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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:

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Hi 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

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Hi 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...

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:

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Dear 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

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If you happen to use R, you can have a look at the last example in this file:

https://github.com/dfsp-spirit/fsbrain/blob/master/tests/testthat/test-vis.R

Running it will give you the attached output image, which is maybe quite close to what you want.

Tim

On February 14, 2020 at 1:44 PM Valentina Mancini Valentina.Mancini@unige.ch wrote:

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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 Caution

Hi 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 Caution

Hi 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 Caution

Dear 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer