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

Kirstie Whitaker kw401 at cam.ac.uk
Thu Apr 14 18:27:02 EDT 2016

Hi Michael,

Sorry for not being clear. 

They're exactly as defined in the Display ROIs example that I linked to.

There aren't any error messages when writing out the file, I just can't load it up in freeview. I'll send a screenshot from freeview tomorrow morning. (I'm on my iPhone now.) Is there anything else that would be good to know?


Sent from my iPhone, please excuse any typos or excessive brevity

> On 14 Apr 2016, at 23:19, Michael Waskom <mwaskom at stanford.edu> wrote:
> 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 pysurfer example.
>> I'd like to be able to overlay the same ROI information in BrainNet (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!
>> 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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