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CT_Skull_Strip_Example.sh
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CT_Skull_Strip_Example.sh
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# Thresholding Image to 0-100
img="Head_Image_1.nii.gz"
intensity=0.01
outfile="Head_Image_1_SS_0.01"
tmpfile=`mktemp`
# Thresholding Image to 0-100
fslmaths "${img}" -thr 0.000000 -uthr 100.000000 "${outfile}"
# Creating 0 - 100 mask to remask after filling
fslmaths "${outfile}" -bin "${tmpfile}";
fslmaths "${tmpfile}.nii.gz" -bin -fillh "${tmpfile}"
# Presmoothing image
fslmaths "${outfile}" -s 1 "${outfile}";
# Remasking Smoothed Image
fslmaths "${outfile}" -mas "${tmpfile}" "${outfile}"
# Running bet2
bet2 "${outfile}" "${outfile}" -f ${intensity} -v
# Using fslfill to fill in any holes in mask
fslmaths "${outfile}" -bin -fillh "${outfile}_Mask"
# Using the filled mask to mask original image
fslmaths "${img}" -mas "${outfile}_Mask" "${outfile}"
######################
## If no pre-smoothing
######################
outfile_nosmooth="Head_Image_1_SS_0.01_nopresmooth"
fslmaths "$img" -thr 0.000000 -uthr 100.000000 "${outfile_nosmooth}"
# Creating 0 - 100 mask to remask after filling
fslmaths "${outfile_nosmooth}" -bin "${tmpfile}";
fslmaths "${tmpfile}" -bin -fillh "${tmpfile}"
# Running bet2
bet2 "${outfile_nosmooth}" "${outfile_nosmooth}" -f ${intensity} -v
# Using fslfill to fill in any holes in mask
fslmaths "${outfile_nosmooth}" -bin -fillh "${outfile_nosmooth}_Mask"
# Using the filled mask to mask original image
fslmaths "$img" -mas "${outfile_nosmooth}_Mask" "${outfile_nosmooth}"