[pymvpa] Error from pymvpa2-prep-afni-surf

Nick Oosterhof n.n.oosterhof at googlemail.com
Tue Oct 13 08:57:39 UTC 2015

>> On 12 Oct 2015, at 23:57, Beau R. Sievers <Beau.R.Sievers.GR at dartmouth.edu> wrote:
>> Hello, PyMVPA users,
>> I am running into an error (two, really) when running pymvpa2-prep-afni-surf to align the surfaces from FreeSurfer’s recon-all to my already-aligned anatomical images. It appears pymvpa2-prep-afni-surf tries to run 3dSurf2Vol with a non-existant option, “-surf” instead of “-surf_1D”, but correcting this apparent bug results in another error: 3dSurf2Vol rejects __tt.1D with a “bad surf data file” error.
> On 13 Oct 2015, at 02:26, Feilong Ma <mafeilong at gmail.com> wrote:
> My intuition is the ANFI version you're using is too old, or the PyMVPA version is too old, or the command pymvpa2-prep-afni-surf hasn't been updated for recent AFNI versions.  It seems the API of the PyMVPA command and that of AFNI is not compatible with each other.

Indeed, going through the AFNI source shows that on 9 Feb 2012 an option "sdata" was added to src/SUMA/SUMA_3dSurf2Vol.c at line 2178 [1]. Maybe your AFNI version is from before that date?
Which version of AFNI are you using? Can you upgrade to the latest version and see if that fixes the issue?

[1] https://github.com/afni/afni/commit/7e0fc62d1b56a8cca8e83055f48453d0bf25bcd8#diff-b28d91a846dda39fcd3530431689e53cR983

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