[pymvpa] Surface searchlight taking 6 to 8 hours

[John Baublitz]

The error upon executing "suma -spec sl.dset" is:

Error SUMA_Read_SpecFile: Your spec file contains uncommented gibberish:
  <AFNI_dataset
Please deal with it.
Error SUMA_Engine: Error in SUMA_Read_SpecFile.

I followed the tutorial on how to generate this so I'm not sure if this is
a bug or maybe a version problem.

On Thu, Jul 23, 2015 at 11:38 AM, Nick Oosterhof <
n.n.oosterhof at googlemail.com> wrote:

>
> > On 23 Jul 2015, at 16:47, John Baublitz <jbaub at bu.edu> wrote:
> >
> > Thank you for the quick response. I tried outputting a surface file file
> before using both niml.write() and surf.write() as my lab would prefer to
> visualize the results on the surface. I mentioned this in a previous email
> and was told that I should be using niml.write() and visualize using SUMA.
> I decided against this because not only would it fail to open with our
> version of SUMA (I can include the error if that would be helpful)
>
> Indeed, that would be helpful.
>
> > but I have found no evidence that .dset files are compatible with
> FreeSurfer. My lab has a hard requirement that whatever we are outputting
> from the analysis must be able to be visualized in FreeSurfer. Is there any
> way to output a FreeSurfer-compatible surface file using PyMVPA?
>
> Not at the moment, but it would be nice to support GIFTI. Currently
> surface anatomy can be exported as GIFTI, but there is no support currently
> for functional files. I’ve added an issue [1], so it may be added in the
> future.
>
> > If not, 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.
>
>
> [1] https://github.com/PyMVPA/PyMVPA/issues/347
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