Can you compare the template_coreg.mgz to the input image; they should be mostly aligned. If not, then the initial registration failed.
On 9/28/2021 2:38 PM, daedalus39@aol.com wrote:
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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.
Any solution or insight would be greatly appreciated
Sincerely, Randolph Andrews
(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
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