I am using mris_fill to create a volume from the lh.pial surface as well as the rh.pial surface. I have 2 questions:
1. How can I combine the 2 separate hemisphere volumes into a single full brain volume that I can export and view in analyze? I only know to use mri_convert on each one separately. Does this need to be done before I run mris_fill, or is there another combined surface that has the same resolution as the pial surfaces that I can run mris_fill on? 2. I know that when I run mris_fill, the volumes that are produced do not contain orientation information. When I load them into Analyze, the volume is mirrored and upside down. I was wondering how I can "get" orientation information back into the volume, and also correct the mirrored and upside down viewing issue.
These results were produced by Freesurfer from standard dicom files from a volumetric scan.
Thanks,
Cochrane Jamison