[pymvpa] Surface searchlight taking 6 to 8 hours

[John Baublitz]

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) and then I tried to load it as a volume
and it didn't load either (no overlay data found in file). I am still
struggling to figure out exactly how I should be loading this data. Is this
a better question for FreeSurfer's mailing list? I'm not entirely sure as
it seems possible that it could be either a format output issue (PyMVPA) or
a FreeSurfer-specific issue.

On Thu, Jul 30, 2015 at 5:27 AM, Nick Oosterhof <
n.n.oosterhof at googlemail.com> wrote:

>
> > 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".
>
>
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