Hi SUMA users,
I'm using SurfSmooth from SUMA version 2004_12_29, and have run into unpredicted behavior. I'm posting in case someone can give me information on this (and in case people run into the same thing in the future)
I am smoothing surface data using the LB_FEM method, and providing the necessary arguments.
When the surf_A argument is specified as a complete path to the surface, I receive:
Error SurfSmooth: Failed to read input surface.
However, when I have the script "change directory" into the directory in which the input surface lives (the surface referred to by surf_A), and refer to the surface in a local path manner, the script works without a glitch.
I am attaching below that two versions of the script that differ only in whether the -surf_A argument is given as a full path or local path.
(1) Working Version:
foreach x (04)
cd /nfs/raidzone/data/NL-ODS/freesurf/subjects/$x/SUMA/
foreach H (lh rh)
SurfSmooth -spec /nfs/raidzone/data/NL-ODS/freesurf/subjects/04/SUMA/ODS_"$x"_"$H"_mesh140_std.spec -surf_A ODS_"$x"_"$H"_mesh140_std.smoothwm.asc -add_index -met LB_FEM -input /nfs/raidzone/data/NL-ODS/freesurf/subjects/"$x"/SUMA/surface.analysis/ODS_"$x"_"$H"_intend-surf.1D\[6] -Niter 100 -fwhm 4 -output /nfs/raidzone/data/NL-ODS/freesurf/subjects/"$x"/SUMA/surface.analysis/smooth.S"$x"_H"$H"_intend.1D
end
end
(2) Non working version
foreach x (04)
cd /nfs/raidzone/data/NL-ODS/freesurf/subjects/$x/SUMA/
foreach H (lh rh)
SurfSmooth -spec /nfs/raidzone/data/NL-ODS/freesurf/subjects/04/SUMA/ODS_"$x"_"$H"_mesh140_std.spec -surf_A /nfs/raidzone/data/NL-ODS/freesurf/subjects/$x/SUMA/ODS_"$x"_"$H"_mesh140_std.smoothwm.asc -add_index -met LB_FEM -input /nfs/raidzone/data/NL-ODS/freesurf/subjects/"$x"/SUMA/surface.analysis/ODS_"$x"_"$H"_intend-surf.1D\[6] -Niter 100 -fwhm 4 -output /nfs/raidzone/data/NL-ODS/freesurf/subjects/"$x"/SUMA/surface.analysis/smooth.S"$x"_H"$H"_intend.1D
end
end
