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Copy pathStructural_Step01_Skullstrip.sh
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Structural_Step01_Skullstrip.sh
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# set your own directory
home=/home/jamielh/Volumes/Hanson/Pitt_PYS/proc/
# basic for i loop
for i in $1
do
# change and making new directories
cd $home
mkdir ${i}
cd ${i}
mkdir anat
cd anat
# doing bias correction in ANTS, then warping in ANTS, and finally warping skull-strip masks to subject space
N4BiasFieldCorrection -d 3 -i ~/Volumes/Hanson/Pitt_PYS/orig/${i}/anat/${i}_t1w.nii.gz -o ${i}_t1w_c.nii.gz -c ["500x500x500x500,.000001"]
ANTS 3 -m CC[/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz,${i}_t1w_c.nii.gz,1,4] -o ${i}_t1w_c_1mm_100100100_ -i 100x100x100 -r Gauss[3,0] -t SyN[0.05]
ANTS 3 -m CC[/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz,${i}_t1w_c.nii.gz,1,4] -o ${i}_t1w_c_1mm_100100100100_ -i 100x100x100x100 -r Gauss[3,0] -t SyN[0.05]
WarpImageMultiTransform 3 /home/jamielh/Volumes/Hanson/Pitt_PYS/proc/archive/MNI152_T1_1mm_brain_mask_filled.nii.gz ${i}_brain_mask_FILLED_100100100.nii.gz -R ${i}_t1w_c.nii.gz -i ${i}_t1w_c_1mm_100100100_Affine.txt ${i}_t1w_c_1mm_100100100_InverseWarp.nii.gz --use-NN
WarpImageMultiTransform 3 /home/jamielh/Volumes/Hanson/Pitt_PYS/proc/archive/MNI152_T1_1mm_brain_mask_filled.nii.gz ${i}_brain_mask_FILLED_100100100100.nii.gz -R ${i}_t1w_c.nii.gz -i ${i}_t1w_c_1mm_100100100100_Affine.txt ${i}_t1w_c_1mm_100100100100_InverseWarp.nii.gz --use-NN
# doing BET-fsl skull script, then flirt/fnirt-ing for warps, and then applying fnirt to skull-strip mask
bet ${i}_t1w_c.nii.gz ${i}_t1w_c_bet.nii.gz -R
flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in ${i}_t1w_c_bet.nii.gz -omat ${i}_affine_transf.mat
fnirt --in=${i}_t1w_c.nii.gz --aff=${i}_affine_transf.mat --cout=${i}_nonlinear_transf --config=T1_2_MNI152_2mm
invwarp --ref=${i}_t1w_c.nii.gz --warp=${i}_nonlinear_transf --out=${i}_fnirt_inv
applywarp --ref=${i}_t1w_c.nii.gz --warp=${i}_fnirt_inv --in=/home/jamielh/Volumes/Hanson/Pitt_PYS/proc/archive/MNI152_T1_1mm_brain_mask_filled.nii.gz --out=${i}_warped_mask_1mm.nii.gz --interp=nn
# using AFNI tool to fix the masks
3dmask_tool -inputs ${i}_brain_mask_FILLED_100100100.nii.gz -dilate_input 1 -fill_holes -prefix ${i}_brain_mask_FILLED_100100100_dil.nii.gz
3dmask_tool -inputs ${i}_brain_mask_FILLED_100100100100.nii.gz -dilate_input 1 -fill_holes -prefix ${i}_brain_mask_FILLED_100100100100_dil.nii.gz
3dmask_tool -inputs ${i}_warped_mask_1mm.nii.gz -dilate_input 1 -fill_holes -prefix ${i}_warped_mask_1mm_dil.nii.gz
# doing AFNI skullstrip
3dSkullStrip -input ${i}_t1w_c.nii.gz -prefix ${i}_t1w_c_ss.nii.gz -mask_vol
fslmaths ${i}_t1w_c_ss.nii.gz -uthr 2 -bin ${i}_subtract.nii.gz
# combining all the masks together
3dmask_tool -inputs ${i}_t1w_c_ss.nii.gz ${i}_t1w_c_bet.nii.gz ${i}_brain_mask_FILLED_100100100.nii.gz ${i}_brain_mask_FILLED_100100100100.nii.gz ${i}_warped_mask_1mm.nii.gz ${i}_brain_mask_FILLED_100100100_dil.nii.gz ${i}_brain_mask_FILLED_100100100100_dil.nii.gz ${i}_warped_mask_1mm_dil.nii.gz -frac .7 -prefix ${i}_MASK_COMBINED.nii.gz
done
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