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Dear Doug, The "template_coreg.mgz" image is also upside-down and rotated 90 degrees (X). Can you suggest how I might troubleshoot the initial registration?
I can send a logfile if it helps (not sure if I attach the textfile it will pass through your email filter)
I saw a section in "Samseg.py" concerning SAMSEG_LEGACY_REGISTRATION but I'm not sure if this is relevant. Sincerely,Randolph Andrews
# ======================================================================================= # # Preprocessing (reading and masking of data) # # =======================================================================================
# Read the image data from disk and crop
# Historically, the template was resaved with a transformed header and the image-to-image transform # was later extracted by comparing the input image and coregistered template transforms, but shear # cannot be saved through an ITK image, so a better method is to pass the image-to-image transform matrix # directly to samseg. If the SAMSEG_LEGACY_REGISTRATION env var is set, this old method is enabled if os.environ.get('SAMSEG_LEGACY_REGISTRATION') is not None: print('INFO: using legacy (broken) registration option') transformedTemplateFileName = os.path.join(self.savePath, 'template_coregistered_legacy.nii') self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImagesLegacy(self.imageFileNames, transformedTemplateFileName) else: self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( self.imageFileNames, os.path.join(self.atlasDir, 'template.nii'), self.imageToImageTransformMatrix )
-----Original Message----- From: Douglas N. Greve dgreve@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Sun, Oct 3, 2021 8:04 am Subject: Re: [Freesurfer] SAMSEG output orientation not the same as input images
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:
External Email - Use Caution 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://secure-web.cisco.com/1Zv7rNvEI4Kb-jCRvS8kJ-QkU8CZDN12WgnjTqh1UpLRFfR...
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