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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu>
Sent: Wednesday, April 10, 2024 10:01 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all stuck at topology fix

 

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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.edu> wrote:



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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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