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 <ayend...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Marena Manierka < > marena.manie...@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 > marena.manie...@gmail.com > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1L-taqivMUIl3IiB7e9YGkgZWz0wlz6JQc4w6sGBCgpI5Gv6NKIrN0DBU0j3hEZZao5OojLhNE4EapJKmYqRH3BeQdgv0twH4Aibi87xSz-gvapJsJZn2lR8xc55BlpLibuNQpV9OYqMqVappHJsgVdCyniqI309osLVhEq521LXg23M_ZMFj9X74iWiylaeN7WkehcXX2G3gBnO1Q4pA82TWaZo5X1EcvA3Xp6o6cFattgVNhM26xl3IVcT_N2gZDpM03CAh0igPxfBcHLrrSA/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 > http://secure-web.cisco.com/1DKhyO0-2nIU-5MafxQam-ttXxxjIcI60MzLLj9eJ1uGXPDAgEIJ32PlrKLX9cj7B95XGsqFOhEsMWETO7Lnb7lEWZAWMcvVwR8j_kgdFq4MOlNlBEGIK2hEjs6NM5RJTtCSQjO_GpRgoapfYSggzm30RwyHTeNZGM6XsGOQCGDH9TukCpo4qTj9mcyrfZzbFDtc_IohiNLiyWzgV675Y5j5CgCKRNSNoUKABaZ8rve9AsJmqtv7VqPsbhljBjPo5I6orHuaVEF9bppQXTZDtiw/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.manie...@gmail.com
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