On Oct 13, 2015, at 4:57 AM, Nick Oosterhof <[email protected]> wrote:
>>> On 12 Oct 2015, at 23:57, Beau R. Sievers <[email protected]> >>> 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 <[email protected]> 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 > I can confirm that this fixes the issue. Thanks Nick and Feilong. A warning for others: 3dSurf2Vol has an incorrect version string in the current version of AFNI, and I had to run the AFNI updating tools more than once to obtain a current 3dSurf2Vol binary. I don’t know if these two problems are related. _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
