Error in importing subcortical region from Brainsuite reconstruction

1

Hello

I updated Brainstorm recently. After that, I am having some issues exporting subcortical regions into brainstorm. The below is the visualization I get when I select the subcortical surface after importing it in brainstorm

image
image572×536 112 KB

When I look at the scout names, I see the below numbers. Prior to the update, it used to show the names of the subcortical structures.

image

Is this a bug in the software or something I am doing wrong? Cortical surfaces are imported using the "Import from folder" option.

2

I'm not sure I understand what you are doing here...
Please describe precisely how you get to what you show, click by click, starting from the subject creation.
Include screen captures of what your database explorer looks like.

3

Hi Fracois, Thanks for the prompt response. Please find the powerpoint attached. brainstorm_issue.pptx (1.4 MB)

4

Hi Francois

I think I figured out the issue. It has to do with mri_getlabels.m code.

In line 78 onwards

if ~isempty(Labels)
    AtlasName = fBase;
% Standard atlases (FreeSurfer/ASEG, BrainSuite/SVREG)
elseif ~isempty(strfind(fBase, 'aseg')) || ~isempty(strfind(fBase, 'aparc')) % *aseg*.mgz
    AtlasName = 'freesurfer';
elseif ~isempty(strfind(fBase, '.svreg.label.'))   % *.svreg.label.nii.gz 
    AtlasName = 'svreg';
end

there is an extra trailing dot at .svreg.label

Once I remove it as follows, the subcortical atlas is loaded properly

if ~isempty(Labels)
    AtlasName = fBase;
% Standard atlases (FreeSurfer/ASEG, BrainSuite/SVREG)
elseif ~isempty(strfind(fBase, 'aseg')) || ~isempty(strfind(fBase, 'aparc')) % *aseg*.mgz
    AtlasName = 'freesurfer';
elseif ~isempty(strfind(fBase, '.svreg.label'))   % *.svreg.label.nii.gz
    AtlasName = 'svreg';
end

Please let me know if this is a correct modification

Balu

5

Hello Francois,

Is it okay to make the above modification? As of now, the code works perfectly for my requirements, but I am not sure whether there are any other dependencies that could be impacted by this modification.

Balu

6

Sorry for the response delay.

Indeed, I could reproduce the error you reported, and the solution you proposed seems perfect.
I pushed it in this commit: https://github.com/brainstorm-tools/brainstorm3/commit/fccbaec4b1054183a8c204b095717355fe0be502
(You'll get it next time you update Brainstorm)

Thank you for reporting and fixing this bug!