mis-registration question

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Nasiriavanaki, Zahra

2 Aug 2019 2 Aug '19

12:17 p.m.

Dear Freesurfers

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

[cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30]

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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Nasiriavanaki, Zahra

5 Aug 5 Aug

12:52 p.m.

Hi experts

I appreciate if you could help me with this question.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

________________________________ From: Nasiriavanaki, Zahra Sent: Friday, August 2, 2019 12:17:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: mis-registration question

Dear Freesurfers

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

[cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30]

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

Greve, Douglas N.,Ph.D.

1:01 p.m.

what is your registration command?

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

Dear Freesurfers

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

[cid:part1.4F74A672.38AE9526@mgh.harvard.edu][cid:part2.AC5CF7F1.14B22350@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

Nasiriavanaki, Zahra

1:33 p.m.

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

________________________________ 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

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

[cid:part1.4F74A672.38AE9526@mgh.harvard.edu][cid:part2.AC5CF7F1.14B22350@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

Greve, Douglas N.,Ph.D.

1:53 p.m.

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

On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:

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

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu Sent: Monday, August 5, 2019 1:01:07 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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

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

[cid:part1.1D7D76D6.30EA461F@mgh.harvard.edu][cid:part2.3980DB9D.DA94E372@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

Nasiriavanaki, Zahra

3 Jan 3 Jan

10:53 a.m.

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

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: 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

On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:

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

what is your registration command?

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

Dear Freesurfers

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

[cid:part1.1D7D76D6.30EA461F@mgh.harvard.edu][cid:part2.3980DB9D.DA94E372@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

Greve, Douglas N.,Ph.D.

11:49 a.m.

Can you send me your project folder and SUBJECTS_DIR?

On 1/3/2020 9:53 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts

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

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu Sent: Monday, August 5, 2019 1:53 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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

On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:

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

what is your registration command?

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

Dear Freesurfers

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

[cid:part6.45E23002.93B55966@mgh.harvard.edu][cid:part7.3AAE7C5F.2E8AFB2D@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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Greve, Douglas N.,Ph.D.
Nasiriavanaki, Zahra