[pymvpa] GIFTI i/o issue [was: Surface searchlight taking 6 to 8 hours]

Nick Oosterhof n.n.oosterhof at googlemail.com
Wed Aug 19 13:07:39 UTC 2015


> On 18 Aug 2015, at 20:25, John Baublitz <jbaub at bu.edu> wrote:
> 
> Sorry for the delay. I have been traveling. I did not try to load them as both at the same time. I tried to load it as a surface and that threw an error in FreeSurfer (mris is NULL)

This error suggests you are trying to use the surface file as an anatomical file (with vertices and faces), and that the vertex and face information is not found. See utils/gifti_local.c [1].

Is that correct? Note that if you want to save an overlay (functional data) from a PyMVPA Dataset with  a .samples field, you should use datasets/gifti. Anatomical surface files are handled through modules in mvpa2.support.nibabel.

> I am still struggling to figure out exactly how I should be loading this data.

Could you please provide more details about what type of data (anatomical or functional) you are trying to export from PyMVPA and import in FreeSurfer?

[1] https://github.com/solleo/freesurfer/blob/master/utils/gifti_local.c


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