/usr/lib/ants/phantomstudy.sh is in ants 2.1.0~rc2+git3-g9103999-4.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | #!/bin/bash
ANTSPATH="/usr/lib/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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