On Jun 28, 2019, at 3:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
I'm not sure I follow. From what I can see the registrations look ok. It looks like you only have a small slab of brain in the fMRI. What am I missing?
On 6/28/2019 10:41 AM, Nasiriavanaki, Zahra wrote:
Thank you so much for your reply.I attached new images.I scrolled through the brain and the worst registration is the last image attached.I'm wondering what else could cause high values of tkregister-sess?
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Zahra (Mona) NasiriavanakiPostdoctoral Research FellowMartinos Center for Biomedical ImagingMassachusetts General Hospital149 13th Street, 149-2615Charlestown, MA, USA, 02129
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, June 28, 2019 10:09:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mis-registartion questionIt is hard to tell from those images, but the registration does not look that bad. It would be more informative to have images that are not on the midline.
On 6/27/2019 4:09 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I checked the functional to anatomical data registration using tkregister-sess -s $subj -fsd bold -per-run -bbr-sum. (The functional data is only collected from parietal and occipital lobes in 7T scanner).The values obtained from tkregister-sess are too high (0.95) for 7 out of 8 runs.When I looked at the snapshots obtained from QA_tools, they looked ok (top row images). But, when I looked at the volumes of the individual runs using tkregister2 command, the registration doesn't look good (bottom row images).tkregister2 --s $subj --mov /$subj/bold/011/template.nii.gz --surf --reg new.dat --regheader .
I'm wondering if I need to do manual edits, and I appreciate any advice on that.
ThanksMona
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<pastedImage.png><pastedImage.png>
Zahra (Mona) NasiriavanakiPostdoctoral Research FellowMartinos Center for Biomedical ImagingMassachusetts General Hospital149 13th Street, 149-2615Charlestown, MA, USA, 02129
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