Hi Salil
This looks like a T2-weighted volume. Recon-all by default assumes T1 weighting. Do you have a T1 you can use (like an MPRAGE or FLASH scan)?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bhole, Salil Sent: Thursday, April 11, 2024 12:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all stuck at topology fix
External Email - Use Caution Here are some images from the patient. I also have the recon-all log posted here is well. This is the same patient but taken from a file where I tried to manually skull strip to fix the issue, however, the same issue persisted. Thank you for your help!
Best, Salil ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Wednesday, April 10, 2024 10:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all stuck at topology fix
* External Email - Caution * 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 <bhole@wustl.edumailto:bhole@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.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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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