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Hi Anastasia,

Thank you so much for your reply. I noticed the truncated temporal lobes in the registered dti_FA.bbr, but I do not see the same problem in either the T1.mgz or the aparc+aseg.mgz when loaded into freeview. In the subject's native space diffusion weighted image (dtifit_FA.nii.gz) it does seem like a portion of the temporal lobes is cut off.

Let me know if there are other files/ screenshots I can provide to help with solving this issue.

Best,
Marena

On Wed, May 26, 2021 at 1:04 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:
Hi Marena - How does the T1 of this subject and its freesurfer segmentation (aparc+aseg) look? In the image the brain looks truncated, is that the case with the T1?

Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marena Manierka <marena.manierka@gmail.com>
Sent: Tuesday, May 25, 2021 8:47 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Tracula registration failure
 

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To the Tracula team:

I am attempting to complete my first project using the Tracula pipeline on a mixed dataset of autism, schizophrenia, and control adult brains. I ran the tracula prep, bedp and path steps for the autistic subject in question without receiving any error messages. However, when I attempt to view the registration of the FA.bbr.nii.gz image to the MNI brain the registered image appears as a completely white, roughly brain-shaped mask. This has not occurred with other subjects from the dataset. I have attached a screenshot from freeview for reference. 
When I load the subject's dtifit_FA.nii.gz in freeview it appears to be relatively normal. Is this a fatal error in the registration process, and is there any way to correct it? 
I have also attached the log file for the subject in case this is helpful.

Thank you for your help,
Marena


--
Marena Manierka, B.Sc
Graduate Student, Integrative Program in Neuroscience
Department of Psychology, MSS 414/ MS0296
University of Nevada, Reno
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--
Marena Manierka, B.Sc
Graduate Student, Integrative Program in Neuroscience
Department of Psychology, MSS 414/ MS0296
University of Nevada, Reno
marena.manierka@gmail.com