/
x.6_surface.sh
executable file
·56 lines (47 loc) · 1.98 KB
/
x.6_surface.sh
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#!/bin/bash
while read subject session min max
do
dir=${rootDir}/${subject}
func_dir=${dir}
## name of the resting-state scan
rest=rest
surfDir=${rootDir}/${subject}/${subject}/surf/SUMA
# Extract func to surf
echo "Extracting surface LH"
3dVol2Surf -spec ${surfDir}/${subject}_lh.spec \
-surf_A ${surfDir}/lh.smoothwm.asc \
-surf_B ${surfDir}/lh.pial.asc \
-sv ${func_dir}/${subject}_SurfVol_WD_Alnd_Exp+orig. \
-grid_parent ${func_dir}/${session}/${rest}_res.aligned.do.dm+orig. \
-map_func ave \
-f_steps 15 -f_index nodes \
-outcols_NSD_format \
-out_niml ${func_dir}/${session}/${subject}_lh_rest.niml.dset
echo "Extracting surface RH"
3dVol2Surf -spec ${surfDir}/${subject}_rh.spec \
-surf_A ${surfDir}/rh.smoothwm.asc \
-surf_B ${surfDir}/rh.pial.asc \
-sv ${func_dir}/${subject}_SurfVol_WD_Alnd_Exp+orig. \
-grid_parent ${func_dir}/${session}/${rest}_res.aligned.do.dm+orig. \
-map_func ave \
-f_steps 15 -f_index nodes \
-outcols_NSD_format \
-out_niml ${func_dir}/${session}/${subject}_rh_rest.niml.dset
# Surface Smoothing
SurfSmooth -met HEAT_07 \
-spec ${surfDir}/${subject}_lh.spec \
-surf_A ${surfDir}/lh.smoothwm.asc \
-input ${func_dir}/${session}/${subject}_lh_rest.niml.dset \
-blurmaster ${func_dir}/${session}/${subject}_lh_rest.niml.dset \
-detrend_master \
-output ${func_dir}/${session}/${subject}_lh_rest_ss.niml.dset \
-target_fwhm 6
SurfSmooth -met HEAT_07 \
-spec ${surfDir}/${subject}_rh.spec \
-surf_A ${surfDir}/rh.smoothwm.asc \
-input ${func_dir}/${session}/${subject}_rh_rest.niml.dset \
-blurmaster ${func_dir}/${session}/${subject}_rh_rest.niml.dset \
-detrend_master \
-output ${func_dir}/${session}/${subject}_rh_rest_ss.niml.dset \
-target_fwhm 6
done<${1}