Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of an FA map that looked truncated, with slices missing from the bottom of the brain (which explains why the error happened for the ILF, which would go through that missing part of the brain). Does dmri/dwi.nii.gz look like that?


Best,

a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.com>
Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
 

        External Email - Use Caution        

If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T. 


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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700


Do the raw images look like that too?

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek <m...@grecsek.com<mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
        External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked 
off the process with -s and -i flags.

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y