Closed Edouard2laire closed 2 months ago
@Edouard2laire, I made some basic tests and everything looks fine. Please check on your side and let me know
Looks great! thanks.
For the tutorial, we might want to copy the warning from freesurfer:
[WARNING: the script in FreeSurfer 7.4 has a small bug when computing the surface label files at the end of the script. Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE. Development versions newer than June 15th 2023 do not have this problem.]
Edit: Link to original warning in FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical
Add support to import the output folder from the FreeSurfer
recon-all-clinical.sh
pipelineRequested here: https://neuroimage.usc.edu/forums/t/47017
Description of the files in the output folder: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical
The standard transformation FreeSurfer=>Brainstorm required for results from
recon-all
is not needed for results fromrecon-all-clinical
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_mri_mgh.m#L140-L146Anatomical atlases have a different size, due to padding in
recon-all-clinical.sh
https://github.com/freesurfer/freesurfer/blob/fdd7a75ae623db77b33ee32b7c13bd161e3e4815/recon_all_clinical/recon-all-clinical.sh#L225Updated tutorial page: https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
[x] Add support in Brainstorm
[x] Document in Brainstorm pages