Do the raw images look like that too?

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.commailto:matt@grecsek.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

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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.

------------------------------------------------ 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