On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:
Hello,
The below solutions sounded like data need to be analyzed with Freesurfer individually to get the registration file?
The anatomical must be analyzed in FS, but not the fMRI. See eg https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
I realized that the stats can be presented in Freeview with the correct locations in T1, but when it comes to inflated surface, the BOLD signals always present in a specific location regardless of dataset (please see the attached figure, looks like it’s a registration issue). I wonder if the data were already analyzed by FSL in group level, is it possible to present the analyzed group data on inflated surface in Freeview?
Yes, see web page above
Thank you again for helping,
Irene
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Wednesday, June 8, 2022 at 11:15 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Freeview GUI overlay and registration
You will need an lta file that maps from the anatomical to the fmri. You can get this with something bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta where template.nii.gz is the fmri motion correction template or the mean fmri (I forgot what it is called in FSL)
On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:
Hi Freesurfer experts, I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed in FSL) and project on the inflated surface. I used the feature “Overlay/Load generic” and was prompted to select overlay file and/or apply registration. The selected overlay file didn’t seem to project on the right spot on the inflated surface as would be seen in T1. If registration was the issue, what registration file should be selected in the Freeview GUI? My Freeview was updated. Thank you very much for helping. Irene _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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