External Email - Use Caution
Ok, thank you!
I'll try in this way and let you know if it works.
Best,
Valentina
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Tim Schäfer ts+ml@rcmd.org Inviato: venerdì 14 febbraio 2020 13:15:29 A: Freesurfer support list Oggetto: Re: [Freesurfer] Desikan and Killiany atlas
External Email - Use Caution
I think one way to do this would be to split the atlas into a set of label files using `mri_annotation2label`. I would do it for the fsaverage subject. This will give you one label file per atlas region. Something like this:
cd /path/to/freesurfer/subjects/ mri_annotation2label --subject fsaverage --hemi lh --outdir fsaverage/label/aparc_labels --annotation aparc # repeat for rh
Then you could first load the fsaverage surfaces (e.g., lh.white and rh.white) into freeview, and then add only the labels of the regions you want to show.
Maybe someone else knows an easier way?
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 February 14, 2020 at 12:29 PM Valentina Mancini Valentina.Mancini@unige.ch wrote:
External Email - Use CautionHi Tim,
yes, exactly something like subfigure B but if possible without the colorcode (i.e. some regions yellow and some others in red) having just one value.
This is because it would not be super correct to use a "summary measure" that doesn't take into account the time and the different frequency bands.
Thank you very much for your help.
Best,
Valentina
Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Tim Schäfer ts+ml@rcmd.org Inviato: venerdì 14 febbraio 2020 12:10:32 A: Freesurfer support list Oggetto: Re: [Freesurfer] Desikan and Killiany atlas
External Email - Use CautionHi Valentina,
Just to be sure I get what you are asking: do you want a visualization like subfigure B in this image?
https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis...
[https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis...]
So you have one value per Desikan atlas region that you want to show?
Best,
Tim
On February 14, 2020 at 11:49 AM Valentina Mancini Valentina.Mancini@unige.ch wrote:
External Email - Use CautionDear Freesurfer experts,
we used the Desikan and Killiany atlas to build individual head models in order to project surface EEG data in the inverse space.
We would like to plot on the cortical surface the regions of the D&K atlas where we find a different functional activation.
As I understand, there is a way to plot statistically significant results with tksurfer, but in our case we cannot show our statistical values because we should take into account also epochs and frequency and we can do that only with a time-frequency plot.
Is there a simple way to get a figure of the cortical surface with a set of predetermined regions of the D&K atlas highlighted only for visualization purpose?
Best regards,
Valentina Mancini _______________________________________________ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer