a bunch of files
18 | % belonging together
19 | ft_hastoolbox('gifti', 1);
20 | g = xmltree(specfile);
21 |
22 | % convert into a structure
23 | s = convert(g);
24 |
25 | if isfield(s, 'FileHeader')
26 | headerinfo = s.FileHeader;
27 | spec = rmfield(s, 'FileHeader');
28 | else
29 | headerinfo = [];
30 | spec = s;
31 | end
32 |
33 | % process the headerinfo
34 | if ~isempty(headerinfo)
35 | if isfield(headerinfo, 'Element')
36 | tmp = headerinfo.Element;
37 | tmp2 = struct([]);
38 | for k = 1:numel(headerinfo.Element)
39 | tmp2(1).(strrep(headerinfo.Element{k}.Name, '-', '_')) = headerinfo.Element{k}.Value;
40 | end
41 | headerinfo = tmp2;
42 | end
43 | end
44 |
45 | % further process the fields in spec
46 | f = fieldnames(spec);
47 |
48 | for k = 1:numel(f)
49 | if isempty(strfind(f{k}, 'study_metadata'))
50 | if iscell(spec.(f{k}))
51 | tmp = spec.(f{k});
52 | tmp2 = {};
53 | for m = 1:numel(tmp)
54 | tmpx = tmp{m};
55 | if isstruct(tmpx)
56 | fn = fieldnames(tmpx)
57 | for i = 1:numel(fn)
58 | tmp2{end+1,1} = tmpx.(fn{i});
59 | end
60 | end
61 | end
62 | spec.(f{k}) = tmp2;
63 | elseif isstruct(spec.(f{k}))
64 | tmp = spec.(f{k});
65 | fn = fieldnames(tmp);
66 | tmp2 = {};
67 | for m = 1:numel(fn)
68 | tmp2{end+1,1} = tmp.(fn{m});
69 | end
70 | spec.(f{k}) = tmp2;
71 | else
72 | % don't know what to do with it
73 | spec = rmfield(spec, f{k});
74 | end
75 | else
76 | % don't know what to do with it
77 | spec = rmfield(spec, f{k});
78 | end
79 | end
80 |
81 | catch
82 |
83 | % process as ASCII-file
84 | fid = fopen(specfile);
85 | line = 'some text';
86 | while isempty(strfind(line, 'EndHeader'))
87 | line = fgetl(fid);
88 | if isempty(strfind(line, 'BeginHeader')) && isempty(strfind(line, 'EndHeader'))
89 | tok = tokenize(line, ' ');
90 | headerinfo.(strrep(tok{1},'-','_')) = tok{2};
91 | end
92 | end
93 | line = fgetl(fid); % empty line
94 |
95 | spec = struct([]);
96 | while 1
97 | line = fgetl(fid);
98 | if ~ischar(line), break, end
99 | tok = tokenize(line, ' ');
100 | if ~isempty(tok{1})
101 | if isfield(spec, tok{1})
102 | spec(1).(tok{1}){end+1,1} = tok{2};
103 | else
104 | spec(1).(tok{1}){1} = tok{2};
105 | end
106 | end
107 | end
108 | fclose(fid);
109 | end
110 |
111 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_ctf_pos.m:
--------------------------------------------------------------------------------
1 | function [fid, pnt, label] = read_ctf_pos(filename)
2 |
3 | % READ_CTF_POS reads Polhemus file created with the CTF digitizer application
4 | %
5 | % Use as
6 | % [fid, pnt, label] = read_ctf_pos(filename)
7 | % Input:
8 | % filename - Polhemus ASCII file containing digitized points
9 | %
10 | % Output:
11 | % fid - fiducial locations of fiducials
12 | % pnt - sensor/headshape locations
13 | % label - labels of the fiducials
14 | %
15 | % IMPORTANT: Note that Polhemus data files should be -ASCII files with
16 | % extension .pos generated by the CTF digitizer
17 |
18 | % Copyright (C) 2012: Jan-Mathijs Schoffelen
19 | % $Id$
20 |
21 | [pth,nam,ext] = fileparts(filename);
22 | if ~strcmp(ext,'.pos')
23 | warndlg(sprintf('Wrong input file format\n'));
24 | return
25 | end
26 |
27 | fid = fopen(filename, 'r');
28 | data = textscan(fid, '%s%f%f%f','headerlines',1);
29 | fclose(fid);
30 |
31 | label = data{1};
32 | pnt = cat(2, data{2:end});
33 |
34 | isfid = false(1,numel(label));
35 | for k = 1:numel(label)
36 | if any(strcmpi(label{k},{'Rcoil','Lcoil','nasion','left','right','lpa','rpa','nas','rc','lc'}))
37 | isfid(k) = true;
38 | end
39 | end
40 | fid = pnt(isfid,:);
41 | label = label(isfid);
42 | pnt = pnt(~isfid,:);
43 |
44 | % average the double occurrences
45 | [u,i1,i2] = unique(label);
46 | newlabel = cell(numel(i1),1);
47 | newfid = zeros(numel(i1),3);
48 | for k = 1:numel(i1)
49 | newlabel{k} = u{k};
50 | newfid(k,:) = mean(fid(i2==k,:),1);
51 | end
52 | fid = newfid;
53 | label = newlabel;
54 |
55 | % rename the fiducials into lpa/rpa/nasion
56 | for k = 1:numel(label)
57 | if any(strcmpi(label{k}, {'nasion' 'nose' 'nz'}))
58 | label{k} = 'nas';
59 | end
60 | if any(strcmpi(label{k}, {'left'}))
61 | label{k} = 'lpa';
62 | end
63 | if any(strcmpi(label{k}, {'right'}))
64 | label{k} = 'rpa';
65 | end
66 | if any(strcmpi(label{k}, {'rc'}))
67 | label{k} = 'Rcoil';
68 | end
69 | if any(strcmpi(label{k}, {'lc'}))
70 | label{k} = 'Lcoil';
71 | end
72 | end
73 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_ctf_shape.m:
--------------------------------------------------------------------------------
1 | function [shape] = read_ctf_shape(filename);
2 |
3 | % READ_CTF_SHAPE reads headshape points and header information
4 | % from a CTF *.shape teh accompanying *.shape_info file.
5 | %
6 | % Use as
7 | % [shape] = read_ctf_shape(filename)
8 | % where filename should have the .shape extension
9 |
10 | % Copyright (C) 2003, Robert Oostenveld
11 | %
12 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
13 | % for the documentation and details.
14 | %
15 | % FieldTrip is free software: you can redistribute it and/or modify
16 | % it under the terms of the GNU General Public License as published by
17 | % the Free Software Foundation, either version 3 of the License, or
18 | % (at your option) any later version.
19 | %
20 | % FieldTrip is distributed in the hope that it will be useful,
21 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
22 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 | % GNU General Public License for more details.
24 | %
25 | % You should have received a copy of the GNU General Public License
26 | % along with FieldTrip. If not, see .
27 | %
28 | % $Id$
29 |
30 | shape = read_ctf_ascii([filename '_info']);
31 |
32 | if ~strcmp(shape.MRI_Info.COORDINATES, 'HEAD')
33 | warning('points on head shape are NOT in headcoordinates')
34 | end
35 |
36 | fid = fopen(filename, 'rt');
37 | num = fscanf(fid, '%d', 1);
38 | shape.pos = fscanf(fid, '%f', inf);
39 | shape.pos = reshape(shape.pos, [3 num])';
40 | fclose(fid);
41 |
42 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_off.m:
--------------------------------------------------------------------------------
1 | function [pnt, tri] = read_off(fn);
2 |
3 | % READ_OFF reads vertices and triangles from a OFF format triangulation file
4 | %
5 | % [pnt, tri] = read_off(filename)
6 | %
7 | % See also READ_TRI, READ_BND
8 |
9 | % Copyright (C) 1998, Robert Oostenveld
10 | %
11 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
12 | % for the documentation and details.
13 | %
14 | % FieldTrip is free software: you can redistribute it and/or modify
15 | % it under the terms of the GNU General Public License as published by
16 | % the Free Software Foundation, either version 3 of the License, or
17 | % (at your option) any later version.
18 | %
19 | % FieldTrip is distributed in the hope that it will be useful,
20 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
21 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 | % GNU General Public License for more details.
23 | %
24 | % You should have received a copy of the GNU General Public License
25 | % along with FieldTrip. If not, see .
26 | %
27 | % $Id$
28 |
29 | fid = fopen(fn, 'rt');
30 | if fid~=-1
31 |
32 | % scan the file type
33 | [s, count] = fscanf(fid, '%s\n', 1);
34 | if ~strcmp(s,'OFF')
35 | msg = sprintf('wrong file type %s', s);
36 | error(msg);
37 | end
38 |
39 | % read the number of vertex points and triangles
40 | [val, count] = fscanf(fid, '%d', 3);
41 | Npnt = val(1)
42 | Ntri = val(2)
43 |
44 | % read the vertex points
45 | pnt = fscanf(fid, '%f', [3, Npnt]);
46 | pnt = pnt(1:3,:)';
47 |
48 | % read the triangles
49 | tri = fscanf(fid, '%d', [4, Ntri]);
50 | tri = (tri(2:4,:)+1)';
51 | fclose(fid);
52 |
53 | else
54 | error('unable to open file');
55 | end
56 |
57 |
58 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_polhemus_fil.m:
--------------------------------------------------------------------------------
1 | function [fid, sens, label] = read_polhemus_fil(Fname_pol,skip)
2 |
3 | % Reads Polhemus files:
4 | % either sensor file or headshape file or both
5 | %
6 | % FORMAT [fid, sens, label] = read_polhemus_fil(Fname_pol,skip)
7 | % Input:
8 | % Fname_pol - Polhemus ASCII file containing sensor locations (cm)
9 | % (headshape can also be considered here instead of sensors)
10 | % skip - first channels to skip
11 | %
12 | % Output:
13 | % fid - fiducial locations (mm) in rows
14 | % sens - sensor/headshape locations (mm) in rows
15 | % label - labels of the fiducials
16 | %
17 | % IMPORTANT: Note that Polhemus data files should be -ASCII files with
18 | % extension .pol
19 | % It is assumed that the .pol file contains the location (cm) of fiducials
20 | % (sampled twice), possibly followed by some additional named points and
21 | % then unnamed location of the sensors. In some instances the first
22 | % few channel locations may pertain to reference channels; the skip
23 | % variable allows these to be skipped if necessary. The fiducial locations
24 | % are flaged with the strings 'NZ','LE' and 'RE'; indicating the Nasion,
25 | % left and right eare respectively.
26 | % _________________________________________________________________________
27 | % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
28 |
29 | % Jeremie Mattout
30 | % $Id$
31 |
32 | % checks and assigments
33 | %--------------------------------------------------------------------------
34 | try, skip; catch, skip = 0; end
35 |
36 | [pth,nam,ext] = fileparts(Fname_pol);
37 | if ~strcmp(ext,'.pol')
38 | warndlg(sprintf('Wrong input file format\n'));
39 | return
40 | end
41 |
42 | % --- READ Polhemus Sensor + fiducial locations ---
43 | %==========================================================================
44 | try
45 | file = textread(Fname_pol,'%s');
46 | catch
47 | file = textread(fullfile(pwd,[nam ext]),'%s');
48 | end
49 | % remove zeros at the end
50 | bool = 0;
51 | while bool == 0
52 | if strcmp(file{end},'0')
53 | file = file(1:end-1);
54 | else
55 | bool = 1;
56 | end
57 | end
58 |
59 | % read fiducials
60 | %--------------------------------------------------------------------------
61 | NZ = [];
62 | LE = [];
63 | RE = [];
64 | label = {};
65 | fid = [];
66 | temp = 0;
67 | nl = 1;
68 |
69 | while temp == 0
70 | if strcmp(file{nl},'NZ')
71 | NZ = [NZ ; str2num(file{nl+1}) str2num(file{nl+2}) str2num(file{nl+3}) ];
72 | nl = nl + 4;
73 | elseif strcmp(file{nl},'LE') | strcmp(file{nl},'OG')
74 | LE = [LE ; str2num(file{nl+1}) str2num(file{nl+2}) str2num(file{nl+3}) ];
75 | nl = nl + 4;
76 | elseif strcmp(file{nl},'RE') | strcmp(file{nl},'OD')
77 | RE = [RE ; str2num(file{nl+1}) str2num(file{nl+2}) str2num(file{nl+3}) ];
78 | nl = nl + 4;
79 | elseif isempty(str2num(file{nl})) % Add possible other named points
80 | label = [label, file(nl)];
81 | fid = [fid; str2num(file{nl+1}) str2num(file{nl+2}) str2num(file{nl+3}) ];
82 | nl = nl + 4;
83 | else
84 | temp = 1;
85 | end
86 | end
87 |
88 | % convert from cm to mm
89 | %--------------------------------------------------------------------------
90 | NZ = mean(NZ,1); LE = mean(LE,1); RE = mean(RE,1);
91 | fid = [NZ; LE; RE; fid];
92 |
93 | label = [{'nas', 'lpa', 'rpa'}, label];
94 |
95 | % read sensor locations or headshape locations
96 | %--------------------------------------------------------------------------
97 | sens = [];
98 | start = nl + skip*3;
99 | for i = start:3:length(file)
100 | sens = [sens; str2num(file{i}) str2num(file{i+1}) str2num(file{i+2})];
101 | end
102 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_stl.m:
--------------------------------------------------------------------------------
1 | function [pnt, tri, nrm] = read_stl(filename)
2 |
3 | % READ_STL reads a triangulation from an ascii or binary *.stl file, which
4 | % is a file format native to the stereolithography CAD software created by
5 | % 3D Systems.
6 | %
7 | % Use as
8 | % [pnt, tri, nrm] = read_stl(filename)
9 | %
10 | % The format is described at http://en.wikipedia.org/wiki/STL_(file_format)
11 | %
12 | % See also WRITE_STL
13 |
14 | % Copyright (C) 2006-2011, Robert Oostenveld
15 | %
16 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
17 | % for the documentation and details.
18 | %
19 | % FieldTrip is free software: you can redistribute it and/or modify
20 | % it under the terms of the GNU General Public License as published by
21 | % the Free Software Foundation, either version 3 of the License, or
22 | % (at your option) any later version.
23 | %
24 | % FieldTrip is distributed in the hope that it will be useful,
25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
27 | % GNU General Public License for more details.
28 | %
29 | % You should have received a copy of the GNU General Public License
30 | % along with FieldTrip. If not, see .
31 | %
32 | % $Id$
33 |
34 | fid = fopen(filename, 'rt');
35 |
36 | % read a small section to determine whether it is ascii or binary
37 | % a binary STL file has an 80 byte asci header, followed by non-printable characters
38 |
39 | section = fread(fid, 160, 'uint8');
40 | fseek(fid, 0, 'bof');
41 |
42 | if printableascii(section)
43 | % the first 160 characters are printable ascii, so assume it is an ascii format
44 |
45 | % solid testsphere
46 | % facet normal -0.13 -0.13 -0.98
47 | % outer loop
48 | % vertex 1.50000 1.50000 0.00000
49 | % vertex 1.50000 1.11177 0.05111
50 | % vertex 1.11177 1.50000 0.05111
51 | % endloop
52 | % endfacet
53 | % ...
54 |
55 | ntri = 0;
56 | while ~feof(fid)
57 | line = fgetl(fid);
58 | ntri = ntri + ~isempty(findstr('facet normal', line));
59 | end
60 | fseek(fid, 0, 'bof');
61 |
62 | tri = zeros(ntri,3);
63 | nrm = zeros(ntri,3);
64 | pnt = zeros(ntri*3,3);
65 |
66 | line = fgetl(fid);
67 | name = sscanf(line, 'solid %s');
68 |
69 | for i=1:ntri
70 | line1 = fgetl(fid);
71 | line2 = fgetl(fid); % outer loop
72 | line3 = fgetl(fid);
73 | line4 = fgetl(fid);
74 | line5 = fgetl(fid);
75 | line6 = fgetl(fid); % endloop
76 | line7 = fgetl(fid); % endfacet
77 | i1 = (i-1)*3+1;
78 | i2 = (i-1)*3+2;
79 | i3 = (i-1)*3+3;
80 | tri(i,:) = [i1 i2 i3];
81 | dum = sscanf(strtrim(line1), 'facet normal %f %f %f'); nrm(i,:) = dum(:)';
82 | dum = sscanf(strtrim(line3), 'vertex %f %f %f'); pnt(i1,:) = dum(:)';
83 | dum = sscanf(strtrim(line4), 'vertex %f %f %f'); pnt(i2,:) = dum(:)';
84 | dum = sscanf(strtrim(line5), 'vertex %f %f %f'); pnt(i3,:) = dum(:)';
85 | end
86 |
87 | else
88 | % reopen the file in binary mode, which does not make a difference on
89 | % UNIX but it does on windows
90 | fclose(fid);
91 | fid = fopen(filename, 'rb');
92 |
93 | fseek(fid, 80, 'bof'); % skip the ascii header
94 | ntri = fread(fid, 1, 'uint32');
95 | tri = reshape(1:(ntri*3),[3 ntri])';
96 | tmp = fread(fid, [12 ntri], '12*float32', 2); % read 12 floats at a time, and skip 2 bytes.
97 | nrm = tmp(1:3,:)';
98 |
99 | tmp = reshape(tmp(4:end,:),[3 3 ntri]); % position info
100 | tmp = permute(tmp,[2 3 1]);
101 | pnt = reshape(tmp, [], 3);
102 |
103 | % the above replaces the below, which is much slower, because it is using
104 | % a for loop across triangles
105 | % tri = zeros(ntri,3);
106 | % nrm = zeros(ntri,3);
107 | % pnt = zeros(ntri*3,3);
108 | % attr = zeros(ntri,1);
109 | % for i=1:ntri
110 | % i1 = (i-1)*3+1;
111 | % i2 = (i-1)*3+2;
112 | % i3 = (i-1)*3+3;
113 | % tri(i,:) = [i1 i2 i3];
114 | % nrm(i,:) = fread(fid, 3, 'float32');
115 | % pnt(i1,:) = fread(fid, 3, 'float32');
116 | % pnt(i2,:) = fread(fid, 3, 'float32');
117 | % pnt(i3,:) = fread(fid, 3, 'float32');
118 | % attr(i) = fread(fid, 1, 'uint16'); % Attribute byte count, don't know what it is
119 | % end % for each triangle
120 | end
121 |
122 | fclose(fid);
123 |
124 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
125 | % SUBFUNCTION
126 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
127 |
128 | function retval = printableascii(num)
129 | % Codes 20hex (32dec) to 7Ehex (126dec), known as the printable characters,
130 | % represent letters, digits, punctuation marks, and a few miscellaneous
131 | % symbols. There are 95 printable characters in total.
132 | num = double(num);
133 | num(num==double(sprintf('\n'))) = double(sprintf(' '));
134 | num(num==double(sprintf('\r'))) = double(sprintf(' '));
135 | num(num==double(sprintf('\t'))) = double(sprintf(' '));
136 | retval = all(num>=32 & num<=126);
137 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/read_vtk.m:
--------------------------------------------------------------------------------
1 | function [pnt, tri] = read_vtk(fn)
2 |
3 | % READ_VTK reads a triangulation from a VTK (Visualisation ToolKit) format file
4 | % Supported are triangles.
5 | %
6 | % Use as
7 | % [pnt, tri] = read_vtk(filename)
8 | %
9 | % See also WRITE_VTK
10 |
11 | % Copyright (C) 2002, Robert Oostenveld
12 | %
13 | % $Id$
14 |
15 | fid = fopen(fn, 'rt');
16 | if fid~=-1
17 |
18 | npnt = 0;
19 | while (~npnt)
20 | line = fgetl(fid);
21 | if ~isempty(findstr(line, 'POINTS'))
22 | npnt = sscanf(line, 'POINTS %d float');
23 | end
24 | end
25 | pnt = zeros(npnt, 3);
26 | for i=1:npnt
27 | pnt(i,:) = fscanf(fid, '%f', 3)';
28 | end
29 |
30 | ntri = 0;
31 | while (~ntri)
32 | line = fgetl(fid);
33 | if ~isempty(findstr(line, 'POLYGONS'))
34 | tmp = sscanf(line, 'POLYGONS %d %d');
35 | ntri = tmp(1);
36 | end
37 | end
38 | tri = zeros(ntri, 4);
39 | for i=1:ntri
40 | tri(i,:) = fscanf(fid, '%d', 4)';
41 | end
42 | tri = tri(:,2:4) + 1;
43 |
44 | fclose(fid);
45 |
46 | else
47 | error('unable to open file');
48 | end
49 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/removefields.m:
--------------------------------------------------------------------------------
1 | function [s] = removefields(s, fields)
2 |
3 | % REMOVEFIELDS makes a selection of the fields in a structure
4 | %
5 | % Use as
6 | % s = removefields(s, fields);
7 | %
8 | % See also KEEPFIELDS, COPYFIELDS
9 |
10 | % Copyright (C) 2014, Robert Oostenveld
11 | %
12 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
13 | % for the documentation and details.
14 | %
15 | % FieldTrip is free software: you can redistribute it and/or modify
16 | % it under the terms of the GNU General Public License as published by
17 | % the Free Software Foundation, either version 3 of the License, or
18 | % (at your option) any later version.
19 | %
20 | % FieldTrip is distributed in the hope that it will be useful,
21 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
22 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 | % GNU General Public License for more details.
24 | %
25 | % You should have received a copy of the GNU General Public License
26 | % along with FieldTrip. If not, see .
27 | %
28 | % $Id$
29 |
30 | if isempty(s)
31 | % this prevents problems if s is an empty double, i.e. []
32 | return
33 | end
34 |
35 | if ischar(fields)
36 | fields = {fields};
37 | elseif ~iscell(fields)
38 | error('fields input argument must be a cell array of strings or a single string');
39 | end
40 |
41 | fields = intersect(fieldnames(s), fields);
42 | for i=1:numel(fields)
43 | s = rmfield(s, fields{i});
44 | end
45 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/renamefields.m:
--------------------------------------------------------------------------------
1 | function b = renamefields(a, old, new)
2 |
3 | % RENAMEFIELDS renames a selection of the fields in a structure
4 | %
5 | % Use as
6 | % b = renamefields(a, old, new);
7 | % which renames the fields with the old name to the new name. Fields that
8 | % are specified but not present will be silently ignored.
9 | %
10 | % See also COPYFIELDS, KEEPFIELDS, REMOVEFIELDS
11 |
12 | % Copyright (C) 2014, Robert Oostenveld
13 | %
14 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
15 | % for the documentation and details.
16 | %
17 | % FieldTrip is free software: you can redistribute it and/or modify
18 | % it under the terms of the GNU General Public License as published by
19 | % the Free Software Foundation, either version 3 of the License, or
20 | % (at your option) any later version.
21 | %
22 | % FieldTrip is distributed in the hope that it will be useful,
23 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
24 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 | % GNU General Public License for more details.
26 | %
27 | % You should have received a copy of the GNU General Public License
28 | % along with FieldTrip. If not, see .
29 | %
30 | % $Id$
31 |
32 | if isempty(a)
33 | % this prevents problems if a is an empty double, i.e. []
34 | return
35 | end
36 |
37 | % these should be cell-arrays
38 | if ischar(old)
39 | old = {old};
40 | end
41 | if ischar(new)
42 | new = {new};
43 | end
44 |
45 | if length(old)~=length(new)
46 | error('the number of field names does not match between old and new');
47 | end
48 |
49 | % keep the fields that were not mentioned
50 | b = keepfields(a, setdiff(fieldnames(a), old));
51 | % copy the fields over with their new name
52 | for i=1:length(old)
53 | if isfield(a, old{i});
54 | b.(new{i}) = a.(old{i});
55 | end
56 | end
57 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/sn2individual.m:
--------------------------------------------------------------------------------
1 | function [warped]= sn2individual(P, input)
2 |
3 | % SN2INDIVIDUAL warps the input coordinates (defined as Nx3 matrix) from
4 | % normalised MNI coordinates to individual headspace coordinates, using the
5 | % warp parameters defined in the structure spmparams.
6 | %
7 | % this is modified from code from nutmeg: nut_mni2mri, which was itself
8 | % modified from code originally written by John Ashburner:
9 | % http://www.sph.umich.edu/~nichols/JG2/get_orig_coord2.m
10 |
11 | % Copyright (C) 2013, Jan-Mathijs Schoffelen
12 | %
13 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
14 | % for the documentation and details.
15 | %
16 | % FieldTrip is free software: you can redistribute it and/or modify
17 | % it under the terms of the GNU General Public License as published by
18 | % the Free Software Foundation, either version 3 of the License, or
19 | % (at your option) any later version.
20 | %
21 | % FieldTrip is distributed in the hope that it will be useful,
22 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
23 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 | % GNU General Public License for more details.
25 | %
26 | % You should have received a copy of the GNU General Public License
27 | % along with FieldTrip. If not, see .
28 | %
29 | % $Id$
30 |
31 | if numel(P.Tr)==0,
32 | % only an affine transformation has been done
33 | T = P.VF.mat*P.Affine/(P.VG.mat);
34 | warped = ft_warp_apply(T, input);
35 | else
36 | % we need the spm_dctmtx function for the nonlinear case
37 | ft_hastoolbox('spm8', 1);
38 |
39 | dim = P.VG.dim(1:3);
40 | xyz = ft_warp_apply(inv(P.VG.mat), input); % goes into voxel coordinates
41 |
42 | basX = spm_dctmtx(dim(1), size(P.Tr,1), xyz(:,1)-1);
43 | basY = spm_dctmtx(dim(2), size(P.Tr,2), xyz(:,2)-1);
44 | basZ = spm_dctmtx(dim(3), size(P.Tr,3), xyz(:,3)-1);
45 |
46 | siz = size(P.Tr);
47 | Tr1 = reshape(P.Tr(:,:,:,1),siz(1)*siz(2),siz(3));
48 | Tr2 = reshape(P.Tr(:,:,:,2),siz(1)*siz(2),siz(3));
49 | Tr3 = reshape(P.Tr(:,:,:,3),siz(1)*siz(2),siz(3));
50 |
51 | xyztmp = zeros(size(xyz));
52 | for i=1:size(xyz,1)
53 | bx = basX(i,:);
54 | by = basY(i,:);
55 | bz = basZ(i,:);
56 | tx = reshape(Tr1*bz', siz(1), siz(2) );
57 | ty = reshape(Tr2*bz', siz(1), siz(2) );
58 | tz = reshape(Tr3*bz', siz(1), siz(2) );
59 | xyztmp(i,:) = [bx*tx*by' bx*ty*by' bx*tz*by'];
60 | end
61 |
62 | T = P.VF.mat*P.Affine;
63 | warped = ft_warp_apply(T, xyz+xyztmp);
64 | end;
65 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/surf_to_tetgen.m:
--------------------------------------------------------------------------------
1 | function surf_to_tetgen(filename, nodes, elements, element_types, attributes_nodes,attributes_elements)
2 | % This function converts a triangulated mesh in FieldTrip format into a
3 | % surface structure readable by Tetgen software
4 |
5 | % Copyright Arno Jannsen, 2011
6 |
7 | %Write the node file
8 | node_filename = [filename '.node'];
9 | precision_str = '%u %.40e %.40e %.40e';
10 |
11 | N_nodes = size(nodes,1);
12 | if(nargin > 4)
13 | N_attributes = size(attributes_nodes,2);
14 | A = [nodes attributes_nodes];
15 | for i=1:N_attributes
16 | precision_str = [precision_str ' %.5e'];
17 | end
18 | precision_str = [precision_str '\n'];
19 | else
20 | N_attributes = 0;
21 | A = nodes;
22 | precision_str = [precision_str '\n'];
23 | end
24 |
25 |
26 | fid = fopen(node_filename, 'w');
27 | fprintf(fid, [num2str(N_nodes) ' 3 ' num2str(N_attributes) ' 0\n']);
28 | for i=1:(N_nodes)
29 | fprintf(fid,precision_str,i,A(i,:));
30 | end
31 | fclose(fid);
32 |
33 | %Write the poly file
34 | poly_filename = [filename '.poly'];
35 |
36 | N_elements = size(elements,1);
37 |
38 | fid = fopen(poly_filename, 'w');
39 | fprintf(fid, ['0 3 ' num2str(N_attributes) ' 0\n']);
40 | fprintf(fid, [num2str(N_elements) ' 1\n']);
41 | for i=1:(N_elements)
42 | switch element_types(i)
43 | case 302
44 | fprintf(fid,['1 0 302 # ' num2str(i) '\n']);
45 | fprintf(fid,'3 %u %u %u\n',elements(i,:));
46 | otherwise
47 | error('currently, only type 302 elements (triangles) are supported')
48 | end
49 | end
50 | fprintf(fid,'0\n');
51 | if(nargin > 5)
52 | N_regions = size(attributes_elements,1);
53 | if(size(attributes_elements,2) < 5)
54 | attributes_elements = [attributes_elements, -1*ones(N_regions,1)];
55 | end
56 | fprintf(fid,[num2str(N_regions) '\n']);
57 | for i=1:N_regions
58 | fprintf(fid,'%u %.3f %.3f %.3f %u %.2f\n',i,attributes_elements(i,:));
59 | end
60 | else
61 | fprintf(fid,'0\n');
62 | end
63 | fclose(fid);
64 |
65 | end
66 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/tokenize.m:
--------------------------------------------------------------------------------
1 | function [tok] = tokenize(str, sep, rep)
2 |
3 | % TOKENIZE cuts a string into pieces, returning the pieces in a cell array
4 | %
5 | % Use as
6 | % t = tokenize(str)
7 | % t = tokenize(str, sep)
8 | % t = tokenize(str, sep, rep)
9 | % where
10 | % str = the string that you want to cut into pieces
11 | % sep = the separator at which to cut (default is whitespace)
12 | % rep = whether to treat repeating separator characters as one (default is false)
13 | %
14 | % With the optional boolean flag "rep" you can specify whether repeated
15 | % separator characters should be squeezed together (e.g. multiple
16 | % spaces between two words). The default is rep=1, i.e. repeated
17 | % separators are treated as one.
18 | %
19 | % See also STRTOK, TEXTSCAN
20 |
21 | % Copyright (C) 2003-2010, Robert Oostenveld
22 | %
23 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
24 | % for the documentation and details.
25 | %
26 | % FieldTrip is free software: you can redistribute it and/or modify
27 | % it under the terms of the GNU General Public License as published by
28 | % the Free Software Foundation, either version 3 of the License, or
29 | % (at your option) any later version.
30 | %
31 | % FieldTrip is distributed in the hope that it will be useful,
32 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
33 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
34 | % GNU General Public License for more details.
35 | %
36 | % You should have received a copy of the GNU General Public License
37 | % along with FieldTrip. If not, see .
38 | %
39 | % $Id$
40 |
41 | % these are for remembering the type on subsequent calls with the same input arguments
42 | persistent previous_argin previous_argout
43 |
44 | str = str(:)';
45 |
46 | if nargin<2
47 | sep = [9:13 32]; % White space characters
48 | end
49 |
50 | if nargin<3
51 | rep = false;
52 | end
53 |
54 | current_argin = {str, sep, rep};
55 | if isequal(current_argin, previous_argin)
56 | % don't do the processing again, but return the previous values from cache
57 | tok = previous_argout;
58 | return
59 | end
60 |
61 | if numel(sep)==1
62 | f = find(str==sep);
63 | else
64 | f = find(ismember(str, sep));
65 | end
66 | f = [0, f, length(str)+1];
67 |
68 | tok = cell(1, length(f)-1);
69 | for i=1:(length(f)-1)
70 | tok{i} = str((f(i)+1):(f(i+1)-1));
71 | end
72 |
73 | if rep
74 | % remove empty cells, which occur if the separator is repeated (e.g. multiple spaces)
75 | tok(cellfun('isempty', tok))=[];
76 | end
77 |
78 | % remember the current input and output arguments, so that they can be
79 | % reused on a subsequent call in case the same input argument is given
80 | current_argout = tok;
81 | previous_argin = current_argin;
82 | previous_argout = current_argout;
83 |
84 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/write_nifti2_hdr.m:
--------------------------------------------------------------------------------
1 | function write_nifti2_hdr(filename, hdr)
2 |
3 | % WRITE_NIFTI2_HDR
4 | %
5 | % Use as
6 | % write_nifti2_hdr(filename, hdr)
7 | % where
8 | % filename = string
9 | % hdr = structure with nifti-2 header information
10 | %
11 | % See also READ_NIFTI_HDR, READ_CIFTI, WRITE_CIFTI
12 |
13 | % Copyright (C) 2013, Robert Oostenveld
14 | %
15 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
16 | % for the documentation and details.
17 | %
18 | % FieldTrip is free software: you can redistribute it and/or modify
19 | % it under the terms of the GNU General Public License as published by
20 | % the Free Software Foundation, either version 3 of the License, or
21 | % (at your option) any later version.
22 | %
23 | % FieldTrip is distributed in the hope that it will be useful,
24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 | % GNU General Public License for more details.
27 | %
28 | % You should have received a copy of the GNU General Public License
29 | % along with FieldTrip. If not, see .
30 | %
31 | % $Id$
32 |
33 | if ischar(filename)
34 | fid = fopen(filename, 'w');
35 | else
36 | fid = filename;
37 | end
38 |
39 | fwrite(fid, 540, 'int32');
40 |
41 | assert(fwrite(fid, hdr.magic , 'int8' )==8 ); % 4 `n', '+', `2', `\0','\r','\n','\032','\n' or (0x6E,0x2B,0x32,0x00,0x0D,0x0A,0x1A,0x0A)
42 | assert(fwrite(fid, hdr.datatype , 'int16' )==1 ); % 12 See file formats
43 | assert(fwrite(fid, hdr.bitpix , 'int16' )==1 ); % 14 See file formats
44 | assert(fwrite(fid, hdr.dim , 'int64' )==8 ); % 16 See file formats
45 | assert(fwrite(fid, hdr.intent_p1 , 'double' )==1 ); % 80 0
46 | assert(fwrite(fid, hdr.intent_p2 , 'double' )==1 ); % 88 0
47 | assert(fwrite(fid, hdr.intent_p3 , 'double' )==1 ); % 96 0
48 | assert(fwrite(fid, hdr.pixdim , 'double' )==8 ); % 104 0,1,1,1,1,1,1,1
49 | assert(fwrite(fid, hdr.vox_offset , 'int64' )==1 ); % 168 Offset of data, minimum=544
50 | assert(fwrite(fid, hdr.scl_slope , 'double' )==1 ); % 176 1
51 | assert(fwrite(fid, hdr.scl_inter , 'double' )==1 ); % 184 0
52 | assert(fwrite(fid, hdr.cal_max , 'double' )==1 ); % 192 0
53 | assert(fwrite(fid, hdr.cal_min , 'double' )==1 ); % 200 0
54 | assert(fwrite(fid, hdr.slice_duration , 'double' )==1 ); % 208 0
55 | assert(fwrite(fid, hdr.toffset , 'double' )==1 ); % 216 0
56 | assert(fwrite(fid, hdr.slice_start , 'int64' )==1 ); % 224 0
57 | assert(fwrite(fid, hdr.slice_end , 'int64' )==1 ); % 232 0
58 | assert(fwrite(fid, hdr.descrip , 'int8' )==80); % 240 All zeros
59 | assert(fwrite(fid, hdr.aux_file , 'int8' )==24); % 320 All zeros
60 | assert(fwrite(fid, hdr.qform_code , 'int32' )==1 ); % 344 NIFTI_XFORM_UNKNOWN (0)
61 | assert(fwrite(fid, hdr.sform_code , 'int32' )==1 ); % 348 NIFTI_XFORM_UNKNOWN (0)
62 | assert(fwrite(fid, hdr.quatern_b , 'double' )==1 ); % 352 0
63 | assert(fwrite(fid, hdr.quatern_c , 'double' )==1 ); % 360 0
64 | assert(fwrite(fid, hdr.quatern_d , 'double' )==1 ); % 368 0
65 | assert(fwrite(fid, hdr.qoffset_x , 'double' )==1 ); % 376 0
66 | assert(fwrite(fid, hdr.qoffset_y , 'double' )==1 ); % 384 0
67 | assert(fwrite(fid, hdr.qOffset_z , 'double' )==1 ); % 392 0
68 | assert(fwrite(fid, hdr.srow_x , 'double' )==4 ); % 400 0,0,0,0
69 | assert(fwrite(fid, hdr.srow_y , 'double' )==4 ); % 432 0,0,0,0
70 | assert(fwrite(fid, hdr.srow_z , 'double' )==4 ); % 464 0,0,0,0
71 | assert(fwrite(fid, hdr.slice_code , 'int32' )==1 ); % 496 0
72 | assert(fwrite(fid, hdr.xyzt_units , 'int32' )==1 ); % 500 0xC (seconds, millimeters)
73 | assert(fwrite(fid, hdr.intent_code , 'int32' )==1 ); % 504 See file formats
74 | assert(fwrite(fid, hdr.intent_name , 'int8' )==16); % 508 See file formats
75 | assert(fwrite(fid, hdr.dim_info , 'int8' )==1 ); % 524 0
76 | assert(fwrite(fid, hdr.unused_str , 'int8' )==15); % 525 All zeros
77 | % disp(ftell(fid)); % 540 End of the header
78 |
79 | if ischar(filename)
80 | fclose(fid);
81 | end
82 |
83 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/write_off.m:
--------------------------------------------------------------------------------
1 | function write_off(filename, pnt, plc)
2 |
3 | % WRITE_OFF writes a set of geometrical planar forms (called piecewise linear complex, PLC)
4 | % to an ascii *.off file, which is a file format created by Princeton Shape Benchmark
5 | %
6 | % Use as
7 | % write_stl(filename, pnt, tri)
8 | %
9 | % See also READ_OFF
10 |
11 | % Copyright (C) 2010, Cristiano Micheli
12 | %
13 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
14 | % for the documentation and details.
15 | %
16 | % FieldTrip is free software: you can redistribute it and/or modify
17 | % it under the terms of the GNU General Public License as published by
18 | % the Free Software Foundation, either version 3 of the License, or
19 | % (at your option) any later version.
20 | %
21 | % FieldTrip is distributed in the hope that it will be useful,
22 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
23 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 | % GNU General Public License for more details.
25 | %
26 | % You should have received a copy of the GNU General Public License
27 | % along with FieldTrip. If not, see .
28 | %
29 | % $Id$
30 |
31 | nedges = 0;
32 | fid = fopen(filename, 'wb');
33 | npnt = size(pnt,1);
34 | nplc = size(plc,1);
35 |
36 | % check that the indexes of plc are correct (0 convention)
37 | if ~sum(any(plc==0))
38 | plc = plc - 1;
39 | end
40 |
41 | fprintf(fid, 'OFF\n');
42 | fprintf(fid, '%d %d %d\n',npnt,nplc,nedges);
43 | for i=1:npnt
44 | fprintf(fid, '%f %f %f\n', pnt(i,1), pnt(i,2), pnt(i,3));
45 | end
46 | for i=1:nplc
47 | str = '%d ';
48 | nvert = size(plc(i,:),2);
49 | str2 = 'nvert,';
50 | for j=1:nvert
51 | str = [str '%d '];
52 | str2 = [str2 'plc(i,' num2str(j) '),'];
53 | end
54 | str = [str '\n''']; str2 = str2(1:end-1);
55 | eval(['fprintf(fid,''' str ',' str2 ');']);
56 | end
57 |
58 | fclose(fid);
59 |
--------------------------------------------------------------------------------
/Sub-function/cifti-matlab-master/private/write_ply.m:
--------------------------------------------------------------------------------
1 | function write_ply(fn, pnt, tri, format)
2 |
3 | % WRITE_PLY writes triangles, tetraheders or hexaheders to a Stanford *.ply format file
4 | %
5 | % Use as
6 | % write_ply(filename, vertex, element)
7 | %
8 | % Documentation is provided on
9 | % http://paulbourke.net/dataformats/ply/
10 | % http://en.wikipedia.org/wiki/PLY_(file_format)
11 | %
12 | % See also READ_PLY, READ_VTK, WRITE_VTK
13 |
14 | % Copyright (C) 2012, Robert Oostenveld
15 | %
16 | % $Id$
17 |
18 | % the element are described as
19 | % Mx3 list of vertices for triangles
20 | % Mx4 list of vertices for tetraheders
21 | % Mx8 list of vertices for hexaheders
22 |
23 | if nargin<4
24 | format = 'ascii';
25 | end
26 |
27 | if size(tri,2)==4
28 | % describe the sides of the tetraheders as polygon surface elements
29 | % see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1836
30 | tri = [
31 | tri(:,[3 2 1])
32 | tri(:,[2 4 1])
33 | tri(:,[3 4 2])
34 | tri(:,[4 3 1])
35 | ];
36 | elseif size(tri,2)==8
37 | % describe the sides of the hexaheders as polygon surface elements
38 | % see http://bugzilla.fcdonders.nl/show_bug.cgi?id=1836
39 | tri = [
40 | tri(:,[4 3 2 1])
41 | tri(:,[1 2 6 5])
42 | tri(:,[3 7 6 2])
43 | tri(:,[4 8 7 3])
44 | tri(:,[5 8 4 1])
45 | tri(:,[6 7 8 5])
46 | ];
47 | end
48 |
49 | if strcmp(format, 'ascii')
50 | fid = fopen(fn, 'wt');
51 | else
52 | fid = fopen(fn, 'wb');
53 | end
54 |
55 | if fid~=-1
56 |
57 | npnt = size(pnt,1);
58 | ntri = size(tri,1);
59 | if numel(tri)>0
60 | % MATLAB indexes start at 1, inside the file they start at 0
61 | tri = tri-1;
62 | end
63 |
64 | % write the header
65 | fprintf(fid, 'ply\n');
66 | if strcmp(format, 'ascii')
67 | fprintf(fid, 'format ascii 1.0\n');
68 | else
69 | [c, m, e] = computer;
70 | if e=='L'
71 | fprintf(fid, 'format binary_little_endian 1.0\n');
72 | elseif e=='B'
73 | fprintf(fid, 'format binary_big_endian 1.0\n');
74 | end
75 | end
76 |
77 | fprintf(fid, 'element vertex %d\n', npnt);
78 | fprintf(fid, 'property float x\n');
79 | fprintf(fid, 'property float y\n');
80 | fprintf(fid, 'property float z\n');
81 | fprintf(fid, 'element face %d\n', ntri);
82 | fprintf(fid, 'property list uchar int vertex_index\n');
83 | fprintf(fid, 'end_header\n');
84 |
85 | if strcmp(format, 'ascii')
86 | % write the vertex points
87 | fprintf(fid, '%f\t%f\t%f\n', pnt');
88 | num = size(tri,2);
89 | switch num
90 | case 3
91 | fprintf(fid, '3\t%d\t%d\t%d\n', tri');
92 | case 4
93 | fprintf(fid, '4\t%d\t%d\t%d\t%d\n', tri');
94 | case 5
95 | fprintf(fid, '5\t%d\t%d\t%d\t%d\n', tri');
96 | case 6
97 | fprintf(fid, '6\t%d\t%d\t%d\t%d\n', tri');
98 | case 7
99 | fprintf(fid, '7\t%d\t%d\t%d\t%d\n', tri');
100 | case 8
101 | fprintf(fid, '8\t%d\t%d\t%d\t%d\n', tri');
102 | case 9
103 | fprintf(fid, '9\t%d\t%d\t%d\t%d\n', tri');
104 | otherwise
105 | error('unsupported size for polygons (%d)', num);
106 | end % case
107 | else
108 | fwrite(fid, pnt', 'single'); % float
109 | num = size(tri,2);
110 | for i=1:size(tri,1)
111 | fwrite(fid, num, 'uint8'); % uchar
112 | fwrite(fid, tri(i,:), 'int32'); % int
113 | end
114 | end
115 |
116 | fclose(fid);
117 |
118 | else
119 | error('unable to open file');
120 | end
121 |
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/Sub-function/cifti-matlab-master/private/write_stl.m:
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1 | function write_stl(filename, pnt, tri, nrm);
2 |
3 | % WRITE_STL writes a triangulation to an ascii *.stl file, which is a file
4 | % format native to the stereolithography CAD software created by 3D Systems.
5 | %
6 | % Use as
7 | % write_stl(filename, pnt, tri, nrm)
8 | % where nrm refers to the triangle normals.
9 | %
10 | % See also READ_STL
11 |
12 | % Copyright (C) 2006, Robert Oostenveld
13 | %
14 | % This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
15 | % for the documentation and details.
16 | %
17 | % FieldTrip is free software: you can redistribute it and/or modify
18 | % it under the terms of the GNU General Public License as published by
19 | % the Free Software Foundation, either version 3 of the License, or
20 | % (at your option) any later version.
21 | %
22 | % FieldTrip is distributed in the hope that it will be useful,
23 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
24 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 | % GNU General Public License for more details.
26 | %
27 | % You should have received a copy of the GNU General Public License
28 | % along with FieldTrip. If not, see .
29 | %
30 | % $Id$
31 |
32 | % solid testsphere
33 | % facet normal -0.13 -0.13 -0.98
34 | % outer loop
35 | % vertex 1.50000 1.50000 0.00000
36 | % vertex 1.50000 1.11177 0.05111
37 | % vertex 1.11177 1.50000 0.05111
38 | % endloop
39 | % endfacet
40 | % ...
41 |
42 | fid = fopen(filename, 'wb');
43 |
44 | ntri = size(tri,1);
45 | fprintf(fid, 'solid unknown\n');
46 |
47 | for i=1:ntri
48 | fprintf(fid, ' facet normal %f %f %f\n', nrm(i,:));
49 | fprintf(fid, ' outer loop\n');
50 | fprintf(fid, ' vertex %f %f %f\n', pnt(tri(i,1),1), pnt(tri(i,1),2), pnt(tri(i,1),3));
51 | fprintf(fid, ' vertex %f %f %f\n', pnt(tri(i,2),1), pnt(tri(i,2),2), pnt(tri(i,2),3));
52 | fprintf(fid, ' vertex %f %f %f\n', pnt(tri(i,3),1), pnt(tri(i,3),2), pnt(tri(i,3),3));
53 | fprintf(fid, ' endloop\n');
54 | fprintf(fid, ' endfacet\n');
55 | end
56 |
57 | fprintf(fid, 'endsolid\n');
58 |
59 | fclose(fid);
60 |
61 |
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/Sub-function/cifti-matlab-master/private/write_vtk.m:
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1 | function write_vtk(fn, pnt, tri)
2 |
3 | % WRITE_VTK writes a triangulation to a VTK (Visualisation ToolKit) format file.
4 | % Supported are triangles, tetraheders and hexaheders.
5 | %
6 | % Use as
7 | % write_vtk(filename, pnt, tri)
8 | %
9 | % See also READ_VTK, WRITE_PLY
10 |
11 | % Copyright (C) 2002, Robert Oostenveld
12 | %
13 | % $Id$
14 |
15 | fid = fopen(fn, 'wt');
16 | if fid~=-1
17 |
18 | npnt = size(pnt,1);
19 | ntri = size(tri,1);
20 |
21 | % write the header
22 | fprintf(fid, '# vtk DataFile Version 2.0\n');
23 | fprintf(fid, 'vtk output\n');
24 | fprintf(fid, 'ASCII\n');
25 | fprintf(fid, 'DATASET POLYDATA\n');
26 | fprintf(fid, '\n');
27 |
28 | % write the vertex points
29 | fprintf(fid, 'POINTS %d float\n', npnt);
30 | fprintf(fid, '%f\t%f\t%f\n', pnt');
31 | fprintf(fid, '\n');
32 |
33 | if size(tri,2)==3
34 | % write the triangles
35 | fprintf(fid, 'POLYGONS %d %d\n', ntri, (3+1)*ntri);
36 | fprintf(fid, '3\t%d\t%d\t%d\n', (tri-1)');
37 | fprintf(fid, '\n');
38 | elseif size(tri,2)==4
39 | % write the tetraheders
40 | fprintf(fid, 'POLYGONS %d %d\n', ntri, (4+1)*ntri);
41 | fprintf(fid, '4\t%d\t%d\t%d\t%d\n', (tri-1)');
42 | fprintf(fid, '\n');
43 | elseif size(tri,2)==8
44 | % write the hexaheders
45 | fprintf(fid, 'POLYGONS %d %d\n', ntri, (8+1)*ntri);
46 | fprintf(fid, '8\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n', (tri-1)');
47 | fprintf(fid, '\n');
48 | end
49 |
50 | fclose(fid);
51 |
52 | else
53 | error('unable to open file');
54 | end
55 |
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/Sub-function/emptyfile.txt:
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1 |
2 |
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/Sub-function/nanconv/license.txt:
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1 | Copyright (c) 2013, Benjamin Kraus
2 | All rights reserved.
3 |
4 | Redistribution and use in source and binary forms, with or without
5 | modification, are permitted provided that the following conditions are
6 | met:
7 |
8 | * Redistributions of source code must retain the above copyright
9 | notice, this list of conditions and the following disclaimer.
10 | * Redistributions in binary form must reproduce the above copyright
11 | notice, this list of conditions and the following disclaimer in
12 | the documentation and/or other materials provided with the distribution
13 |
14 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
15 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
16 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
17 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
18 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
19 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
20 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
21 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
22 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
23 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
24 | POSSIBILITY OF SUCH DAMAGE.
25 |
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/Sub-function/nanconv/nanconv.m:
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1 | function c = nanconv(a, k, varargin)
2 | % NANCONV Convolution in 1D or 2D ignoring NaNs.
3 | % C = NANCONV(A, K) convolves A and K, correcting for any NaN values
4 | % in the input vector A. The result is the same size as A (as though you
5 | % called 'conv' or 'conv2' with the 'same' shape).
6 | %
7 | % C = NANCONV(A, K, 'param1', 'param2', ...) specifies one or more of the following:
8 | % 'edge' - Apply edge correction to the output.
9 | % 'noedge' - Do not apply edge correction to the output (default).
10 | % 'nanout' - The result C should have NaNs in the same places as A.
11 | % 'nonanout' - The result C should have ignored NaNs removed (default).
12 | % Even with this option, C will have NaN values where the
13 | % number of consecutive NaNs is too large to ignore.
14 | % '2d' - Treat the input vectors as 2D matrices (default).
15 | % '1d' - Treat the input vectors as 1D vectors.
16 | % This option only matters if 'a' or 'k' is a row vector,
17 | % and the other is a column vector. Otherwise, this
18 | % option has no effect.
19 | %
20 | % NANCONV works by running 'conv2' either two or three times. The first
21 | % time is run on the original input signals A and K, except all the
22 | % NaN values in A are replaced with zeros. The 'same' input argument is
23 | % used so the output is the same size as A. The second convolution is
24 | % done between a matrix the same size as A, except with zeros wherever
25 | % there is a NaN value in A, and ones everywhere else. The output from
26 | % the first convolution is normalized by the output from the second
27 | % convolution. This corrects for missing (NaN) values in A, but it has
28 | % the side effect of correcting for edge effects due to the assumption of
29 | % zero padding during convolution. When the optional 'noedge' parameter
30 | % is included, the convolution is run a third time, this time on a matrix
31 | % of all ones the same size as A. The output from this third convolution
32 | % is used to restore the edge effects. The 'noedge' parameter is enabled
33 | % by default so that the output from 'nanconv' is identical to the output
34 | % from 'conv2' when the input argument A has no NaN values.
35 | %
36 | % See also conv, conv2
37 | %
38 | % AUTHOR: Benjamin Kraus (bkraus@bu.edu, ben@benkraus.com)
39 | % Copyright (c) 2013, Benjamin Kraus
40 | % $Id: nanconv.m 4861 2013-05-27 03:16:22Z bkraus $
41 |
42 | % Process input arguments
43 | for arg = 1:nargin-2
44 | switch lower(varargin{arg})
45 | case 'edge'; edge = true; % Apply edge correction
46 | case 'noedge'; edge = false; % Do not apply edge correction
47 | case {'same','full','valid'}; shape = varargin{arg}; % Specify shape
48 | case 'nanout'; nanout = true; % Include original NaNs in the output.
49 | case 'nonanout'; nanout = false; % Do not include NaNs in the output.
50 | case {'2d','is2d'}; is1D = false; % Treat the input as 2D
51 | case {'1d','is1d'}; is1D = true; % Treat the input as 1D
52 | end
53 | end
54 |
55 | % Apply default options when necessary.
56 | if(exist('edge','var')~=1); edge = false; end
57 | if(exist('nanout','var')~=1); nanout = false; end
58 | if(exist('is1D','var')~=1); is1D = false; end
59 | if(exist('shape','var')~=1); shape = 'same';
60 | elseif(~strcmp(shape,'same'))
61 | error([mfilename ':NotImplemented'],'Shape ''%s'' not implemented',shape);
62 | end
63 |
64 | % Get the size of 'a' for use later.
65 | sza = size(a);
66 |
67 | % If 1D, then convert them both to columns.
68 | % This modification only matters if 'a' or 'k' is a row vector, and the
69 | % other is a column vector. Otherwise, this argument has no effect.
70 | if(is1D);
71 | if(~isvector(a) || ~isvector(k))
72 | error('MATLAB:conv:AorBNotVector','A and B must be vectors.');
73 | end
74 | a = a(:); k = k(:);
75 | end
76 |
77 | % Flat function for comparison.
78 | o = ones(size(a));
79 |
80 | % Flat function with NaNs for comparison.
81 | on = ones(size(a));
82 |
83 | % Find all the NaNs in the input.
84 | n = isnan(a);
85 |
86 | % Replace NaNs with zero, both in 'a' and 'on'.
87 | a(n) = 0;
88 | on(n) = 0;
89 |
90 | % Check that the filter does not have NaNs.
91 | if(any(isnan(k)));
92 | error([mfilename ':NaNinFilter'],'Filter (k) contains NaN values.');
93 | end
94 |
95 | % Calculate what a 'flat' function looks like after convolution.
96 | if(any(n(:)) || edge)
97 | flat = conv2(on,k,shape);
98 | else flat = o;
99 | end
100 |
101 | % The line above will automatically include a correction for edge effects,
102 | % so remove that correction if the user does not want it.
103 | if(any(n(:)) && ~edge); flat = flat./conv2(o,k,shape); end
104 |
105 | % Do the actual convolution
106 | c = conv2(a,k,shape)./flat;
107 |
108 | % If requested, replace output values with NaNs corresponding to input.
109 | if(nanout); c(n) = NaN; end
110 |
111 | % If 1D, convert back to the original shape.
112 | if(is1D && sza(1) == 1); c = c.'; end
113 |
114 | end
115 |
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/Sub-function/parcellation_template.mat:
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/Sub-function/parcellation_template7.mat:
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/Sub-function/preproc_fRMI.m:
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1 | function [sigValid,posValid,nanChans] = preproc_fRMI(data,pos,fs) ;
2 | % load in the signals from HCP and extract the valid surface cortex data
3 | % input: data from nii file;
4 | % pos from surf.nii file;
5 | % output: sigValid and posValid, valid cortex data
6 |
7 | disp('start preprocessing...');
8 | surfData = data.dtseries ;
9 | surfPos = data.pos ;
10 |
11 | % cortex position
12 | % for i=1:21
13 | % data.brainstructurelabel{i}
14 | % end
15 | % cortex is the region we are interested but the pos is from surface.gii
16 | % file
17 |
18 | % find the cortex
19 | cortexLIdx = find(data.brainstructure == 1) ;
20 | startL = min(cortexLIdx) ;
21 | endL = max(cortexLIdx) ;
22 | cortexRIdx = find(data.brainstructure == 2) ;
23 | startR = min(cortexRIdx) ;
24 | endR = max(cortexRIdx) ;
25 |
26 | %% Get the valid region (cortex)
27 | %patch('Faces',posLC.faces,'Vertices',posLC.vertices)
28 | %axis equal
29 | rangeC = startL:endL ; % left brain
30 | % rangeC = startR:endR ; % right brain
31 |
32 | tic
33 | % check the valid region in time
34 | % figure;
35 | % plot((1:size(surfData,2))/fs,surfData(startL,:))
36 | % hold on
37 | % plot((1:size(surfData,2))/fs,surfData(startL+1000,:))
38 | % hold on
39 | % plot((1:size(surfData,2))/fs,surfData(startL+10000,:))
40 | % title('check three lines of data to confirm the valid region')
41 |
42 | % get rid of the first and the last 10s
43 | % timeRange = fix(10*fs): size(surfData,2)-fix(10*fs) ;
44 | timeRange = 1: size(surfData,2) ;
45 | sigRange = surfData(rangeC,:) ;
46 | sigOri = sigRange(:,timeRange) ;
47 | % sigOri = zscore(surfData(rangeC,timeRange),[],2) ;
48 | nanChans = any(isnan(sigOri(:,:)),2);
49 |
50 | sigValid = sigOri;
51 | sigValid(nanChans,:) = [] ;
52 | posValid = pos ;
53 | posValid.vertices(nanChans,:) = [] ;
54 |
55 | % figure;
56 | % plot(posValid.vertices(1:10:end,1),posValid.vertices(1:10:end,2),'o')
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/Sub-function/spaceFreq_fMRI.m:
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1 | function sigSSpec_reshape=spaceFreq_fMRI(posValid,dataIn,xCord,yCord,...
2 | flagPlotSpe, flagCheckIntp,mask)
3 |
4 | %% re-interpolate data (time consuming)
5 | [X,Y] = meshgrid(xCord, yCord);
6 | sigSSpec = dataIn ;
7 |
8 | sigSSpec_reshape = [] ;
9 | disp('start interpolation (downsample)...')
10 | tic
11 | if sum(mask(:))~= 0
12 | flagMask = 1 ;
13 | end
14 | for iTime=1:size(sigSSpec,2)
15 | % sigSSpec_reshape(:,:,iTime) = griddata(double(posValid.vertices(1:10:end,1)),...
16 | % double(posValid.vertices(1:10:end,2)),sigSSpec(1:10:end,iTime),X,Y,'cubic') ;
17 | sigSSpec_reshape(:,:,iTime) = griddata(double(posValid.vertices(:,1)),...
18 | double(posValid.vertices(:,2)),sigSSpec(:,iTime),X,Y,'cubic') ;
19 | if flagMask
20 | sigSSpec_reshape(:,:,iTime) = sigSSpec_reshape(:,:,iTime).*mask ;
21 | end
22 | end
23 | toc
24 |
25 | %% plot the spatial spectrum
26 | if flagPlotSpe
27 | [Pxx,F] = pmtm(zscore(sigSSpec_reshape(100,:,1)),[],[],1e3) ;
28 | figure;
29 | coeffs = polyfit(log(F(F>10)),log(Pxx(F>10)),1);
30 | fittedX = log(F);
31 | fittedLogY = polyval(coeffs, fittedX);
32 | fittedY = exp(fittedLogY) ;
33 |
34 | loglog(F,Pxx)
35 | hold on
36 | loglog(F,fittedY)
37 | end
38 |
39 | %% check the re-interpolation by visualisation
40 | if flagCheckIntp
41 | %% original data
42 | sigIn = sigSSpec ; % angle(sigSSpec) ;
43 | numColor = 1000 ;
44 | tempColor = jet(numColor) ;
45 | maxData = max(sigIn(:)) ;
46 | minData = min(sigIn(:)) ;
47 | colorAxis = linspace(minData,maxData/2,numColor) ;
48 | idxColor1 = zeros(size(sigIn)) ;
49 | disp('start visulisation 1 ...')
50 | tic
51 | for iTime = 1:size(sigIn,2)
52 | % [cordI,cordJ] = ind2sub(size(sigIn),iData) ;
53 | [~,idxColor1(:,iTime)] = min(abs(sigIn(:,iTime)-ones(size(sigIn,1),1)*colorAxis),[],2) ;
54 | % disp([num2str(iTime/size(sigIn,2)),'%'])
55 | end
56 | toc
57 | %% interpolated data
58 | sigIn = sigSSpec_reshape ; % angle(sigSSpec_reshape) ; % notice the size change
59 | % numColor = 1000 ;
60 | % tempColor = jet(numColor) ;
61 | % maxData = max(sigIn(:)) ;
62 | % minData = min(sigIn(:)) ;
63 | % colorAxis = linspace(minData,maxData/2,numColor) ;
64 | sigIn = reshape(sigIn,size(sigIn,1)*size(sigIn,2),size(sigIn,3)) ;
65 | idxColor2 = zeros(size(sigIn)) ;
66 | disp('start visulisation 2 ...')
67 | tic
68 | for iTime = 1:size(sigIn,2)
69 | % [cordI,cordJ] = ind2sub(size(sigIn),iData) ;
70 | [~,idxColor2(:,iTime)] = min(abs(sigIn(:,iTime)-ones(size(sigIn,1),1)*colorAxis),[],2) ;
71 | % disp([num2str(iTime/size(sigIn,2)),'%'])
72 | end
73 | toc
74 | X_list = reshape(X,size(X,1)*size(X,2),1) ;
75 | Y_list = reshape(Y,size(Y,1)*size(Y,2),1) ;
76 |
77 | iTime = 100 ;
78 | figure;
79 | scatter(posValid.vertices(:,1),posValid.vertices(:,2),4,tempColor(idxColor1(:,iTime),:)) ;
80 | xlim([xCord(1) xCord(end)])
81 | ylim([yCord(1) yCord(end)])
82 |
83 | figure;
84 | scatter(X_list,Y_list,4,tempColor(idxColor2(:,iTime),:)) ;
85 |
86 |
87 | end
88 |
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