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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 <dgr...@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, daedalu...@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
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