Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay
files are already in full fsaverage space with ~164k vertices.
I also thought that mri_convert doesn’t take .gii as output, but the command
that Tim suggested below does indeed seem to work.
Thanks,
Yuta
On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Glasser, Matthew" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
glass...@wustl.edu> wrote:
External Email - Use Caution
Is GIFTI a legal output type for mri_convert? I though it only could be
outputted by mris_convert (which does appear to allow .mgh and .gii).
Matt.
On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Tim Schäfer" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ts...@rcmd.org> wrote:
* External Email - Caution *
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" <glass...@wustl.edu>
wrote:
>
>
> External Email - Use Caution
>
> The 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-boun...@nmr.mgh.harvard.edu> on behalf of "Katsumi,
Yuta" <ykats...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Glasser,
Matthew" <glass...@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 Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Katsumi,
Yuta" <ykats...@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#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
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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please immediately notify the sender via telephone or return mail.
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