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#!/bin/bash
#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 $x "
ANTS 2 -m PR[ phantomtemplate.jpg,$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]
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:
StackSlices volo.hdr -1 -1 0 *$1
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{$count}logjac.nii 1 "
CreateJacobianDeterminantImage 2 TEST{$count}Warp.nii TEST{$count}logjac.nii 1
# SmoothImage 2 TEST{$count}logjac.nii 1 TEST{$count}logjac.nii
done
ThresholdImage 2 phantomtemplate.jpg mask.nii 100 200
# use the GLM with mask
GLM 2 mask.nii designmat.txt contrast.txt Result.nii 1000 TEST*logjac.nii
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