[pymvpa] Surface based pattern analysis problems

[Nick Oosterhof]

On 24 February 2015 at 21:06, Xixi Wang <wangxixi577 at gmail.com> wrote:

> I'm trying to perform some surfaced-based pattern analysis and I'm not
> sure how to correlate the 3D volumetric coordinates with the 2D surface
> coordinates.
>
> [...]
>     -  I found out that coregistration results were pretty good and the
> activation maps were projected on the surface reasonably
>

That is reassuring.


> 5) *My question is: For each voxel of interest inside of the VT cortex,
> I'd like to get the corresponding surface coordinates. My impression is
> that SUMA is used for visualization only, so is there any method that I
> could use to extract certain information? *
>

See mvpa2.misc.surfing.volgeom, and the ijk2xyz and xyz2ijk methods. For
example:

from mvpa2.suite import *
ds=fmri_dataset('my_nifti_file.nii')

# instantiate volgeom instance from fmri dataset
vg=volgeom.from_any('my_nifti_file.nii')   # can also take 'ds' directly

# convert voxel indices in 'ds' to 3D coordinates
xyz=vg.ijk2xyz(ds.fa.voxel_indices)
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