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#!/bin/bash
count=0
for x in phantomA phantomB phantomC phantomD phantomE phantomF phantomG phantomH
do
count=`expr $count + 1` # Increment the counter
echo " $x "
echo " LaplacianThickness ${x}wm.hdr ${x}gm.hdr 15 TEST{$count}thick.hdr 1 0.5 "
ThresholdImage 2 ${x}wmgm.jpg ${x}wm.nii 245 290
ThresholdImage 2 ${x}wmgm.jpg ${x}gm.nii 111 133
LaplacianThickness ${x}wm.nii ${x}gm.nii 15 TEST{$count}thick.hdr 5 3
WarpImageMultiTransform 2 TEST{$count}thick.hdr TEST{$count}thickreg.hdr TEST{$count}Warp.nii TEST{$count}Affine.txt
# SmoothImage 2 TEST{$count}thickreg.hdr 1 TEST{$count}thickreg.hdr
done
StudentsTestOnImages 2 THICK2.hdr 4 4
~/Code/bin/ants/GLM 2 mask.nii designmat.txt contrastvec.txt temp.hdr 1000 TEST{1}thickreg.hdr TEST{2}thickreg.hdr TEST{3}thickreg.hdr TEST{4}thickreg.hdr TEST{5}thickreg.hdr TEST{6}thickreg.hdr TEST{7}thickreg.hdr TEST{8}thickreg.hdr
MultiplyImages 2 THICK2.hdr phantomtemplate.jpg THICK2.hdr
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