
all images and masks in this folder were copied from
/autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/ADC_manual_skull_stripping_byKalli/

--------------------------------------------------------


cp cua_series10057772_010W_ADC.nii.gz Template1.nii.gz
cp cua_series10057772_010W_ADC_yomask.nii.gz Template1_mask.nii.gz
cp kan_series10477798_002D_ADC.nii.gz Template2.nii.gz
cp kan_series10477798_002D_ADC_yomask.nii.gz Template2_mask.nii.gz
cp lat_series11267377_018M_ADC.nii.gz Template3.nii.gz
cp lat_series11267377_018M_ADC_yomask.nii.gz Template3_mask.nii.gz
cp les_series13984090_012M_ADC.nii.gz Template4.nii.gz
cp les_series13984090_012M_ADC_yomask.nii.gz Template4_mask.nii.gz
cp mcc_series10573872_004D_ADC.nii.gz Template5.nii.gz
cp mcc_series10573872_004D_ADC_yomask.nii.gz Template5_mask.nii.gz
cp san_series14975928_003Y_ADC.nii.gz Template6.nii.gz
cp san_series14975928_003Y_ADC_yomask.nii.gz Template6_mask.nii.gz

cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/week2/3T/series4394644.nii.gz Template7.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/month1/3T/s36804.nii.gz Template8.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/month4/3T/series38968.nii.gz Template9.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year0.5-1/3T/series5057403.nii.gz Template10.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year0.5-1/3T/series6102999.nii.gz Template11.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year0.5-1/3T/series5019216.nii.gz Template12.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year4-5/3T/series4972688.nii.gz Template13.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year5-6/3T/series5148563.nii.gz Template14.nii.gz
cp /autofs/cluster/mi2b2/4/Pediatric_Brain_Atlas/nifti/ADC/year3-4/3T/series5810004.nii.gz Template15.nii.gz



==========================
on 6/19/2018, with the intension to make picasso.sh applicable to ADC maps
==========================

###############################
# step 1. padding images and label images (inferior and superior)

for i in {1..15}; do
        3dZeropad -I 15 -S 15 -A 15 -P 15 -L 15 -R 15 -prefix Template${i}_padded.nii.gz Template${i}.nii.gz
        3dZeropad -I 15 -S 15 -A 15 -P 15 -L 15 -R 15 -prefix Template${i}_padded_label.nii.gz Template${i}_label.nii.gz
done


# check before removing
for i in {1..15}; do
        \rm Template${i}.nii.gz Template${i}_label.nii.gz
done


##############################
# step2. check if any image has negative values

for i in {1..15}; do
        fslmaths Template${i}_padded.nii.gz -bin -mul Template${i}_padded.nii.gz haha.nii.gz
        mv haha.nii.gz Template${i}_padded.nii.gz
done


##############################
# step 3. normalize FOV by registering brain masks, not the brain image from MNI152

# compute affine matrix by brain masks
for i in {1..15}; do
        flirt -in ../MNI152atlas/MNI152_T1_1mm_padded_brain.nii.gz -ref Template${i}_padded_label.nii.gz -omat MNI152_to_Template${i}_brain.mat &
done

# apply the affine transform to warp with-skull images
for i in {1..15}; do
        flirt -in ../MNI152atlas/MNI152_T1_1mm_padded.nii.gz -ref Template${i}_padded.nii.gz -out MNI152_to_Template${i}_padded_bybrainonly.nii.gz -init MNI152_to_Template${i}_brain.mat -applyxfm &
done

# apply the affine transform to warp the MNI152 FOV
for i in {1..15}; do
        flirt -in ../MNI152atlas/MNI152_T1_1mm_padded_FOV.nii.gz -ref Template${i}_padded.nii.gz -out Template${i}_padded_normalizedFOVmask.nii.gz -init MNI152_to_Template${i}_brain.mat -applyxfm -interp nearestneighbour &
done




############################
# step 4: further verifications

# make sure the brain mask and FOV masks are all 0-1 (not 0-255) and all in uint8 data type
for i in {1..15}; do
        fslmaths Template${i}_padded_label.nii.gz -bin Template${i}_padded_label.nii.gz -odt char
        fslmaths Template${i}_padded_normalizedFOVmask.nii.gz -bin Template${i}_padded_normalizedFOVmask.nii.gz -odt char
done


# check if the masks files have the same dimensions as the image
for i in {1..15}; do
        echo $i
        fslinfo Template${i}_padded.nii.gz; echo ""
        fslinfo Template${i}_padded_label.nii.gz; echo ""
        fslinfo Template${i}_padded_normalizedFOVmask.nii.gz
        read a
done


# need to visualize all images, brain masks and FOV masks to check
for i in {1..15}; do
        fslview Template${i}_padded.nii.gz Template${i}_padded_label.nii.gz -l yellow -t 0.5 Template${i}_padded_normalizedFOVmask.nii.gz -l green -t 0.5 &
done



