Great, thanks so much again for your input, Matt/Tim/Bruce.
Yuta
On 6/19/20, 1:37 PM, "Glasser, Matthew" <glass...@wustl.edu> wrote:
External Email - Use Caution
After you convert to GIFTI at fsaverage 164k, you can use these
instructions to get to fs_LR:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiyj9jetI7qAhWNVs0KHR5gCtEQFjABegQIBBAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
Matt.
On 6/19/20, 10:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Fischl, Bruce" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
bfis...@mgh.harvard.edu> wrote:
* External Email - Caution *
In general almost all of our binaries will read or write almost all
formats we support. There are some exceptions to this, but it is generally true
Cheers
Bruce
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the
HCP format
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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