Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce
On Apr 10, 2024, at 7:05 PM, Bhole, Salil <bh...@wustl.edu> wrote:
External Email - Use Caution
Hello,
I have tried to process this MRI a few times now and it always seems to get
stuck on the step I have pasted below here. I have tried to fix the defect
myself by editing the voxels manually, but that has also not seemed to help.
I've looked through the MRI and there are no obvious deformities/defects. Any
help with the next steps would be much appreciated.
Best,
Salil
49 defects to be corrected
0 vertices coincident
reading input surface
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
-face loglikelihood: -8.8808 (-4.4404)
-vertex loglikelihood: -7.5174 (-3.7587)
-normal dot loglikelihood: -3.4734 (-3.4734)
-quad curv loglikelihood: -5.9156 (-2.9578)
Total Loglikelihood : -25.7872
CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)
________________________________
From: Bhole, Salil
Sent: Wednesday, April 10, 2024 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Recon-all stuck at topology fix
Hello,
I have tried to process this MRI a few times now and it always seems to get
stuck on the step I have pasted below here. I have tried to fix the defect
myself by editing the voxels manually, but that has also not seemed to help.
I've looked through the MRI and there are no obvious deformities/defects. Any
help with the next steps would be much appreciated.
Best,
Salil
49 defects to be corrected
0 vertices coincident
reading input surface
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
-face loglikelihood: -8.8808 (-4.4404)
-vertex loglikelihood: -7.5174 (-3.7587)
-normal dot loglikelihood: -3.4734 (-3.4734)
-quad curv loglikelihood: -5.9156 (-2.9578)
Total Loglikelihood : -25.7872
CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)
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