External Email - Use Caution
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 CautionHi 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 aresubsets
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 fsaverage5surface 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 andthreshold 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 afterperforming
diffusion embedding map
on fMRI > data. > > > > I am now using the SurfStat toolbox(Matlab) inorder
to obtain p-value maps to
compare > between > > two groups. > > > > After obtaining the p-value map, I would like tolabel
the surface in order to
> identify the > > regions of significant difference between bothgroups.
> > > > Would it be possible to use Freview in order todo it?
> > If so, which format should I use for my SurfStatPoutput p-value map?
> > How would you do it, (tools to convert into aspecific
format, surfaces and
atlas to > load on > > Freeview, which format for those ones)? > > I would be very grateful if you could detail abit, 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.eduhttps://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
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