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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 marena.manierka@gmail.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1L-taqivMUIl3IiB7e9YGkgZWz0wlz6JQc4w6sGBCgpI5Gv... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1DKhyO0-2nIU-5MafxQam-ttXxxjIcI60MzLLj9eJ1uGXPDA... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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.commailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marena Manierka <marena.manierka@gmail.commailto:marena.manierka@gmail.com> Sent: Tuesday, May 25, 2021 8:47 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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 marena.manierka@gmail.commailto:marena.manierka@gmail.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1LDd5MsrztbHpVGjKftRDr9ofphqfDSzmEAwMmtMuXOHkLKE3xOpRsLTvE-NeXNKjDV9eCsF8oPIkmfLrtHkInK8AInc0CadwDeemj-0zPZO-HJmACcdw3ziLTcdNtuRUXcQYZGWN7EZn6oycr2eT3Fxhrn5rJ6yepj7exlJeua71WJQg1xzMEzcgksbZBQpJpV0CL__hLJQ2UDeu5DuilvRvDDkhFCNfCX8fIj4kFJCErlXhs7jTc-I6iN717yDQbdC5W2D58eGmQhao7Bijdw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1-c7UY348j9-LDtjFFdGTs_uGqZ9ogrTO4m0sA1treUqdq5JyI-TC2JSH70vswRN_rGvoGl9XaDXI678GI0d8hjpJSoDELNODDlkQGH_D7xfv_0kKKA4Uw7XU6gBvVX4cpzKDU266ns4Q08WG2ROxise5Vu8eqMjJeA740C5jqr7H5ZYPGgNtYdJuerglGUWICTREtjAOVK6OaHUiMuDOgeUAF-q1ycXQm2ADZRvTQ4lU0wyIJPvadql9r2dsilSJAktuAog3xF58CUtGBuggXQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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

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