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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Monday, August 5, 2019 1:01:07 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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 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 [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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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