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

[Michael Waskom]

Hi Kirstie,

What do the vtx_data, ctab, and names that you are passing look like?

Best,
Michael

On Thu, Apr 14, 2016 at 2:57 PM, Kirstie Whitaker <kw401 at cam.ac.uk> wrote:

> 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
> example.
>
> 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
> <http://nipy.org/nibabel/reference/nibabel.freesurfer.html#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!
> 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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>
>
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