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?
[cid:f6b0a970-f350-4604-a6cc-6d906087867c][cid:fb697ced-f05c-45a0-bee6-f36b8a82c006][cid:03f08852-7577-4b4c-91d1-d508dbb637f6][cid:54169995-eaf7-4781-b63b-4dd0177af3eb]
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, 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 question
It 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.
Thanks Mona
[cid:part1.F07CDD4A.AF97105B@mgh.harvard.edu][cid:part2.D6E3E6E4.1B7A8679@mgh.harvard.edu]
[cid:part3.070DE0A8.07061B0F@mgh.harvard.edu][cid:part4.6C462CD0.17C35CEF@mgh.harvard.edu]
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
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