Hi Marena - If the registration between the diffusion and T1 images is reasonable, this should work. You should bypass any pathways that lie mostly in the truncated part of the diffusion scans.

Best,
Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marena Manierka <marena.manierka@gmail.com>
Sent: Wednesday, June 2, 2021 12:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula registration failure
 

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Hello Anastasia,

Not sure if you've had a chance to look at my previous message. I've manually gone through the registrations of all the subjects in my dataset now in Freeview. Although the anatomical scans appear to be complete, the dtifit images show significant clipping of the temporal lobes in almost every individual (even those scans where tracula prep, bedp and path steps worked without casting an error). Is it still possible for me to run tracula on this dataset? Should I be re-processing all subjects with the config file set up to exclude the ILF tracts, or can I pull the data and simply exclude those tracts running through temporal lobes in my final analysis?

Any advice would be greatly appreciated. I'm new to this type of analysis and no one in my lab has published using TRACULA previously.

Thanks very much,
Marena

On Wed, May 26, 2021 at 1:47 PM Marena Manierka <marena.manierka@gmail.com> wrote:
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
 

        External Email - Use Caution        

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, B.Sc
Graduate Student, Integrative Program in Neuroscience
Department of Psychology, MSS 414/ MS0296
University of Nevada, Reno