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" <[email protected]> > To: "[email protected]" < > [email protected]> > 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 > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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