We have recently installed FS-7.1 and have tested a few “ADNI” images with SAMSEG.  The process runs to completion, but the output (seg.mgz) appears upside-down and rotated about 90 about the X-axis.  We are passing seg.mgz through BrainStorm to create NiFTI images.  We do not believe that this is a BrainStorm issue inasmuch as the same images run through recon-all (fully separate proc) yield output images in the same orientation as the original images.  I found a thread from 2012 with a similar output orientation issue, but the I did not see a response that resolved this.

 

(PS. listserv item from 2012)

Re: [Freesurfer] integrating FSL and Freesurfer

Chris Filo Gorgolewski Tue, 09 Oct 2012 01:03:57 -0700

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24896.html