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

[John Baublitz]

I am trying to export functional data from PyMVPA. Our lab is specifically
trying to load functional data from the analysis (a list of vertices and a
value associated with each vertex from the analysis) and visualize it in
FreeSurfer. As I understand it, I have been saving it as functional data
(using map2gifti) based on the update to PyMVPA that you committed.
Unfortunately there seems to be an issue where FreeSurfer will not load an
overlay with an extension .gii. I am happy to email FreeSurfer if this is
more of a FreeSurfer issue but it seems that the .gii file output by PyMVPA
does not really work with any FreeSurfer utils, not just the visualization
as I mentioned with mris_convert. I am still unsure of where this issue is
coming from: FreeSurfer or PyMVPA.

On Wed, Aug 19, 2015 at 9:07 AM, Nick Oosterhof <
n.n.oosterhof at googlemail.com> wrote:

>
> > 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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