Re: [Freesurfer] -normalization2 does not run mri_mask

Dear Freesurfer team,

is mri_mask actually a part of normalization2 as stated here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02175.html?

while trying to run freesurfer stepwise, the normalization2 step "recon-all -subjid subject -normalization2" is not executing "mri_mask" when it is called separately (while running "recon-all -subjid subject -all" executes indeed mri_mask). This is preventing "recon-all -subjid subject -finalsurfs" later from running successfully. Do you have any suggestion/idea/workaround how to solve/fix this? is there something like "recon-all -s subject -mri_mask" or shall I run mri_mask directly from the command line?

Thanking you in advance for your reply Yassene