External Email - Use Caution
Hi Bruce,
I am reaching out to you, as I am trying to load the surface scalar values of diffusion embedding for overlay on a pial surface in Freeview.
I used save_mgh to save a scalar matrix containing surface embedding values in an .mgz format. However I can't load it in freeview, be either only half of the matrix data (one hemisphere I assume) or the whole matrix saved in the same file.
Is there anything specific I need to do in order to be able to visualize a scalar overlay on a surface? Is .mgz a wrong format for scalar values? I also tried with .nii.gz, or .mgh. I am not even sure save_mgh can do all this...
Thanks in advance,
Sincerely,
Loïc
Le lun. 27 mai 2019 à 11:54, Loïc Daumail loic.daumail@gmail.com a écrit :
Hi Tim,
Your link works perfectly, it's awesome! Thanks a lot,
Best,
Loïc
Le lun. 27 mai 2019 à 11:43, Loïc Daumail loic.daumail@gmail.com a écrit :
Hi Tim,
'mean_rest' is a diffusion embedding map, which contains scores for every vertex on fsaverage5 surface resolution. 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also tried forjust lh hemisphere, but it gives me the same result...
Thanks for the link!
Best,
Loïc
Le lun. 27 mai 2019 à 11:20, Tim Schäfer ts+ml@rcmd.org a écrit :
External Email - Use CautionHi Loïc,
that does not look correct, the data is definitely off. I'm not sure where the variables `mean_rest` and `surf.b` come from in your code, and I suspect that something is wrong with them.
In the meantime, I got interested in this myself and put together some code that will load the Desikan data for both hemispheres and display it in surfstat. Feel free to use it, there also is an example screenshot of the results:
https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On May 27, 2019 at 11:01 AM Loïc Daumail loic.daumail@gmail.com
wrote:
External Email - Use CautionHi Tim,
Thanks a lot for your help, indeed, this is exactly what I needed! I wrote this : " subjects_dir = '/home/loic/Documents/recon_all_success/freesurfer/'; subject_id = 'sub-004'; hemi = 'lh';
aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', sprintf("%s.aparc.annot", hemi)); [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); fprintf("Read aparc parcellation file '%s' containing %d regions.\n", aparc_file_this_hemi, length(colortable.struct_names)); for sidx = 1:length(colortable.struct_names) region = colortable.struct_names{sidx}; struct_code = colortable.table(sidx, 5); vertices_of_struct_roi = find(label == struct_code); fprintf("Found region '%s' with %d verts.\n", region, length(vertices_of_struct_roi)); end fig1 = figure(); SurfStatView(mean_rest, surf.b); SurfStatColormap(colortable.table(:,1:3)/255); " However, the image I obtain seems a bit fuzzy...( see attached) Is it because of my data?
Thanks in advance,
Loïc
Le jeu. 23 mai 2019 à 17:20, Tim Schäfer ts+ml@rcmd.org a écrit :
External Email - Use CautionAfaik SurfStat is not maintained anymore and I think it's been this
way
for quite a while now. Maybe someone else knows better?
The website is at http://www.math.mcgill.ca/keith/surfstat/ and it
says
'Updated 26 September 2008'. I'm not sure whether that's really
true, but
at least for the last 14 months (the only time frame I know about),
there
have not been any changes to that website or any new releases of
SurfStat.
Tim
On May 23, 2019 at 4:36 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote:
Hi Loic
sorry, can you ask whoever maintains surfstat? Or maybe someone
else on
the
list knows? I don't. You can label surfaces manually with the dev
version
of freeview if you want.
cheers Bruce
On Thu, 23 May 2019, Loïc Daumail wrote:
> > External Email - Use Caution > > Hi Bruce, > > I am coming back to this request as I was wondering: > would it be possible to load freesurfer surface atlases in
surfstat in
order to label my surfaces?
> Is their format compatible? I saw surfstat only accepts a limited
array of formats...
> > Thanks, > Best, > > Loïc > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
a écrit :
> sure. All the fsaverages are in the same space (they are
subsets
of
> fsaverage) > On Mon, 20 May 2019, Loïc Daumail wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > Thanks for your response. Is it also fine for fsaverage5
surface or I need to switch
> my data to > > fsaverage? > > > > Thanks, > > > > Sincerely, > > > > Loïc > > > > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> a écrit :
> > Hi Loic > > > > if you are on the fsaverage surface you can save
the
-log10(p) values
> > using save_mgh.m, then load them in freeview and
threshold them or
> > whatever > > > > cheers > > Bruce > > On Mon, 20 May 2019, Loïc Daumail wrote: > > > > > > > > External Email - Use Caution > > > > > > Also, one more thing: > > > > > > My data is on fsaverage5 resolution. > > > > > > Thanks in advance, > > > > > > Sincerely, > > > > > > Loïc > > > > > > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <
loic.daumail@gmail.com> a écrit :
> > > Dear Freesurfer community, > > > > > > I obtained score matrices of surfaces after
performing
diffusion embedding map
> on fMRI > > data. > > > > > > I am now using the SurfStat toolbox(Matlab) in
order
to obtain p-value maps to
> compare > > between > > > two groups. > > > > > > After obtaining the p-value map, I would like to
label
the surface in order to
> > identify the > > > regions of significant difference between both
groups.
> > > > > > Would it be possible to use Freview in order to
do it?
> > > If so, which format should I use for my SurfStatP
output p-value map?
> > > How would you do it, (tools to convert into a
specific
format, surfaces and
> atlas to > > load on > > > Freeview, which format for those ones)? > > > I would be very grateful if you could detail a
bit, as
I am new to these
> tools! > > > > > > Thanks in advance, > > > > > > Loïc Daumail > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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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