Dear Freesurfer experts

I have a follow up question about mis-registration and I appreciate if you could please reply.

I am having trouble fixing the registration for one of my subjects in highres scan.

The tkregister-sess values looked bad (around 0.8). So I checked the registration with tkregister2 and it looked off too.

I ran this command: "register-sess -s $subj -per-run -delete-dat -dof 6 -fsd bold4 -init-header -bbr-xopts bbr.xopts -d $all_subjects", with  --brute1max 20 --brute1delta 4 ! which took a long while to finish! but still the registration is off.

Could you please help me with that?

Thanks

MOna 

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: Monday, August 5, 2019 1:53 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mis-registration question

Can you send a pointer to the data so I can have a look? Include the folder were you run tkregister-sess from as well as the $SUBJECTS_DIR

Thanks for your reply.

preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold -init-header -d .

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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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: Monday, August 5, 2019 1:01:07 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mis-registration question

 

what is your registration command?

On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

Hi

I have a subject that the registration is not done correctly in two runs (run 12 and run 15) .

The tkregister-sess values for this subject is shown below. 

Subject 1 10 0.2628

Subject 1 11 0.3038

Subject 1 12 0.7639

Subject 1 13 0.3364

Subject 1 14 0.3346

Subject 1 15 0.9361

Subject 1 16 0.2584

Subject 1 17 0.2488

I attached the screen shots from tkregister2 to this email. The functional data is only collected in a slab of parietal and occipital lobe.

I appreciate if you let me know how to fix them. 

Thanks

Mona

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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