Error 'add scouts to atlas'

gnicolas1223 · March 18, 2021, 1:06pm

Hello,

I have an issue when I want to import a MNI scout from spm12 (.nii) in a new atlas. I selected 'Volume mask or atlas (dilated, MNI space)' and then I have this error :

Capture d’écran 2021-03-18 140306

It's the first time I have this issue, I have never had it before. The only thing that has changed is that I updated my version of brainstorm. I never had this error with the old version of brainstorm.

I try with many .nii scouts and with different subjects. I quit brainstorm and then reopen it but it's always the same error.

Thank you in advance for your help.

Francois · March 18, 2021, 3:23pm

I fixed the source of the error (update Brainstorm to get the fix):
https://github.com/brainstorm-tools/brainstorm3/commit/767ec9bdbd2636009b20f8803ee44719b731a54b

But I don't understand how you got to this point in the code.
This is a switch case for hdr/img old Analyze file format... Is the file you are reading with a .hdr or .img extension? Is so, time to update to .nii files.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_mri_nii.m#L93


        hdrFilename = bst_fullfile(filepath, [baseName '.hdr']);

        imgFilename = bst_fullfile(filepath, [baseName '.img']);

        if ~file_exist(hdrFilename), disp(sprintf('in_mri_nii : Missing header file (%s)', hdrFilename)); return; end

        if ~file_exist(imgFilename), disp(sprintf('in_mri_nii : Missing image file (%s)', imgFilename)); return; end

        % Read header file

        [fid, byteOrder] = nifti_open_hdr(hdrFilename);

        if fid==-1, disp(sprintf('in_mri_nii : Error opening header file')); return; end

        hdr = nifti_read_hdr(fid, isReadMulti);

        if isempty(hdr), disp(sprintf('in_mri_nii : Error reading header file')); return; end

        fclose(fid);

        % Read image file

        [fid, message] = fopen(imgFilename, 'r', byteOrder);

        if fid == -1, disp(sprintf('in_mri_nii : %s', message)); return; end

        data = nifti_read_img(fid, hdr, 0);

        fclose(fid);

        

    otherwise

        error('Unsupported file format');

end



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