├── .DS_Store ├── COPYING ├── EULA ├── README.md ├── Share ├── .DS_Store ├── NIfTI_20140122 │ ├── FAQ.pdf │ ├── NIfTI_tools.pdf │ ├── UseANALYZE.pdf │ ├── affine.m │ ├── bipolar.m │ ├── bresenham_line3d.m │ ├── clip_nii.m │ ├── collapse_nii_scan.m │ ├── examples.txt │ ├── expand_nii_scan.m │ ├── extra_nii_hdr.m │ ├── flip_lr.m │ ├── get_nii_frame.m │ ├── license.txt │ ├── load_nii.m │ ├── load_nii_ext.m │ ├── load_nii_hdr.m │ ├── load_nii_img.m │ ├── load_untouch0_nii_hdr.m │ ├── load_untouch_header_only.m │ ├── load_untouch_nii.m │ ├── load_untouch_nii_hdr.m │ ├── load_untouch_nii_img.m │ ├── make_ana.m │ ├── make_nii.m │ ├── mat_into_hdr.m │ ├── pad_nii.m │ ├── reslice_nii.m │ ├── rri_file_menu.m │ ├── rri_orient.m │ ├── rri_orient_ui.m │ ├── rri_select_file.m │ ├── rri_xhair.m │ ├── rri_zoom_menu.m │ ├── save_nii.m │ ├── save_nii_ext.m │ ├── save_nii_hdr.m │ ├── save_untouch0_nii_hdr.m │ ├── save_untouch_header_only.m │ ├── save_untouch_nii.m │ ├── save_untouch_nii_hdr.m │ ├── save_untouch_slice.m │ ├── unxform_nii.m │ ├── verify_nii_ext.m │ ├── view_nii.m │ ├── view_nii_menu.m │ └── xform_nii.m ├── emma-master │ ├── CHANGES │ ├── MANIFEST │ ├── MANIFEST.SKIP │ ├── Makefile │ ├── Makefile.develop │ ├── Makefile.irix4 │ ├── Makefile.irix5 │ ├── Makefile.irix6 │ ├── Makefile.linux │ ├── Makefile.macosx │ ├── Makefile.msvc-win32 │ ├── Makefile.site │ ├── Makefile.sun4 │ ├── Makefile.version │ ├── README │ ├── doc │ │ ├── Makefile │ │ ├── emma-help.tex │ │ ├── emma.tex │ │ ├── flow.xfig │ │ ├── gen_html_docs │ │ ├── leastsq.tex │ │ ├── matlab_activities.txt │ │ ├── rCBF_activities.txt │ │ ├── rcbf-help.tex │ │ ├── rcbf.tex │ │ ├── simul.tex │ │ ├── state_of_the_world.txt │ │ └── structure.xfig │ ├── matlab │ │ ├── fdg │ │ │ ├── cnvCa.m │ │ │ ├── fdg.m │ │ │ ├── getFDG_CPI.m │ │ │ ├── getFDGplasma.m │ │ │ ├── igrate.m │ │ │ ├── shift_1.m │ │ │ └── solveFDG.m │ │ ├── general │ │ │ ├── Contents.m │ │ │ ├── blurimage.m │ │ │ ├── calpix.m │ │ │ ├── check_sf.m │ │ │ ├── closeimage.m │ │ │ ├── deriv.m │ │ │ ├── dispimage.m │ │ │ ├── emma_table.m │ │ │ ├── emmahelp.m │ │ │ ├── gecolour.m │ │ │ ├── getblooddata.m │ │ │ ├── getcwd.m │ │ │ ├── getimageinfo.m │ │ │ ├── getimages.m │ │ │ ├── getmask.m │ │ │ ├── getpixel.m │ │ │ ├── gettaggedhist.m │ │ │ ├── gettaggedregion.m │ │ │ ├── getvolumehist.m │ │ │ ├── getvoxeltoworld.m │ │ │ ├── handlefield.m │ │ │ ├── hotmetal.m │ │ │ ├── howbig.m │ │ │ ├── kernel.m │ │ │ ├── loadtagfile.m │ │ │ ├── loadxfmfile.m │ │ │ ├── lookup.m │ │ │ ├── maketac.m │ │ │ ├── miinquire.m │ │ │ ├── mireadimages.m │ │ │ ├── mireadvar.m │ │ │ ├── miwriteatt.m │ │ │ ├── miwriteimages.m │ │ │ ├── nconv.m │ │ │ ├── newimage.m │ │ │ ├── nfmins.m │ │ │ ├── nframeint.m │ │ │ ├── ntrapz.m │ │ │ ├── openimage.m │ │ │ ├── pixelindex.m │ │ │ ├── putimages.m │ │ │ ├── resampleblood.m │ │ │ ├── rescale.m │ │ │ ├── smooth.m │ │ │ ├── spectral.m │ │ │ ├── tempfilename.m │ │ │ ├── threshimage.m │ │ │ ├── viewimage.m │ │ │ ├── voxeltoworld.m │ │ │ └── worldtovoxel.m │ │ ├── rcbf │ │ │ ├── b_curve.m │ │ │ ├── correctblood.m │ │ │ ├── findintconvo.m │ │ │ ├── fit_b_curve.m │ │ │ ├── rcbf1.m │ │ │ ├── rcbf2.m │ │ │ ├── rcbfanalysis.m │ │ │ └── rcbfdemo.m │ │ └── roi │ │ │ ├── drawboxroi.m │ │ │ ├── drawpolyroi.m │ │ │ ├── drawroi.m │ │ │ ├── getroi.m │ │ │ ├── makeroimask.m │ │ │ └── transferroi.m │ ├── mexrc.sh │ └── source │ │ ├── bldtobnc │ │ ├── 00Description │ │ ├── Makefile │ │ └── bldtobnc.c │ │ ├── bloodtonc │ │ ├── 00Description │ │ ├── Makefile │ │ └── bloodtonc.c │ │ ├── delaycorrect │ │ ├── 00Description │ │ ├── Makefile │ │ └── delaycorrect.c │ │ ├── include │ │ ├── ParseArgv.h │ │ ├── cvterr │ │ ├── emmageneral.h │ │ ├── emmaproto.h │ │ ├── mexutils.h │ │ ├── mierrors.h │ │ ├── mincutil.h │ │ ├── ncblood.h │ │ └── time_stamp.h │ │ ├── includeblood │ │ ├── 00Description │ │ ├── Makefile │ │ └── includeblood.c │ │ ├── libsource │ │ ├── .depend │ │ ├── 00Description │ │ ├── Makefile │ │ ├── ParseArgv.c │ │ ├── createnan.c │ │ ├── intframes.c │ │ ├── lookup12.c │ │ ├── mexutils.c │ │ ├── mincutil.c │ │ ├── monotonic.c │ │ ├── time_stamp.c │ │ └── trapint.c │ │ ├── lookup │ │ ├── 00Description │ │ ├── Makefile │ │ └── lookup.c │ │ ├── makefile.cmex │ │ ├── makefile.std │ │ ├── mexec │ │ ├── Makefile │ │ └── mexec.c │ │ ├── micreate │ │ ├── 00Description │ │ ├── Makefile │ │ └── micreate.c │ │ ├── micreatedim │ │ ├── 00Description │ │ ├── Makefile │ │ └── micreatedim.c │ │ ├── micreateimage │ │ ├── 00Description │ │ ├── Makefile │ │ ├── args.c │ │ ├── args.h │ │ ├── dimensions.c │ │ ├── dimensions.h │ │ ├── micreateimage.c │ │ └── micreateimage.h │ │ ├── micreatevar │ │ ├── 00Description │ │ ├── Makefile │ │ └── micreatevar.c │ │ ├── miinquire │ │ ├── 00Description │ │ ├── Makefile │ │ └── miinquire.c │ │ ├── mireadimages │ │ ├── 00Description │ │ ├── Makefile │ │ └── mireadimages.c │ │ ├── mireadvar │ │ ├── 00Description │ │ ├── Makefile │ │ └── mireadvar.c │ │ ├── miwriteatt │ │ ├── 00Description │ │ ├── Makefile │ │ └── miwriteatt.c │ │ ├── miwriteimages │ │ ├── 00Description │ │ ├── Makefile │ │ └── miwriteimages.c │ │ ├── miwritevar │ │ ├── 00Description │ │ ├── Makefile │ │ └── miwritevar.c │ │ ├── nfmins │ │ ├── 00Description │ │ ├── Makefile │ │ └── nfmins.c │ │ ├── nframeint │ │ ├── 00Description │ │ ├── Makefile │ │ └── nframeint.c │ │ ├── ntrapz │ │ ├── 00Description │ │ ├── Makefile │ │ └── ntrapz.c │ │ └── rescale │ │ ├── 00Description │ │ ├── Makefile │ │ └── rescale.c └── surfstat │ └── stat_threshold.m ├── Ui ├── VoxelStats.m ├── chooseFile.m ├── chooseVariable.m ├── runRFT.m ├── runVS.m ├── saveRes.m └── viewRes.m ├── UtilFncs ├── .DS_Store ├── VoxelStatsDoRFT.m ├── VoxelStatsShow.m ├── VoxelStatsShowOnTemplate.m ├── VoxelStatsWriteMinc.m ├── VoxelStatsWriteNifti.m ├── getMaskSlicesMinc.m ├── getMaskSlicesNifti.m ├── getMultiVarData.m ├── getMultiVarForSlice.m ├── getMultiVarMapForSliceMultiVar.m ├── getVoxelStructFromMask.m ├── readMaskSlices.m ├── 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