Dear Chao-Gan,
I assume that these files are obtained from fmriprep? I don't know if
things have changed in the meantime but rereading an email exchange I
had with Chris and Oscar on this topic a year ago, the surface
(geometry) meshes for fsnative (native subject specific surface) are in
../anat/sub-*_T1w_midthickness.*.surf.gii while the other surfaces (like
fsaverage5) are standard FreeSurfer surfaces and are therefore to be
found in your FreeSurfer installation (possibly in a different file format).
Best regards,
Guillaume.
On 08/11/2018 00:06, YAN Chao-Gan wrote:
> Dear Guillaume,
>
> Thank you very much for your code example. I just wonder where can I
> find 'mesh.surf.gii' in your example?
>
> For a functional image like
> "sub-001_task-rest_space-fsaverage5_hemi-R.func.gii", I think I should
> find some thing like "fsaverage5_hemi-R_midthickness.surf.gii". Do you
> happen to know where would "fsaverage5_hemi-R_midthickness.surf.gii" exist?
>
> Thank you very much!
>
> Best,
>
> Chao-Gan
>
>
> On Fri, Oct 13, 2017 at 11:04 PM Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Patrick,
>
> Then, given you're not using them for proper inference, it probably
> doesn't matter too much - it's just that the separation in two
> hemispheres is an artefact of the preprocessing pipeline (eg you would
> rarely do that with volumetric data).
>
> To combine the surface meshes, you can do something like this:
>
> M = gifti({'L.surf.gii','R.surf.gii'});
> M = spm_mesh_join(M);
> save(gifti(M),'mesh.surf.gii')
>
> and for the functional data it would be something like:
>
> gl = gifti('L.func.gii');
> gr = gifti('R.func.gii');
> for i=1:size(gr.cdata,2)
> gg = gifti([gl.cdata(:,i);gr.cdata(:,i)]);
> gg.private.metadata =
> struct('name','SurfaceID','value','mesh.surf.gii');
>
> save(gg,spm_file('mesh.func.gii','suffix',sprintf('_%05d',i)),'ExternalFileBinary');
> end
>
> As with the previous snippet, I haven't tried it so it might require
> adjustments...
>
> Best regards,
> Guillaume.
>
>
> On 13/10/17 15:39, Patrick Sadil wrote:
> > Hello Guillaume,
> > I see. We had only been planning on using these data as a
> really rough localizer, grabbing voxels that were active as
> determined by an uncorrected p-value threshold. But, it sounds like
> even that would be improved by analyzing the entire hemisphere
> together. Sorry, to keep asking questions about this, but do you
> know of a reliable way to combine these hemispheres?
> >
> > Best,
> > Patrick
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
>
>
> --
> Chao-Gan YAN, Ph.D.
> Professor, Principal Investigator
> Deputy Director, Magnetic Resonance Imaging Research Center
> Institute of Psychology, Chinese Academy of Sciences
> 16 Lincui Road, Chaoyang District, Beijing 100101, China
> -
> Initiator
> <http://rfmri.org/DPARSF>DPABI
> <http://rfmri.org/DPABI><http://rfmri.org/DPARSF>,
> <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN
> <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org>
> (RFMRI.ORG <http://rfmri.org/>)
> http://rfmri.org/yan
> http://scholar.google.com/citations?user=lJQ9B58AAAAJ
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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