afni.nimh.nih.gov

Hi-

OK, that is odd. The following works for me, which should be basically emulating your command (I'm using output from the AFNI Bootcamp dir plus having run the s03* script example for afni_proc.py processing on a surface):

#!/bin/tcsh

# working version

set subj = FT

set idir = ~/CD/AFNI_data6/FT_analysis/FT/SUMA

3dVol2Surf                          \
    -spec    ${idir}/std.141.${subj}_rh.spec   \
    -surf_A  std.141.rh.smoothwm.gii \
    -surf_B  std.141.rh.pial.gii     \
    -map_func ave                   \
    -f_steps 15                     \
    -f_index voxels                 \
    -sv          ${subj}.surf_SurfVol_Alnd_Exp+orig.HEAD \
    -grid_parent ${subj}.surf_SurfVol_Alnd_Exp+orig.HEAD \
    -oob_value 0.0                  \
    -oob_index 0.0                  \
    -out_niml rh_${subj}_TEST_D.niml.dset

Note how there is the path to the *.spec file, but *not* to the *.gii ones-- those are basically assumed to be in the same spot as the *.spec file. However, if I tried putting a path to each of the "-surf_* .." files as well, like this:

#!/bin/tcsh

# *broken* version

set subj = FT

set idir = ~/CD/AFNI_data6/FT_analysis/FT/SUMA

3dVol2Surf                          \
    -spec    ${idir}/std.141.${subj}_rh.spec   \
    -surf_A  ${idir}/std.141.rh.smoothwm.gii \
    -surf_B  ${idir}/std.141.rh.pial.gii     \
    -map_func ave                   \
    -f_steps 15                     \
    -f_index voxels                 \
    -sv          ${subj}.surf_SurfVol_Alnd_Exp+orig.HEAD \
    -grid_parent ${subj}.surf_SurfVol_Alnd_Exp+orig.HEAD \
    -oob_value 0.0                  \
    -oob_index 0.0                  \
    -out_niml rh_${subj}_TEST_D.niml.dset

... then I got a similar error to yours:

** surface name '/home/ptaylor/CD/AFNI_data6/FT_analysis/FT/SUMA/std.141.rh.smoothwm.gii' not found

In your 3dVol2Surf command, have you copied files around? I don't see how all your inputs are in the same directory location.

--pt