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Brainstorm software: MEG, EEG, fNIRS, ECoG, sEEG and electrophysiology
http://neuroimage.usc.edu/brainstorm
GNU General Public License v3.0
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Bugs CAT12 v1728/1732 #352

Closed ftadel closed 3 years ago

ftadel commented 4 years ago

1. catROIs...xml vs catROI...xml ?

Execution of the following segmentation batch:

    matlabbatch{1}.spm.tools.cat.estwrite.data = {[NiiFile ',1']};
    matlabbatch{1}.spm.tools.cat.estwrite.data_wmh = {''};    % NEW 1728 
    matlabbatch{1}.spm.tools.cat.estwrite.useprior = '';      % NEW 1728
    matlabbatch{1}.spm.tools.cat.estwrite.nproc = 0;   % Blocking call to CAT12
    matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {TpmNii};
    matlabbatch{1}.spm.tools.cat.estwrite.opts.affreg = 'mni';
    matlabbatch{1}.spm.tools.cat.estwrite.opts.biasstr = 0.5;   % OLD
    matlabbatch{1}.spm.tools.cat.estwrite.opts.biasacc = 0.5;   % NEW 1716
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.APP = 1070;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.spm_kamap = 0;   % NEW 1716
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.LASstr = 0.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.gcutstr = 2;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.WMHC = 1;   % NEW 1716
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.dartel.darteltpm = {dartelTpm};   % OLD
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.shooting.shootingtpm = {shootingTpm};  % NEW 1716 
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.shooting.regstr = 0.5;  % NEW 1716 
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.vox = 1.5;
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.restypes.optimal = [1 0.1];  % NEW 1716 
    matlabbatch{1}.spm.tools.cat.estwrite.extopts.ignoreErrors = 1;  % NEW 1716 
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.labelnative = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.jacobianwarped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [1 1];      % Changed from [0 0] with NEW 1728
    matlabbatch{1}.spm.tools.cat.estwrite.output.rmat = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.ownatlas = {''};

On Windows 10 / Matlab 2020b: Runs correctly, but prints an error message:

  Remove "C:\Users\franc\.brainstorm\tmp\cat12\label\catROI_CAT12_1001_2020-11.xml" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list 
and following batches will may not work correctly!

The file C:\Users\franc.brainstorm\tmp\cat12\label\ catROIs _CAT12_1001_2020-11.xml exists. But not C:\Users\franc.brainstorm\tmp\cat12\label\ catROI _CAT12_1001_2020-11.xml. Is there an error somewhere?

2. CAT_ResampleSurf: Vertex index out of range

Trying to interpolate the Destrieux parcellation on the subject's surfaces, on Windows 10 / Matlab 2020b: 

>> cat_surf_map_atlas('C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.central.CAT12_1001_2020-11.gii', 'C:\Work\Dev\Divers\spm12\toolbox\cat12\atlases_surfaces\lh.aparc_a2009s.freesurfer.annot')

Translates into the system call:  
>> C:\Work\Dev\Divers\spm12\toolbox\cat12\CAT.w32\CAT_ResampleSurf
"C:\Work\Dev\Divers\spm12\toolbox\cat12\templates_surfaces\lh.central.freesurfer.gii" 
"C:\Work\Dev\Divers\spm12\toolbox\cat12\templates_surfaces\lh.sphere.freesurfer.gii" 
"C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.sphere.reg.CAT12_1001_2020-11.gii" 
"NULL" 
"C:\Work\Dev\Divers\spm12\toolbox\cat12\atlases_surfaces\lh.aparc_a2009s.freesurfer.annot" 
"C:\Users\franc\.brainstorm\tmp\cat12\label\lh.aparc_a2009s.CAT12_1001_2020-11.annot"'

Produces the following warning in the terminal:
Vertex index out of range

Followed by an error without any error message in Matlab:
** >cat_check_system_output.m at 27
** >cat_surf_map_atlas.m at 47

The same error arises for all the annotation files in spm12\toolbox\cat12\atlases_surfaces\, except for lh.aparc_DK40.freesurfer.annot. However, when reading this file with FreeSurfer's read_annotation.m, it crashes with the following error message, therefore the .annot file is invalid.

>> cat_surf_map_atlas('C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.central.CAT12_1001_2020-11.gii', 'C:\Work\Dev\Divers\spm12\toolbox\cat12\atlases_surfaces\lh.aparc_DK40.freesurfer.annot')
Save C:\Users\franc\.brainstorm\tmp\cat12\label\lh.aparc_DK40.CAT12_1001_2020-11.annot
Save C:\Users\franc\.brainstorm\tmp\cat12\label\rh.aparc_DK40.CAT12_1001_2020-11.annot

>> read_annotation('C:\Users\franc\.brainstorm\tmp\cat12\label\lh.aparc_DK40.CAT12_1001_2020-11.annot')
Error using zeros
Requested 1107296256x5 (41.3GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive.
Error in read_annotation (line 126)
        colortable.table = zeros(numEntries,5);

>> read_annotation('C:\Users\franc\.brainstorm\tmp\cat12\label\rh.aparc_DK40.CAT12_1001_2020-11.annot')
Error using fread
Invalid size.
Error in read_annotation (line 123)
        colortable.orig_tab = fread(fp, len, '*char')';

Christian Gaser:

This is somewhat weird. I am cross-compiling the code using the same compiler. However, probably this is a Windows issue.

Testing with Ubuntu 18 (WSL) / Matlab 2018b. Using the exact same call, SPM/CAT installation and input files (C: drive mounted on the Linux system as /mnt/c). => It does not crash. There is something different between the Windows and Linux binaries, indeed.

cat_surf_map_atlas('/mnt/c/Users/franc/.brainstorm/tmp/cat12/surf/lh.central.CAT12_1001_2020-11.gii', '/mnt/c/Work/Dev/Divers/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot')

Translates to:
/mnt/c/Work/Dev/Divers/spm12/toolbox/cat12/CAT.glnx86/CAT_ResampleSurf 
"/mnt/c/Work/Dev/Divers/spm12/toolbox/cat12/templates_surfaces/lh.central.freesurfer.gii" 
"/mnt/c/Work/Dev/Divers/spm12/toolbox/cat12/templates_surfaces/lh.sphere.freesurfer.gii" 
"/mnt/c/Users/franc/.brainstorm/tmp/cat12/surf/lh.sphere.reg.CAT12_1001_2020-11.gii" "NULL" 
"/mnt/c/Work/Dev/Divers/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot" 
"/mnt/c/Users/franc/.brainstorm/tmp/cat12/label/lh.aparc_a2009s.CAT12_1001_2020-11.annot"

Output in the Matlab command window:
Save /mnt/c/Users/franc/.brainstorm/tmp/cat12/label/lh.aparc_a2009s.CAT12_1001_2020-11.annot
Save /mnt/c/Users/franc/.brainstorm/tmp/cat12/label/rh.aparc_a2009s.CAT12_1001_2020-11.annot

However, it still doesn't work as expected. If we try to read the files with FreeSurfer's read_annotation.m, we get an error:

>> [vertices, labels, colortable] = read_annotation('/mnt/c/Work/RawData/Test/fem/A1001_cat12_2020-11/label/lh.aparc_a2009s.CAT12_1001_2020-11.annot',1)

Reading from version 2
Index exceeds the number of array elements (76).
Error in read_annotation (line 163)
            if(~isempty(colortable.struct_names{structure}))

The .annot file is saved with a structure that can't be read by read_annotation.m. From the second strucutre on, the values that are read from the file are wrong. This happens both on Windows 10/Matlab 2020b and Ubuntu 18/Matlab 2018b, with read_annotation.m from FreeSurfer 6. => There is probably something to fix in the CAT function that generates the .annot files.

ftadel commented 4 years ago

@i5gach FYI

ftadel commented 4 years ago

Updated the script that runs CAT12 in Brainstorm in this commit: https://github.com/brainstorm-tools/brainstorm3/commit/5212b573192212cc661caf9661b459323ae7f469

The SPM batch generated by Brainstorm is now the following:

    matlabbatch{1}.spm.tools.cat.estwrite.data = {'C:\Users\franc\.brainstorm\tmp\cat12\CAT12_ICBM152.nii,1'};
    matlabbatch{1}.spm.tools.cat.estwrite.data_wmh = {''};
    matlabbatch{1}.spm.tools.cat.estwrite.useprior = '';
    matlabbatch{1}.spm.tools.cat.estwrite.nproc = 0;                % Blocking call to CAT12
    matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {'C:\Users\franc\.brainstorm\defaults\spm\TPM.nii'};      % User-defined TPM atlas
    matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [1 1];     % Save deformation fields: [forward inverse]
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native   = 1;   % GM tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.warped   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod      = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native   = 1;   % WM tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.warped   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod      = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 1;   % Tissue classes 4-6 to create own TPMs
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod    = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native  = 1;   % CSF tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped  = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod     = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel  = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1;  % Label: background=0, CSF=1, GM=2, WM=3, WMH=4
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0;  % No volume atlases
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40             = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra              = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers            = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 2;   % 1: lh+rh, 2:lh+rh+cerebellum
    matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1;   % Cortical thickness

    matlabbatch{2}.spm.tools.cat.stools.surfextract.data_surf(1) = cfg_dep('CAT12: Segmentation (current release): Left Central Surface', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','lhcentral', '()',{':'}));
    matlabbatch{2}.spm.tools.cat.stools.surfextract.GI = 1;     % Gyrification index
    matlabbatch{2}.spm.tools.cat.stools.surfextract.SD = 1;     % Sulcal depth
    matlabbatch{2}.spm.tools.cat.stools.surfextract.nproc = 0;  % Blocking call to CAT12

However, all the errors mentioned above are still there. Additionally, I confirm that when running the atlas projection with the GUI menu Surface Tools > Map Surface Atlas to Individual Surface, we get exactly the same errors as above:

Error using cat_check_system_output (line 27)

Error in cat_surf_map_atlas (line 47)
      [ST, RS] = cat_system(cmd); cat_check_system_output(ST,RS);

Error in spm (line 1004)
    evalin('base',CB)

Error while evaluating UIControl Callback.
ftadel commented 4 years ago

Execution example on the MNI ICBM152 template: https://neuroimage.usc.edu/forums/t/cat12-missing-files/23121/3

ChristianGaser commented 3 years ago

@ftadel

1. catROIs...xml vs catROI...xml ?

In order to disable ROI processing for volumes the ROI structure should have the following syntax: matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.noROI = struct([]);

Please note that surface extraction for the cerebellum is still experimental and does not reliably work and should only be used with great care. Currently, I cannot recommend regular use and this should be disabled which also holds for the experimental surface_measure flag (thickness will be saved anyway): matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 1; %matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1;

2. CAT_ResampleSurf: Vertex index out of range

I couldn't get this to work on Windows systems, and after trying for days to solve the problem, I gave up and implemented an alternative approach. This is available in r1732.

ftadel commented 3 years ago
  • In order to disable ROI processing for volumes the ROI structure should have the following syntax:
  • Please note that surface extraction for the cerebellum is still experimental
  • also holds for the experimental surface_measure flag (thickness will be saved anyway)

Thank you for your comments. I made the cerebellum extraction a discreet option (disabled by default) and adjusted the SPM batch based on your recommendations. We might need the deformation fields and the volume atlases in the future, but not immediately. https://github.com/brainstorm-tools/brainstorm3/commit/0f6ad98d6d613f36d8fcc4cb3aa2baaf88572593

The "advanced" interface in Brainstorm now looks like this: image

And the default batch is the following:

    matlabbatch{1}.spm.tools.cat.estwrite.data = {'C:\Users\franc\.brainstorm\tmp\cat12\CAT12_1001_2020_11_1732.nii,1'};
    matlabbatch{1}.spm.tools.cat.estwrite.data_wmh = {''};
    matlabbatch{1}.spm.tools.cat.estwrite.useprior = '';
    matlabbatch{1}.spm.tools.cat.estwrite.nproc = 0;                % Blocking call to CAT12
    matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {'C:\Users\franc\.brainstorm\defaults\spm\TPM.nii'};      % User-defined TPM atlas
    matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.warps       = [0 0]; % Skip deformation fields for the moment: [forward inverse]
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native   = 1;   % GM tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.warped   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod      = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native   = 1;   % WM tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.warped   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod      = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel   = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 1;   % Tissue classes 4-6 to create own TPMs
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod    = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native  = 1;   % CSF tissue maps
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped  = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod     = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel  = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1;  % Label: background=0, CSF=1, GM=2, WM=3, WMH=4
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.noROI = struct([]);   % CGaser comment: Correct syntax to disable ROI processing for volumes   
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0;  % No volume atlases
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40             = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra              = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers            = 0;
    matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 1;

I couldn't get this to work on Windows systems, and after trying for days to solve the problem, I gave up and implemented an alternative approach. This is available in r1732.

Not sure how to make this work. There are issues with the handling of the file separators on Windows.

>> cat_surf_map_atlas('C:\Work\RawData\Test\fem\A1001_cat12_2020-11_1728\surf\lh.central.CAT12_1001_2020-11.gii', 'C:\Work\Dev\Divers\spm12\toolbox\cat12\atlases_surfaces\lh.aparc_a2009s.freesurfer.annot')
Error using cat_check_system_output (line 27)
Error:  could not open file "C:WorkRawDataTestfemA1001_cat12_2020-11_1728surflh.aparc_a2009s.txt".
System message: No such file or directory
Cannot read values in C:\Work\RawData\Test\fem\A1001_cat12_2020-11_1728\surf\lh.aparc_a2009s.txt.

Error in cat_surf_map_atlas (line 54)
      [ST, RS] = cat_system(cmd); cat_check_system_output(ST,RS);

This calls translates to the system call:

CAT_ResampleSurf -label 
"C:\Work\Dev\Divers\spm12\toolbox\cat12\templates_surfaces\lh.central.freesurfer.gii" 
"C:\Work\Dev\Divers\spm12\toolbox\cat12\templates_surfaces\lh.sphere.freesurfer.gii" 
"C:\Work\RawData\Test\fem\A1001_cat12_2020-11_1728\surf\lh.sphere.reg.CAT12_1001_2020-11.gii" 
"NULL" 
"C:\Work\RawData\Test\fem\A1001_cat12_2020-11_1728\surf\lh.aparc_a2009s.txt" "C:\Work\RawData\Test\fem\A1001_cat12_2020-11_1728\surf\lh.aparc_a2009s.CAT12_1001_2020-11.txt"

Note that there were issues on Linux as well: not compatible with FreeSurfer's read_annotation.m. (I haven't checked if this was working with r1732).

I rather use the surf folder for the annot files because this is necessary to display these files with the surf display tool in CAT12. It’s mandatory that texture (e.g. thickness) and annotation files are in the same folder for the surface files (which are necessary for displaying).

But then the output is not compatible with freesurfer processing tools. Other people using CAT outputs for other purposes than displaying them in CAT would have to move the files back to the label folder (they are actually labels and not surfaces). I also noticed that you switched from the .annot to a .txt format.

Could you make these two changes optional?
=> Additional input parameters to cat_surf_map_atlas to select between the FreeSurfer-style (label/.annot) and the CAT-style (surf/.txt) (one single option for both or two separate options in )

ChristianGaser commented 3 years ago

Sorry for the mess. The new r1733 should hopefully run.

The new settings look fine. These line scan be deleted because the ROI structure is set to not saving any ROI atlases: matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0; % No volume atlases matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 0; matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 0; matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 0;

ftadel commented 3 years ago

Everything seems to be working both on Windows and Linux with r1733! Only 45min for the segmentation+interpolation of the FsAverage atlases, this is unbeatable! :-)

I pushed the last modifications to the CAT12 wrapper + importer, it's all online: https://github.com/brainstorm-tools/brainstorm3/commit/6de6b3d8d9e219d5e4bbd47f2fb029821781dc4d

Thank you very much for your help.

ftadel commented 3 years ago

PS: I also changed the import code so that it looks for .annot file anywhere with the CAT segmentation folder, so it doesn't matter anymore if the .annot are in /surf or /label.