Hi Tapsya, try adding "-no-subcort-mask" to your mkanalysis-sess command line. doug

tapsya@nmr.mgh.harvard.edu wrote:

Hi Doug,

http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes states that "FSFAST

• now masks the volume-based analysis to include only subcortical areas"

and indeed, it looks like our group level volume results are in subcortical space only.

We always use volume (native space full brain) analysis especially for sanity checks. At the group level, looking at analysis results in full volume (default brain mask) is essential for quality control and getting a feel of what is going on with the data.

Is there a way to set up the volume analysis so that it is run for the whole brain (brain mask) at group level?

Thank you!

Best regards,

Tapsya

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer