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- #!/bin/tcsh
- #
- ## ----------------------------------------------------------------------
- ## Convert a drawn surface ROI to the volume (and back?).
- ##
- ## In suma, draw an ROI and save it as (prefix) tuna.lh ,
- ## then run this script.
- ##
- ## This script runs ROI2dataset to convert the tuna ROI into a
- ## surface dataset (NIML), and then runs 3dSurf2Vol to project
- ## that into the volume domain, filling the volxels between the
- ## smooth WM and pial surfaces.
- ##
- ## Afterwards, one could view the volume ROI in afni, 'talk' to
- ## suma, and see how the volume ROI maps back to the surface.
- ## ----------------------------------------------------------------------
- # ------------------------------
- # note input dataset name
- if ( $#argv > 0 ) then
- set prefix = $argv[1]
- else
- set prefix = tuna
- endif
- # ------------------------------
- # be sure input exists
- if ( ! -f $prefix.lh.niml.roi ) then
- echo "** missing input dataset: $prefix.lh.niml.roi"
- echo " please 'draw' in suma to create it (save -> $prefix.lh)"
- echo ""
- exit 1
- endif
- # ------------------------------
- # 1. convert to proper surface dataset (not ROI),
- # with only one value per node
- # 2. map to volume
- ROI2dataset -prefix $prefix.lh.niml.dset -input $prefix.lh.niml.roi
- # consider also @surf_to_vol_spackle
- 3dSurf2Vol \
- -spec std.141.FT_lh.spec \
- -surf_A smoothwm \
- -surf_B pial \
- -sv FT_SurfVol.nii \
- -grid_parent FT_SurfVol.nii \
- -map_func mode \
- -f_steps 12 \
- -sdata $prefix.lh.niml.dset \
- -prefix $prefix.lh.s2v.roi
- if ( $status ) then
- echo "** failed 3dSurf2Vol"
- echo 1
- endif
- echo ""
- echo "++ created $prefix.lh.s2v.roi"
- echo ""
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