[pymvpa] Surface searchlight taking 6 to 8 hours

[John Baublitz]

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 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. 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. Is there any way to work around these
problems?

On Jul 28, 2015 8:01 AM, "Nick Oosterhof" <n.n.oosterhof at googlemail.com>
wrote:

>
> > On 23 Jul 2015, at 17:38, Nick Oosterhof <n.n.oosterhof at googlemail.com>
> wrote:
> >
> >
> >> is there a utility to convert from SUMA surface files to FreeSurfer
> surface files included in PyMVPA?
> >
> > ConvertDset (included with AFNI) can convert between NIML and GIFTI, and
> mris_convert (included with Freesufer) can convert between GIFTI and a
> variety of other file formats used in FreeSurfer.
>
> With the latest code on github [1] there is now basic support for GIFTI
> datasets in PyMVPA [2].
>
> [1] https://github.com/PyMVPA/PyMVPA
> [2]
> https://github.com/PyMVPA/PyMVPA/commit/05ebdda025401148425a7894b3a14ea73b932dfc
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