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I’m more familiar with volume than surface based methods so I cannot answer your below question, but I would highly recommend that you check out CAT12 by Christian Gaser and folks. The viewer included with that toolbox (called directly via “cat_surf_display” or also accessible by the GUI) provides extremely nice rendering of images with some additional tweaks, like the ability to inflate surfaces, etc. SurfIce by Chris Rorden is a standalone that also works very nicely for visualization. Of course, SPM does a great job rendering as well, as Guillame has suggested.
Peter
From: SPM (Statistical Parametric Mapping) <[log in to unmask]> On Behalf Of YAN Chao-Gan
Sent: Friday, November 16, 2018 7:17 PM
To: [log in to unmask]
Subject: [External] Re: [SPM] unsure why SPM12 unable to load GIFTI files during 1st-level Analysis
Dear Guillaume,
Thank you very much for your response and introducing the nice tool of MRIcroS.
I have a further question regarding to how to put data back to GIfTI cdata.
1. Just directly put back, there would be a problem.
gl = gifti('sub-Sub001_task-rest_space-fsaverage5_hemi-L.func.gii');
Data=gl.cdata;
gl.cdata=Data;
Error using gifti/subsasgn (line 130)
Syntax not implemented.
2. Use a for loop
gl = gifti('sub-Sub001_task-rest_space-fsaverage5_hemi-L.func.gii');
Data=gl.cdata;for i=1:size(Data,2)
gl.cdata(:,i)=Data(:,i);
endIndex in position 2 exceeds array bounds (must not exceed 1).
Error in gifti/subsasgn (line 115)
this.data{idx(k)}.data =
single(builtin('subsasgn',this.data{idx(k)}.data,s,A(:,k)));This error occurred when i=58.
Do you have any hints?
Thanks,
Chao-Gan
On Fri, Nov 16, 2018 at 6:21 PM Flandin, Guillaume <[log in to unmask]> wrote:
Dear Chao-Gan,
Use spm_mesh_render instead:
spm_mesh_render('Left1.gii')
otherwise, with gifti/plot, you need to do this:
plot(gifti('lh.white.gii'),gifti('Left1.gii'));
I will update gifti/plot to match spm_mesh_render's behaviour but have a
look at the contextual menu with spm_mesh_render as it gives you a lot
more functionalities.
Concerning a MATLAB-based viewer for GIfTI files, there is MRIcroS from
the prolific Chris Rorden:
https://www.nitrc.org/projects/mricros/
otherwise if there is a viewer you like but does not support GIfTI, we
should be able to find a way to export the data in a suitable format.
Best regards,
Guillaume.
On 16/11/2018 03:52, YAN Chao-Gan wrote:
> Hi Rouhi and Guillaume,
>
> Thank you very much for your response!
>
> When I saved the gifti file as demonstrated by Guillaume, I can not plot
> it. Please see below for my codes and the error message, could you
> please give me some hints?
> gl = gifti('sub-Sub001_task-rest_space-fsaverage5_hemi-L.func.gii');
> ggl = gifti(gl.cdata(:,1));
> ggl.private.metadata = struct('name','SurfaceID','value','lh.white.gii');
> save(ggl,'Left1.gii','ExternalFileBinary');
> Left1=gifti('Left1.gii');
> plot(Left1)
> Error using gifti/subsref (line 24)
> Reference to non-existent field 'vertices'.
>
> Error in gifti/plot (line 48)
> 'vertices', subsref(this,struct('type','.','subs','vertices')),...
>
> BTW, do you know if there is any nice matlab-based Viewer for gifti
> files? (I know I can view them in freeview, but trying to find a
> matlab-based one).
>
> Thanks,
>
> Chao-Gan
>
>
>
>
>
> On Sat, Nov 10, 2018 at 7:53 AM Rouhollah Abdollahi <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Chao-Gan,
>
> Freesurfer does not make the mid thickness surfaces. However you can
> do it yourself by loading the pial and white surfaces in Matlab and
> average them to make the mid thickness surface. Also I have to
> mention for the point of visualization the fsavrage surface is
> pretty good and you don’t need the mid surface one.
>
> Hope it helps
>
> Best
> Rouhi
>
> On Sat 10. Nov 2018 at 00:17, YAN Chao-Gan <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Guillaume,
>
> Thank you very much for your response!
>
> Yes, this comes from fmriprep. Indeed there is a
> sub-001_hemi-L_midthickness.surf.gii for each subject, however,
> there is no midthickness file under the fsaverage5 in freesurfer.
>
> I am also ccing Chris to see if he has any suggestions. Hi
> Chris, any insights?
>
> Thanks,
>
> Chao-Gan
>
> On Fri, Nov 9, 2018 at 6:41 PM Flandin, Guillaume
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> 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]>
> > <mailto:[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
> <https://maps.google.com/?q=12+Queen+Square+%0D%0A+%C2%A0+%C2%A0+%C2%A0London+WC1N+3BG&entry=gmail&source=g>
> <https://maps.google.com/?q=12+Queen+Square+%0D%0A+%C2%A0+%C2%A0+%C2%A0London+WC1N+3BG&entry=gmail&source=g>>
> London WC1N 3BG
> <https://maps.google.com/?q=12+Queen+Square+%0D%0A+%C2%A0+%C2%A0+%C2%A0London+WC1N+3BG&entry=gmail&source=g>
> >
> >
> >
> > --
> > 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
> <https://maps.google.com/?q=16+Lincui+Road,+Chaoyang+District,+Beijing+100101,+China&entry=gmail&source=g>
> > -
> > 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/>)
> > 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
>
>
>
> --
> 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
> <https://maps.google.com/?q=16+Lincui+Road,+Chaoyang+District,+Beijing+100101,+China&entry=gmail&source=g>
> -
> 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
>
> --
> Sent from Gmail Mobile
>
>
>
> --
> 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
--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-
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