├── LICENSE ├── README.md └── preprocessing_BIDS_SPM12.m /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # fMRI-preprocessing-SPM12 2 | This is a SPM12 batch script that runs a standard fMRI preprocessing pipeline on a BIDS formatted data-set. 3 | 4 | ## Included preprocessing steps 5 | - defacing 6 | - field map esimtation 7 | - realignment and unwarping 8 | - slice-time correction 9 | - normalization 10 | - smoothing 11 | 12 | ## Requirements 13 | - a BIDS formatted fMRI data-set See http://bids.neuroimaging.io/ for more information. 14 | - a T1 anatomical image 15 | - a field map 16 | - at least 1 functional run (saved as a 4D nifti file) 17 | The scripts are written with the imaging sequences used at the GIfMI (http://gifmi.ugent.be/) in mind. 18 | 19 | ## Bugs / Improvements 20 | If you find bugs in this script or have suggestions for improvement, please report both here https://github.com/CCN-github/fMRI-preprocessing-SPM12/issues 21 | 22 | ## Import raw data in the BIDS format 23 | If you are interested in importing your data according to BIDS standards, go check out the scripts here https://github.com/NeuroStat/CustomFormatBIDS 24 | 25 | ## Contact 26 | david.wisniewski@ugent.be 27 | 28 | -------------------------------------------------------------------------------- /preprocessing_BIDS_SPM12.m: -------------------------------------------------------------------------------- 1 | function preprocessing_BIDS (sub) 2 | 3 | %{ 4 | This functions runs a standard preprocessing pipeline in SPM12. Make sure SPM12 is in your matlab path. 5 | 6 | The scripts requires a BIDS formatted dataset. See http://bids.neuroimaging.io/ 7 | It also assumes you acquired a T1 analtomical image, at least 1 functional run saved as a 4D nifti file, and a field map (which I highly recommend). 8 | 9 | In order to run this script, call the preprocessing_BIDS function, giving it one subject numer. 10 | The script will then run the preprocessing for that subejct. 11 | 12 | 23/01/2018 v.0.9.0: - stable version 13 | 01/07/2018 v.1.0.0: - adapted to multi-band sequence 14 | - added segmentation step (both by: Carlos Gonzalez-Garcia, carlos.gonzalezgarcia@ugent.be) 15 | 16 | David Wisniewski (david.wisniewski@ugent.be) 17 | %} 18 | 19 | 20 | %% FLAGS 21 | %{ 22 | The script is partly modular. You can switch specific preprocessing step on (=1) or off (=0) here. 23 | The order of the steps is fixed at the moment though. It is assumed that you run your preprocessing 24 | in the order: deface -> fieldmap -> realign and unwarp -> slice time correction -> coregistration -> segmentation -> normalization -> smoothing 25 | %} 26 | 27 | do_deface = 1; % deface the anatomical image to anonymize the data 28 | do_fieldmap = 1; % calculate fieldmap (vdm file) 29 | do_realign_unwarp = 1; % realignment (get rid of movement artifacts) + unwarping (account for disortions in the magnetic field using the fieldmap) 30 | do_slice_time = 1; % slice time correction 31 | do_coregister = 1; % coregistration of T1 to EPI images 32 | do_segment = 1; % segment T1 and create inverse and forward models 33 | do_norm=1; % normalize images to MNI space 34 | do_smooth=1; % smooth images 35 | 36 | %% PARAMETERS 37 | %{ 38 | specify the paramters of your dataset here 39 | %} 40 | % specify the number of functional runs acquired 41 | nruns=5; 42 | % slice time corrections 43 | param.st.nslices = 50; % number of slices per volume 44 | param.st.tr = 1.73; %TR in sec 45 | param.st.ta = 1.73-(1.73/50); %time of acquisition for one slice, i.e. TR - (TR./nslices) 46 | param.st.so = [0.82, 0, 0.8875, 0.0675, 0.9575, 0.1375, 1.025, 0.205, 1.0925, 0.2725, 1.1625, 0.3425, 1.23, 0.41, 1.3, 0.4775, 1.3675, 0.5475, 1.435, 0.615, 1.505, 0.6825, 1.5725, 0.7525, 1.64, 0.82, 0, 0.8875, 0.0675, 0.9575, 0.1375, 1.025, 0.205, 1.0925, 0.2725, 1.1625, 0.3425, 1.23, 0.41, 1.3, 0.4775, 1.3675, 0.5475, 1.435, 0.615, 1.505, 0.6825, 1.5725, 0.7525, 1.64]*1000; % slice acquisition order 47 | param.st.refslice = max(param.st.so)/2; % reference slice, for fMRI usually the middle slice 48 | % smoothing 49 | param.smooth.fwhm = [8 8 8]; % define the smoothing kernel in mm 50 | 51 | %% DIRECTORIES 52 | % convert subject number into a string for easier handling 53 | substr=num2str(sub,'%.2d'); 54 | % specify the directory in which your BIDS compatible raw data are localized 55 | basedir = '\\folder\BIDS'; 56 | % specify the directory to which all derivatives of the raw data are to be saved 57 | % side note: BIDS splits your data into the raw unprocessed images, and derivatives. The latter are all images derived from the raw data, e.g. preprocessed images. 58 | derivativesdir = '\\folder\derivatives'; 59 | subdir=['\sub-' substr]; 60 | % please also check below as well. The fieldmap and segmentation steps require you to change folders in the respective code segments as well. 61 | 62 | %% RUN THE ANALYSIS 63 | 64 | %% DEFACE T1 65 | % in order to guarantee anaonymity, we deface the anatomical images 66 | if do_deface 67 | % run the defacing step 68 | matlabbatch{1}.spm.util.deface.images = cellstr(spm_select('FPList',[basedir subdir '\anat\'],'^sub.*.nii$')); 69 | spm_jobman('run', matlabbatch); 70 | clear matlabbatch; 71 | % file management 72 | % delete original file with the face still intact 73 | delete (spm_select('FPList',[basedir subdir '\anat\'],'^sub.*.nii$')); 74 | % rename anonimized file 75 | fname=spm_select('FPList',[basedir subdir '\anat\'],'^anon.*.nii$'); 76 | newname= regexprep(fname,'anon_',''); 77 | movefile (fname,newname); 78 | % copy anonymized file to \derivates folder 79 | destination = regexprep(newname,'BIDS','derivatives'); 80 | copyfile (newname,destination) ; 81 | end 82 | 83 | 84 | %% FIELDMAP 85 | % estimate a field map 86 | if do_fieldmap 87 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.presubphasemag.phase = cellstr(spm_select('FPList',[basedir subdir '\fmap\'],'^sub.*phase2.nii$')); 88 | % of the two magnitude images, use the one with the shorter TE,which will have greater signal 89 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.data.presubphasemag.magnitude = cellstr(spm_select('FPList',[basedir subdir '\fmap\'],'^sub.*magnitude2.nii$')); 90 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.et = [5.19 7.56]; 91 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.maskbrain = 0; 92 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.blipdir = -1; 93 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.tert = 32.64; 94 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.epifm = 0; 95 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.ajm = 0; 96 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.method = 'Mark3D'; 97 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.fwhm = 10; 98 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.pad = 0; 99 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.uflags.ws = 1; 100 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.template = {'F:\Data\Programs Scripts\spm12\toolbox\FieldMap\T1.nii'}; % change the folder here 101 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.fwhm = 5; 102 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.nerode = 2; 103 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.ndilate = 4; 104 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.thresh = 0.5; 105 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.defaults.defaultsval.mflags.reg = 0.02; 106 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.session.epi = cellstr(spm_select('FPList',[basedir subdir '\func'],'^sub.*run-1_bold.nii$')); 107 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.matchvdm = 1; 108 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.sessname = 'session'; 109 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.writeunwarped = 0; 110 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.anat = ''; 111 | matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj.matchanat = 0; 112 | spm_jobman('run', matlabbatch); 113 | clear matlabbatch; 114 | 115 | %file management: move newly generated files into derivatives 116 | %folder 117 | fname=spm_select('FPList',[basedir subdir '\fmap\'],'^fpm.*.nii$'); 118 | destination = regexprep(fname,'BIDS','derivatives'); 119 | movefile (fname,destination) ; 120 | fname=spm_select('FPList',[basedir subdir '\fmap\'],'^scsub.*.nii$'); 121 | destination = regexprep(fname,'BIDS','derivatives'); 122 | movefile (fname,destination) ; 123 | fname=spm_select('FPList',[basedir subdir '\fmap\'],'^vdm.*.nii$'); 124 | destination = regexprep(fname,'BIDS','derivatives'); 125 | movefile (fname,destination) ; 126 | fname=spm_select('FPList',[basedir subdir '\func\'],'^usub.*.nii$'); 127 | destination = regexprep(fname,'BIDS','derivatives'); 128 | movefile (fname,destination) ; 129 | fname=spm_select('FPList',[basedir subdir '\func\'],'^wfmag.*.nii$'); 130 | destination = regexprep(fname,'BIDS','derivatives'); 131 | movefile (fname,destination); 132 | 133 | end 134 | 135 | %% REALIGN & UNWARP 136 | % correct for movement artifacts and magnetic field inhomogeneities. The latter requires the estimated field map from the previous step. 137 | if do_realign_unwarp 138 | clear matlabbatch; 139 | 140 | vdmfile = cellstr(spm_select('FPList',[derivativesdir subdir '\fmap\'],'^vdm.*\phase2.nii$')); 141 | for run=1:nruns 142 | filter = ['^sub.*run-' num2str(run) '_bold.nii$'] ; 143 | matlabbatch{1}.spm.spatial.realignunwarp.data(run).scans = cellstr(spm_select('FPList',[basedir subdir '\func\'],filter)); 144 | matlabbatch{1}.spm.spatial.realignunwarp.data(run).pmscan = vdmfile; 145 | end 146 | 147 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.quality = 0.9; 148 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.sep = 3; 149 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.fwhm = 5; 150 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.rtm = 0; 151 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.einterp = 4; 152 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.ewrap = [0 0 0]; 153 | matlabbatch{1}.spm.spatial.realignunwarp.eoptions.weight = ''; 154 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.basfcn = [12 12]; 155 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.regorder = 1; 156 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.lambda = 100000; 157 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.jm = 0; 158 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.fot = [4 5]; 159 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.sot = []; 160 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.uwfwhm = 4; 161 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.rem = 1; 162 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.noi = 5; 163 | matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.expround = 'Average'; 164 | matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.uwwhich = [2 1]; 165 | matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.rinterp = 4; 166 | matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.wrap = [0 0 0]; 167 | matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.mask = 1; 168 | matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.prefix = 'u'; 169 | 170 | spm_jobman('run', matlabbatch); 171 | clear matlabbatch; 172 | 173 | % file management 174 | % move files to /derivatives folder 175 | fname=cellstr(spm_select('FPList',[basedir subdir '\func\'],'^usub.*.nii$')); 176 | destination = regexprep(fname,'BIDS','derivatives'); 177 | for i = 1:length(fname) 178 | movefile (fname{i},destination{i}); 179 | end 180 | fname=spm_select('FPList',[basedir subdir '\func\'],'^mean.*.nii$'); 181 | destination = regexprep(fname,'BIDS','derivatives'); 182 | movefile (fname,destination); 183 | fname=cellstr(spm_select('FPList',[basedir subdir '\func\'],'^*.mat$')); 184 | destination = regexprep(fname,'BIDS','derivatives'); 185 | for i = 1:length(fname) 186 | movefile (fname{i},destination{i}); 187 | end 188 | fname=cellstr(spm_select('FPList',[basedir subdir '\func\'],'^*.txt$')); 189 | destination = regexprep(fname,'BIDS','derivatives'); 190 | for i = 1:length(fname) 191 | movefile (fname{i},destination{i}); 192 | end 193 | end 194 | 195 | %% SLICE TIME CORRECTION 196 | % corrects for slice acquisition order 197 | if do_slice_time 198 | clear matlabbatch img_files; 199 | img_files = [{cellstr(spm_select('FPList', [derivativesdir subdir '\func\'], '^usub.*.nii$'))}]; 200 | matlabbatch{1}.spm.temporal.st.scans = img_files; 201 | matlabbatch{1}.spm.temporal.st.nslices = param.st.nslices; % check this again 202 | matlabbatch{1}.spm.temporal.st.tr = param.st.tr; 203 | matlabbatch{1}.spm.temporal.st.ta = param.st.ta; 204 | matlabbatch{1}.spm.temporal.st.so = param.st.so; % check this again whther this is actually true. also see 205 | % https://static.healthcare.siemens.com/siemens_hwem-hwem_ssxa_websites-context-root/wcm/idc/groups/public/@global/@imaging/@mri/documents/download/mdaz/nzmy/~edisp/mri_60_graessner-01646277.pdf 206 | matlabbatch{1}.spm.temporal.st.refslice = param.st.refslice; 207 | matlabbatch{1}.spm.temporal.st.prefix = 'a'; 208 | spm_jobman('run', matlabbatch); 209 | clear matlabbatch; 210 | end 211 | 212 | 213 | %% COREGISTRATION 214 | % in order to normalize the functional images, first coregister the T1 to the mean EPI image. 215 | if do_coregister 216 | clear matlabbatch; 217 | % use the mean EPI as the stationary reference image 218 | matlabbatch{1}.spm.spatial.coreg.estwrite.ref = cellstr(spm_select('FPList', [derivativesdir subdir '\func\'], '^mean.*.nii$')); 219 | % use the MPRAGE as the source image that will be warped to match the mean EPI 220 | matlabbatch{1}.spm.spatial.coreg.estwrite.source = cellstr(spm_select('FPList', [basedir subdir '\anat\'], '^sub.*.nii$')); 221 | matlabbatch{1}.spm.spatial.coreg.estwrite.other = {''}; 222 | matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.cost_fun = 'nmi'; 223 | matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.sep = [4 2]; 224 | matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001]; 225 | matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.fwhm = [7 7]; 226 | matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.interp = 4; 227 | matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.wrap = [0 0 0]; 228 | matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.mask = 0; 229 | matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.prefix = 'r'; 230 | spm_jobman('run', matlabbatch); 231 | clear matlabbatch; 232 | 233 | %file management: move newly generated files into derivatives 234 | %folder 235 | fname=spm_select('FPList',[basedir subdir '\anat\'],'^rsub.*.nii$'); 236 | destination = regexprep(fname,'BIDS','derivatives'); 237 | movefile (fname,destination) ; 238 | 239 | end 240 | 241 | %% SEGMENTATION 242 | % segment T1 with inverse and forward models 243 | if do_segmentation == 1 244 | clear matlabbatch; 245 | matlabbatch{1}.spm.spatial.preproc.channel.vols = cellstr(spm_select('FPList', [derivativesdir subdir '\anat\'], '^rsub.*.nii$')); 246 | matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001; 247 | matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60; 248 | matlabbatch{1}.spm.spatial.preproc.channel.write = [0 0]; 249 | matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,1'}; % change the folders here 250 | matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1; 251 | matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0]; 252 | matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [0 0]; 253 | matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,2'}; % and here 254 | matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1; 255 | matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0]; 256 | matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0]; 257 | matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,3'}; % and here 258 | matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2; 259 | matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0]; 260 | matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0]; 261 | matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,4'}; % and here 262 | matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3; 263 | matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0]; 264 | matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0]; 265 | matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,5'}; % and here 266 | matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4; 267 | matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0]; 268 | matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0]; 269 | matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'D:\Data\Programs_Scripts\spm12\tpm\TPM.nii,6'}; % and here 270 | matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2; 271 | matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0]; 272 | matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0]; 273 | matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1; 274 | matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1; 275 | matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2]; 276 | matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni'; 277 | matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0; 278 | matlabbatch{1}.spm.spatial.preproc.warp.samp = 3; 279 | matlabbatch{1}.spm.spatial.preproc.warp.write = [1 1]; 280 | spm_jobman('run', matlabbatch); 281 | clear matlabbatch; 282 | end 283 | 284 | 285 | %% NORMALIZATION 286 | %normalize the images to MNI space 287 | if do_norm 288 | clear matlabbatch; 289 | % new normaization, using deformation fields from segmentation 290 | img_files = cellstr(spm_select('FPList', [derivativesdir subdir '\func\'], '^ausub.*\.nii$')); 291 | matlabbatch{1}.spm.spatial.normalise.write.subj.def = cellstr(spm_select('FPList', [derivativesdir subdir '\anat\'], '^y.*.nii$')); 292 | matlabbatch{1}.spm.spatial.normalise.write.subj.resample = img_files; 293 | matlabbatch{1}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 294 | 78 76 85]; 295 | matlabbatch{1}.spm.spatial.normalise.write.woptions.vox = [2 2 2]; 296 | matlabbatch{1}.spm.spatial.normalise.write.woptions.interp = 4; 297 | matlabbatch{1}.spm.spatial.normalise.write.woptions.prefix = 'w'; 298 | spm_jobman('run', matlabbatch); 299 | end 300 | 301 | %% SMOOTHING 302 | % smooth the images 303 | if do_smooth 304 | clear matlabbatch; 305 | img_files = [cellstr(spm_select('FPList', [derivativesdir subdir '\func\'], '^wausub.*.nii$'))]; 306 | matlabbatch{1}.spm.spatial.smooth.data = img_files; 307 | matlabbatch{1}.spm.spatial.smooth.fwhm = param.smooth.fwhm; 308 | matlabbatch{1}.spm.spatial.smooth.dtype = 0; 309 | matlabbatch{1}.spm.spatial.smooth.im = 0; 310 | matlabbatch{1}.spm.spatial.smooth.prefix = 's'; 311 | spm_jobman('run', matlabbatch); 312 | clear matlabbatch; 313 | end 314 | 315 | --------------------------------------------------------------------------------