[Neuroimaging] [PySurfer][Nibabel] Write annot from roi display

Kirstie Whitaker kw401 at cam.ac.uk
Thu Apr 14 17:57:07 EDT 2016

Hi Pysurfer and Nibabel teams,

I have some code that is heavily stolen from the Display ROI values
<https://pysurfer.github.io/examples/plot_parc_values.html> pysurfer

I'd like to be able to overlay the same ROI information in BrainNet
<https://www.nitrc.org/projects/bnv/> (as they allow plotting a network on
top of a freesurfer image and because my colleague already uses it!) and so
I tried to use the write_annot
command in nibabel.

The command was (at the end of the example linked above)

nib.freesurfer.io.write_annot('output.annot', vtx_data, ctab, names)

Unfortunately this file does not load up in freeview. I have a feeling
that's because I'm passing the wrong information to the write_annot command.

Any suggestions on what to do?

Thank you!

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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