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#!/bin/bash
ANTSPATH="/Users/stnava/Code/bin/ants/"
#initialization, here, is unbiased
count=0
for x in phantomAwmgm.jpg phantomBwmgm.jpg phantomCwmgm.jpg phantomDwmgm.jpg phantomEwmgm.jpg phantomFwmgm.jpg phantomGwmgm.jpg phantomHwmgm.jpg
do
count=`expr $count + 1` # Increment the counter
echo " count is $count and file is $x "
${ANTSPATH}/ANTS 2 -m PR[phantomtemplate.jpg,$x,1,4] -i 20x161x161x161 -o TEST{$count} -t SyN[2] -r Gauss[3,0.]
#
# -t SyN[1,2,0.05] -r Gauss[3,0.25]
${ANTSPATH}/WarpImageMultiTransform 2 $x TEST{$count}registered.nii TEST{$count}Warp.nii TEST{$count}Affine.txt
done
# to look at the stack of results, do this:
${ANTSPATH}/StackSlices volo.hdr -1 -1 0 *$1
${ANTSPATH}/StackSlices volr.hdr -1 -1 0 *registered.nii
count=0
for x in phantomAwmgm.jpg phantomBwmgm.jpg phantomCwmgm.jpg phantomDwmgm.jpg phantomEwmgm.jpg phantomFwmgm.jpg phantomGwmgm.jpg phantomHwmgm.jpg
do
count=`expr $count + 1` # Increment the counter
echo " count is $count and file is $x "
echo " CreateJacobianDeterminantImage 2 TEST{$count}Warp.nii TEST{$count}logjac.nii 1 "
${ANTSPATH}/CreateJacobianDeterminantImage 2 TEST{$count}Warp.nii TEST{$count}logjac.nii 1
# ${ANTSPATH}/SmoothImage 2 TEST{$count}logjac.nii 1 TEST{$count}logjac.nii
done
${ANTSPATH}/ThresholdImage 2 phantomtemplate.jpg mask.nii 100 200
# use the GLM with mask
${ANTSPATH}/GLM 2 mask.nii designmat.txt contrast.txt Result.nii 1000 TEST*logjac.nii
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