Dear FreeSurfer community,

I'm using the mri_label2vol, the output is in .mgz. I then use mri_convert to convert it to .nii.gz.
When I do so, the output is corrupted (see attached images). Some colleagues told me that it was because my FreeSurfer had a bug so I uninstalled and installed it back again but nothing changed. I then tried to run it on some other colleague's machine and it worked fine (on one subject just to test).

Any ideas what could be the problem ? I tried to flip the image 90 degrees but it won't flip, nothing changes.

Here are the commands I'm launching :

mri_label2vol --seg ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz

mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz


The data looks fine when I open it with tkmedit but it's inverted and cut when opened with fslview.

I cannot continue my analyses even if the data looks fine on tkmedit. When I apply a flirt transformation on the data I get the same cut and inverted brain than on fslview (see flirt attached image).

Is it a problem with my FreeSurfer or a command I'm running the wrong way ? Is there another software to convert .mgz to .nii.gz ?


Thank you very much !


Jimmy