Yes, if you want to run it now, use samseg --i orig.mgz --i T2.mgz --o samsegdir And don't use the T1.mgz I have fixed this bug in the version that we will release. I mostly wanted to make sure that samseg itself would run.
On 2/25/2020 3:08 PM, Antonin Skoch wrote:
External Email - Use Caution
Dear experts,
I began to test beta v7 version of FreeSurfer.
I noticed that some entries in recon-all-status.log seem missing (i.e. white and pial surface placement - there is entry Cortical Parc while following entry is Refine Pial Surfs).
Running samseg` --t1w $s/mri/T1.mgz --t2w $s/mri/T2.mgz --s $s --refmode t1w exits with error in samseg2recon since command
set segvol = `find "$samsegdir" -iname "*crispSegmentation.nii" -print`
results with empty string set to segvol variable.
Antonin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer