External Email - Use Caution
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 CautionTo 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.