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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I guess what I’m concerned about is the high values of tkregister-sess even though the registration looks normal. I have checked tkregister values in other subjects with the same slab of functional data, and their values are within the normal range (~0.2-0.3), but for this subject the values of each run is about 0.95.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

Thanks for your time

On Jun 28, 2019, at 3:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto: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?

<pastedImage.png><pastedImage.png><pastedImage.png><pastedImage.png>

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Friday, June 28, 2019 10:09:22 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

<pastedImage.png><pastedImage.png> <pastedImage.png><pastedImage.png>

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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