[pymvpa] Surface searchlight taking 6 to 8 hours

[Nick Oosterhof]

> On 29 Jul 2015, at 20:57, John Baublitz <jbaub at bu.edu> wrote:
> 
> Thank you very much for the support. Unfortunately I have tried using this GIFTI file that it outputs with FreeSurfer as an overlay and surface

Both at the same time?

> and it throws errors for all FreeSurfer utils and even AFNI utils. FreeSurfer mris_convert outputs:
> 
> mriseadGIFTIfile: mris is NULL! found when parsing file f_mvpa_rh.func.gii
> 
> This seems to indicate that it is not saving it as a surface file. Likewise AFNI's gifti_tool outputs:
> 
> ** failed to find coordinate/triangle structs
> 
> How exactly is the data being stored in the GIFTI file? It seems that it is not saving it as triangles and coordinates even based on the code you linked to in the github commit given that the NIFTI intent codes are neither NIFTI_INTENT_POINTSET nor NIFTI_INTENT_TRIANGLE by default.

For your current purposes (visualizing surface-based data), consider there are two types of "surface" GIFTI files:

1) "functional" node-data, where each node is associated with the same number of values. Examples are time series data or statistical maps. Typical extensions are .func.gii or .time.gii.
2) "anatomical" surfaces, that have coordinates in 3D space (with NIFTI_INTENT_POINTSET) and node indices in face information (with NIFTI_INTENT_TRIANGLE). The typical extension is surf.gii.

In PyMVPA:
(1) "functional" surface data is handled through mvpa2.datasets.gifti. Data is stored in a Dataset instance.
(2) "anatomical" surfaces are handled through mvpa2.support.nibabel.surf (for GIFTI, mvpa2.support.nibabel.surf_gifti). Vertex coordinates and face indices are stored in a Surface instance (from mvpa2.support.nibabel.surf)

(I'm aware that documentation about this distinction can be improved in PyMVPA).

> I've also run into a problem where the dataset that I've loaded has no intent codes and unfortunately it appears that this means that the NIFTI intent code is set to NIFTI_INTENT_NONE.

Why is that a problem? What are you trying to achieve? If the dataset has no intent, then NIFTI_INTENT_NONE seems valid to me, as the GIFTI standard describes this as "Data intent not specified".