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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 FreesurferChris Filo Gorgolewski Tue, 09 Oct 2012 01:03:57 -0700https://http://secure-web.cisco.com/1bJm-kJVNOrTUaWjoqVk32d_m43kHXTpDrk8lcY-0m9IZL70ouR0Amj-rARrWUqpHqs37bd05gpqsZ5ysfX2IwhyEvB-jtySLbpgfVIwI9odls_4K82Kvhw3QUndLV0gJI7R_qOETwN5R8IsMiDFIovreM-3E6uNLDr9ua3ZEczUFu9zQt9L__yWHK3owmBE4NgW7-Jnn33sNGKV7QlzDb88gcre-4JwPKkrKdRylwImRU0aoDyCaRRFgoCRV_0jNFU_SZCrwzKcpPOyFWMzFRA/http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg24896.html
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