Hi FS gurus,
For whatever reason, BET worked better on my structural image than mri_watershed, so I used a BET image with recon-all -autorecon1 -noskullstrip. Here is a summary of the codes that I used:
bet structural.nii structural_brain.nii.gz recon-all -i structural.nii -s {subjid} recon-all -autorecon1 -noskullstrip -s {subjid} mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid {subjid}
Stage 1 ran without errors. Stage 2 ran with errors, but when I checked the log (see attached), and the only message that resembled error to me was the following: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH
Is there something I did wrong? Thanks.
Best, Richard