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Implemented method to register lesion mask to MT space #95

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Implemented method to register lesion mask to MT space #95

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47afaa3
Implemented method to register lesion mask to MT space
jcohenadad May 23, 2024
35855d6
Fetch subject basename
jcohenadad May 23, 2024
632bdab
Upsample PSIR to get better registration results
jcohenadad May 31, 2024
69e9183
Added code to estimate MTR excluding lesion mask
jcohenadad May 31, 2024
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54 changes: 52 additions & 2 deletions lisa/spine.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,19 @@
# Usage: sh spine.sh <ABSOLUTE_PATH_SUBJECT> <qc>
# Example command line: sh spine.sh /Users/msresearch/Downloads/canproco/data/CAN-01-CON-039-M0 /Users/msresearch/Downloads/canproco/data/qc
#
# Tested with Spinal Cord Toolbox - Version 5.7
# Tested with Spinal Cord Toolbox - Version 6.3
#
# Author: Lisa Eunyoung Lee

SUBJECT=$1
qc=$2

SUBJECT_BASENAME=`basename ${SUBJECT}`


# Display start time
echo "${SUBJECT}: spine.sh started at $(date +%x_%r)";
echo "Subject: ${SUBJECT_BASENAME}"
start=$(date +%s);

# T2
Expand Down Expand Up @@ -48,6 +52,20 @@ sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0 -qc $qc;
sct_process_segmentation -i t2_seg.nii.gz -vert 2:4 -vertfile ./label/template/PAM50_levels.nii.gz -o csa_c2c4.csv -append 0;


# PSIR
# ===========================================================================================

cd ${SUBJECT}/psir;

# Upsample PSIR image

sct_resample -i psir.nii.gz -mm 0.7x0.7x0.7;

# Segment spinal cord on upsampled PSIR image

sct_deepseg -i psir_r.nii.gz -task seg_sc_contrast_agnostic -qc $qc;


# MT
# ===========================================================================================

Expand Down Expand Up @@ -81,17 +99,49 @@ sct_register_multimodal -i mt1.nii.gz -d mt_t1.nii.gz -dseg mt_t1_seg.nii.gz -m

sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_reg.nii.gz;

# Register PSIR -> mt_t1

sct_register_multimodal -i ../psir/psir_r.nii.gz -iseg ../psir/psir_r_seg.nii.gz -d mt_t1.nii.gz -dseg mt_t1_seg.nii.gz -param step=1,type=seg,algo=centermass -x spline -o psir_r_reg.nii.gz -qc $qc;

# Bring lesion mask onto mt_t1 space
# TODO: extract subject name from absolute PATH

sct_apply_transfo -i ../../derivatives/lesion_masks/${SUBJECT_BASENAME}_lesion.nii.gz -d mt_t1.nii.gz -w warp_psir_r2mt_t1.nii.gz -x linear -o lesion.nii.gz

# Extract MTR in whole cord, GM, WM, WM regions (DC, LF, VF, CST) averaged between C2-C4

mkdir -p ${SUBJECT}/mt/csv;

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 50 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_cord.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 52 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_gm.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 51 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_wm.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 53 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_dc.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 54 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_lf.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 55 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_vf.csv -append 0;

# Generate labels without lesions
# First, invert lesion mask
sct_maths -i lesion_new.nii.gz -sub 1 -o lesion_new_inv.nii.gz
sct_maths -i lesion_new_inv.nii.gz -mul -1 -o lesion_new_inv.nii.gz
# Then, loop through all the atlas files and multiply it by the inverted lesion mask
mkdir label/atlas_nolesion
for file in label/atlas/*; do
# Check if it's a file (not a directory)
if [[ "$file" == *.nii.gz ]]; then
new_file="${file//atlas/atlas_nolesion}"
sct_maths -i $file -mul lesion_new_inv.nii.gz -o $new_file
fi
done
# Finally, copy infor_label.txt to atlas_nolesion
cp label/atlas/info_label.txt label/atlas_nolesion/info_label.txt

# Extract MTR in whole cord, GM, WM, WM regions (DC, LF, VF, CST) averaged between C2-C4 without lesion
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 50 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_cord_nolesion.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 52 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_gm_nolesion.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 51 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_wm_nolesion.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 53 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_dc_nolesion.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 54 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_lf_nolesion.csv -append 0;
sct_extract_metric -i mtr.nii.gz -f label/atlas_nolesion -method map -l 55 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_vf_nolesion.csv -append 0;

# Display end time

echo "${SUBJECT}: spine.sh finished at $(date +%x_%r)";
Expand Down