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

[Feilong Ma]

Hi Beau,

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.

Best,
Feilong

---------- Forwarded message ----------
> From: "Beau R. Sievers" <Beau.R.Sievers.GR at dartmouth.edu>
> To: "pkg-exppsy-pymvpa at lists.alioth.debian.org" <
> pkg-exppsy-pymvpa at lists.alioth.debian.org>
> Cc:
> Date: Mon, 12 Oct 2015 21:57:14 +0000
> Subject: [pymvpa] Error from pymvpa2-prep-afni-surf
> 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.
>
> Detail follows, including the errors copied from the output logs:
>
> Running: makesurfmasks
> ** Will execute the following commands:
> ** - cd /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk
> ** - 1deval -1D: -num 163841 -expr 1 > __t.1D
> ** - 1dtranspose __t.1D > __tt.1D
> **>> Starting now:
> **<< ... completed execution
> ** Will execute the following commands:
> ** - cd /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk
> ** - 3dSurf2Vol -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec
> -surf_A smoothwm -sv anat_final_kk_ss+orig -grid_parent
> anat_final_kk_ss+orig. -prefix __m2_lh -sdata __tt.1D -overwrite
> **>> Starting now:
> Traceback (most recent call last):
>   File "/afs/
> dbic.dartmouth.edu/usr/local/common/bin/pymvpa2-prep-afni-surf", line 25,
> in <module>
>     run_prep_afni_surf(vars(d))
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/site-packages/mvpa2/support/afni/lib_prep_afni_surf.py",
> line 1208, in run_prep_afni_surf
>     run_all(config, environment)
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/site-packages/mvpa2/support/afni/lib_prep_afni_surf.py",
> line 1116, in run_all
>     step2func[step](config, env)
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/site-packages/mvpa2/support/afni/lib_prep_afni_surf.py",
> line 964, in run_makesurfmasks
>     utils.run_cmds('cd %s;%s' % (refdir, cmd))
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/site-packages/mvpa2/support/afni/afni_utils.py",
> line 116, in run_cmds
>     subprocess.check_call(cmd, env=env, shell=True)
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/subprocess.py",
> line 540, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command 'cd
> /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk;3dSurf2Vol
> -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec -surf_A smoothwm
> -sv anat_final_kk_ss+orig -grid_parent anat_final_kk_ss+orig. -prefix
> __m2_lh -sdata __tt.1D -overwrite' returned non-zero exit status 255
>
>
> Running the 3dSurf2Vol command to determine the reason for failure gives
> this exit message error:
>
> > 3dSurf2Vol -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec
> -surf_A smoothwm -sv anat_final_kk_ss+orig -grid_parent
> anat_final_kk_ss+orig. -prefix __m2_lh -sdata __tt.1D -overwrite
> invalid option <-sdata>
>   usage: 3dSurf2Vol [options] -spec SPEC_FILE -surf_A SURF_NAME \
>              -grid_parent AFNI_DSET -sv SURF_VOL \
>              -map_func MAP_FUNC -prefix OUTPUT_DSET
> usage: 3dSurf2Vol -help
>
>
> I created a new version of the pymvpa2-prep-afni-surf script that corrects
> this error, by changing “-sdata” to “-sdata_1D", but running this resulted
> in another set of errors:
>
> Running: makesurfmasks
> ** Will execute the following commands:
> ** - cd /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk
> ** - 1deval -1D: -num 163841 -expr 1 > __t.1D
> ** - 1dtranspose __t.1D > __tt.1D
> **>> Starting now:
> **<< ... completed execution
> ** Will execute the following commands:
> ** - cd /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk
> ** - 3dSurf2Vol -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec
> -surf_A smoothwm -sv anat_final_kk_ss+orig -grid_parent
> anat_final_kk_ss+orig. -prefix __m2_lh -sdata_1D __tt.1D -overwrite
> **>> Starting now:
> Traceback (most recent call last):
>   File "/afs/
> dbic.dartmouth.edu/usr/wheatley/beau/bouncing_ball_pipeline/pymvpa2-prep-afni-surf-fixed",
> line 25, in <module>
>     run_prep_afni_surf(vars(d))
>   File "/afs/
> dbic.dartmouth.edu/usr/wheatley/beau/bouncing_ball_pipeline/lib_prep_afni_surf_fixed.py",
> line 1186, in run_prep_afni_surf
>     run_all(config, environment)
>   File "/afs/
> dbic.dartmouth.edu/usr/wheatley/beau/bouncing_ball_pipeline/lib_prep_afni_surf_fixed.py",
> line 1097, in run_all
>     step2func[step](config, env)
>   File "/afs/
> dbic.dartmouth.edu/usr/wheatley/beau/bouncing_ball_pipeline/lib_prep_afni_surf_fixed.py",
> line 945, in run_makesurfmasks
>     utils.run_cmds('cd %s;%s' % (refdir, cmd))
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/site-packages/mvpa2/support/afni/afni_utils.py",
> line 116, in run_cmds
>     subprocess.check_call(cmd, env=env, shell=True)
>   File "/afs/
> dbic.dartmouth.edu/usr/pkg/python/python_v2.7/@sys/lib/python2.7/subprocess.py",
> line 540, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command 'cd
> /flash/wheatley/bouncing_ball_testing/pymvpa_afni_surf_output_kk;3dSurf2Vol
> -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec -surf_A smoothwm
> -sv anat_final_kk_ss+orig -grid_parent anat_final_kk_ss+orig. -prefix
> __m2_lh -sdata_1D __tt.1D -overwrite' returned non-zero exit status 253
>
>
> Now running the 3dSurf2Vol command manually to determine the problem gives
> this exit message:
>
> > 3dSurf2Vol -map_func mask2 -data_expr "a*2" -spec lh_ico128_al.spec
> -surf_A smoothwm -sv anat_final_kk_ss+orig -grid_parent
> anat_final_kk_ss+orig. -prefix __m2_lh -sdata_1D __tt.1D -overwrite
> ** bad (163842 x 1) surf data 1D file '__tt.1D'
>
>
> And now I’m in over my head. Any ideas about what the underlying issue
> might be?
>
> Thanks!
> Beau Sievers
>
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