mri_surf2surf will do it, but you are probably better off going directly to fsaverage rather than downsampling and upsampling
cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tim Schäfer Sent: Friday, June 19, 2020 9:00 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
External Email - Use Caution
I can't telt you how to get your data from 16k fsaverage to the full 162k fsaverage mesh, but once you have the full fsaverage version, to convert to gifti, just do:
mri_convert yourfile.mgh yourfile.func.gii
Best,
Tim
On June 19, 2020 at 1:10 PM "Glasser, Matthew" glasserm@wustl.edu wrote:
External Email - Use CautionThe appropriate GIFTI extension for that would be .func.gii. What fsaverage# space is that? Hopefully FreeSurfer provides a tool to convert that to GIFTI in full resolution fsaverage space and from there we can help you get it to CIFTI in fs_LR.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 10:43 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
Hi Matt,
For instance, I have a statistical map (e.g., showing magnitude of functional connectivity at each vertex) that has been computed in 16k fsaverage space that I want to display on a fs_LR surface. I was wondering if there’s a way to convert this file (which is in .mgh extension now) to .dscalar so it’d be CIFTI/wb compatible.
Thanks, Yuta
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Glasser, Matthew" glasserm@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 10:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
External Email - Use CautionWhat kind of data does one display in an “OVERLAY” file?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Katsumi, Yuta" YKATSUMI@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 18, 2020 at 5:43 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
Dear FreeSurfer community,
I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA...) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task.
Thanks, Yuta
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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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