Hi Kirstie,

Nibabel has a write_annot function that should work: http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot

Best,

Michael

On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker <kw401@cam.ac.uk> wrote:

Thank you Michael! I <3 Pysurfer.

(and freesurfer of course!)

The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet which can show the network nicely on top of freesurfer files.

Here's the wiki for my pysurfer wrapper: https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer

And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py

Unfortunately I don't use BrainNet so I'm having difficulty helping my lab mate make his pretty plots of network nodes and edges overlayed on top of surface colors (eg: modular partition)!

Is there a way of writing out an annot file from pysurfer into freesurfer format? Maybe that would bring the two packages closer together....

Kx

On 29 March 2016 at 16:29, Michael Waskom <mwaskom@stanford.edu> wrote:

Hi Kirstie,

Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html

Hope that helps,

Michael

On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwakeman@gmail.com> wrote:

Hi Kirstie,

You could write your own CLUT file with the color corresponding to the
correlation you want to show?
Just open up the file and play with the values in the color columns.
Then simply load the color table in Freeview and use it to visualize
the annotation.

There are of course other ways, but this is probably the quickest.

hth
d

On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw401@cam.ac.uk> wrote:
> Hi,
>
> I'd like to show correlation coefficients by region on the brain surface. So
> for example, if I've calculated a modular decomposition in a network
> analysis for each region of the D-K atlas I'd like to be able to color each
> atlas region according to the module it has been assigned to.
>
> It seems like I have to do something with the ?h.aparc.annot files and a
> colour lookup table but I'm not sure exactly what.
>
> Thank you!
> Kx
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> Mailing Address
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> Phone: +44 7583 535 307
> Website: www.kirstiewhitaker.com
>

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--

Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com

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The information in this e-mail is intended only for the person to whom it is
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The information in this e-mail is intended only for the person to whom it is
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