organize processing by script

.gitignore

@@ -0,0 +1 @@
+.idea/

crop_data.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+#
+# Pipeline for spinal cord tumor data.
+#
+# Generate sc segmentation, preprocess data before training.
+#
+# Note: All images have .nii extension.
+#
+# Usage:
+#   sct_run_batch <FILEPARAM> process_data.sh
+#
+# Author: Andreanne Lemay
+
+# Uncomment for full verbose
+# set -v
+
+# Immediately exit if error
+set -e
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+FILEPARAM=$2
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# shellcheck disable=SC1090
+source $FILEPARAM
+# Go to results folder, where most of the outputs will be located
+cd $PATH_RESULTS
+# Copy source images and segmentations
+mkdir -p data/derivatives/labels
+cd data
+
+cp -r $PATH_DATA/$SUBJECT .
+cp -r $PATH_DATA/derivatives/labels/$SUBJECT $PATH_RESULTS/data/derivatives/labels
+
+# Go to data folder
+cd $PATH_RESULTS/data/$SUBJECT/anat/
+## Setup file names
+file_t2w=${SUBJECT}_T2w
+file_t1w=${SUBJECT}_T1w
+
+path_t1w=`pwd`/${file_t1w}.nii.gz
+
+# Oversample to avoid losing slice info when cropping
+sct_resample -i ${file_t2w}.nii.gz -vox 512x512x100 -x spline -o ${file_t2w}.nii.gz;
+
+sct_get_centerline -i ${file_t2w}.nii.gz -c t2;
+sct_create_mask -i ${file_t2w}.nii.gz -p centerline,${file_t2w}_centerline.nii.gz;
+sct_crop_image -i ${file_t2w}.nii.gz -m mask_${file_t2w}.nii.gz -o ${file_t2w}.nii.gz;
+cropped_img=`pwd`/${file_t2w}.nii.gz;
+
+
+if [ -f ${path_t1w} ]; then
+  sct_resample -i ${file_t1w}.nii.gz -vox 512x512x100 -x spline -o ${file_t1w}.nii.gz;
+  sct_crop_image -i ${file_t1w}.nii.gz -ref ${cropped_img} -o ${file_t1w}.nii.gz;
+  sct_resample -i ${file_t1w}.nii.gz -vox 96x512x16 -x spline -o ${file_t1w}.nii.gz;
+fi
+
+cd $PATH_RESULTS/data/derivatives/labels/$SUBJECT/anat/
+
+file_t2w_seg=${SUBJECT}_T2w_seg-tumor
+file_t1w_seg=${SUBJECT}_T1w_seg-tumor
+
+if [ -f ${path_t1w} ]; then
+  sct_resample -i ${file_t1w_seg}.nii.gz -vox 512x512x100 -x linear -o ${file_t1w_seg}.nii.gz;
+  sct_crop_image -i ${file_t1w_seg}.nii.gz -ref ${cropped_img} -o ${file_t1w_seg}.nii.gz;
+  sct_resample -i ${file_t1w_seg}.nii.gz -vox 96x512x16 -x linear -o ${file_t1w_seg}.nii.gz;
+  sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9
+  sct_image -i ${file_t1w_seg}.nii.gz -setorient AIL;
+fi
+
+sct_resample -i ${file_t2w_seg}.nii.gz -vox 512x512x100 -x linear -o ${file_t2w_seg}.nii.gz;
+sct_crop_image -i ${file_t2w_seg}.nii.gz -ref ${cropped_img} -o ${file_t2w_seg}.nii.gz;
+sct_resample -i ${file_t2w_seg}.nii.gz -vox 96x512x16 -x linear -o ${file_t2w_seg}.nii.gz;
+sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+sct_image -i ${file_t2w_seg}.nii.gz -setorient AIL;
+
+cd $PATH_RESULTS/data/$SUBJECT/anat/
+sct_resample -i ${file_t2w}.nii.gz -vox 96x512x16 -x spline -o ${file_t2w}.nii.gz;

merge_labels.sh

@@ -0,0 +1,81 @@
+#!/bin/bash
+#
+# Pipeline for spinal cord tumor data.
+#
+# Generate sc segmentation, preprocess data before training.
+#
+# Note: All images have .nii extension.
+#
+# Usage:
+#   sct_run_batch <FILEPARAM> process_data.sh
+#
+# Author: Andreanne Lemay
+
+# Uncomment for full verbose
+# set -v
+
+# Immediately exit if error
+set -e
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+FILEPARAM=$2
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# shellcheck disable=SC1090
+source $FILEPARAM
+# Go to results folder, where most of the outputs will be located
+cd $PATH_RESULTS
+# Copy source images and segmentations
+mkdir -p data/derivatives/labels
+cd data
+
+cp -r $PATH_DATA/$SUBJECT .
+cp -r $PATH_DATA/derivatives/labels/$SUBJECT $PATH_RESULTS/data/derivatives/labels
+
+# Go to data labels folder
+cd $PATH_RESULTS/data/derivatives/labels/$SUBJECT/anat/
+
+file_t2w_seg=${SUBJECT}_T2w_seg-tumor
+file_t1w_seg=${SUBJECT}_T1w_seg-tumor
+file_t1w_edema=${SUBJECT}_T1w_edema
+file_t1w_cavity=${SUBJECT}_T1w_cavity
+file_t2w_edema=${SUBJECT}_T2w_edema
+file_t2w_cavity=${SUBJECT}_T2w_cavity
+
+sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+sct_image -i ${file_t2w_seg}.nii.gz -setorient AIL;
+
+sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;
+sct_image -i ${file_t1w_seg}.nii.gz -setorient AIL;
+
+path_edema=`pwd`/${file_t1w_edema}.nii.gz
+if [ -f ${path_edema} ]; then
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+  sct_image -i ${file_t2w_seg}.nii.gz -setorient AIL;
+
+  sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;
+  sct_image -i ${file_t1w_seg}.nii.gz -setorient AIL;
+
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -add ${file_t2w_edema}.nii.gz;
+  sct_maths -i ${file_t1w_edema}.nii.gz -o ${file_t1w_edema}.nii.gz -add ${file_t1w_edema}.nii.gz;
+fi
+
+path_cavity=`pwd`/${file_t1w_cavity}.nii.gz
+if [ -f ${path_cavity} ]; then
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+  sct_image -i ${file_t2w_seg}.nii.gz -setorient AIL;
+
+  sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;
+  sct_image -i ${file_t1w_seg}.nii.gz -setorient AIL;
+
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -add ${file_t2w_cavity}.nii.gz;
+  sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -add ${file_t1w_cavity}.nii.gz;
+fi
+
+sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;

parameters/parameters.sh

@@ -4,19 +4,21 @@
 # Set every other path relative to this path for convenience
 # Do not add "/" at the end. Path should be absolute (i.e. do not use "~")
 # Example:
-export PATH_PARENT="/home/GRAMES.POLYMTL.CA/anlemj/results/dataset"
+
+export PATH_PARENT="/home/andreanne/Documents/dataset"
 
 
 # Path to the folder containing the BIDS dataset.
 # Do not add "/" at the end. Path should be absolute (i.e. do not use "~")
-export PATH_DATA="$PATH_PARENT/sctumor_BIDS"
+export PATH_DATA="$PATH_PARENT/new_labels320/data"
 
 # If each subject folder starts with a prefix, indicate it here. Otherwise, set to ""
 SUBJECT_PREFIX="sub-"
 
 # Paths to where to save the new dataset.
 # Do not add "/" at the end. Path should be absolute (i.e. do not use "~")
-export PATH_RESULTS="$PATH_PARENT/results"
+# Endroit où seront copiees les données
+export PATH_RESULTS="$PATH_PARENT/reg"
 export PATH_QC="$PATH_RESULTS/qc"
 export PATH_LOG="$PATH_RESULTS/log"
 
@@ -36,8 +38,8 @@ export PATH_LOG="$PATH_RESULTS/log"
 # Number of jobs for parallel processing
 # To know the number of available cores, run: getconf _NPROCESSORS_ONLN
 # We recommend not using more than half the number of available cores.
-export JOBS=4
+export JOBS=1
 
 # Number of jobs for ANTs routine. Set to 1 if ANTs functions crash when CPU saturates.
-export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
 

process_data.sh

@@ -26,6 +26,7 @@ FILEPARAM=$2
 
 # SCRIPT STARTS HERE
 # ==============================================================================
+# shellcheck disable=SC1090
 source $FILEPARAM
 # Go to results folder, where most of the outputs will be located
 cd $PATH_RESULTS
@@ -36,19 +37,75 @@ cd data
 cp -r $PATH_DATA/$SUBJECT .
 cp -r $PATH_DATA/derivatives/labels/$SUBJECT $PATH_RESULTS/data/derivatives/labels
 
-cd $PATH_RESULTS/data/derivatives/labels/$SUBJECT/anat/
-
-file_t2w_seg=${SUBJECT}_T2w_seg-tumor
-file_t1w_seg=${SUBJECT}_T1w_seg-tumor
-#
-sct_resample -i ${file_t2w_seg}.nii.gz -vox 512x512x11 -x spline -o ${file_t2w_seg}.nii.gz
-sct_resample -i ${file_t1w_seg}.nii.gz -vox 512x512x11 -x spline -o ${file_t1w_seg}.nii.gz
-
 # Go to data folder
 cd $PATH_RESULTS/data/$SUBJECT/anat/
 ## Setup file names
 file_t2w=${SUBJECT}_T2w
 file_t1w=${SUBJECT}_T1w
-sct_resample -i ${file_t2w}.nii.gz -vox 512x512x11 -x spline -o ${file_t2w}.nii.gz
-sct_resample -i ${file_t1w}.nii.gz -vox 512x512x11 -x spline -o ${file_t1w}.nii.gz
+
+path_t1w=`pwd`/${file_t1w}.nii.gz
+
+sct_image -i ${file_t2w}.nii.gz -setorient AIL
+sct_resample -i ${file_t2w}.nii.gz -vox 320x320x16 -x spline -o ${file_t2w}.nii.gz;
+sct_maths -i ${file_t2w}.nii.gz -o ${file_t2w}.nii.gz -bin 0.9;
+
+if [ -f ${path_t1w} ]; then
+  sct_image -i ${file_t1w}.nii.gz -setorient AIL
+  sct_resample -i ${file_t1w}.nii.gz -vox 320x320x16 -x spline -o ${file_t1w}.nii.gz;
+  sct_maths -i ${file_t1w}.nii.gz -o ${file_t1w}.nii.gz -bin 0.9;
+fi
+
+cd $PATH_RESULTS/data/derivatives/labels/$SUBJECT/anat/
+
+file_t2w_seg=${SUBJECT}_T2w_seg-tumor
+file_t1w_seg=${SUBJECT}_T1w_seg-tumor
+file_t1w_edema=${SUBJECT}_T1w_edema
+file_t1w_cavity=${SUBJECT}_T1w_cavity
+file_t2w_edema=${SUBJECT}_T2w_edema
+file_t2w_cavity=${SUBJECT}_T2w_cavity
+
+
+sct_resample -i ${file_t2w_seg}.nii.gz -vox 320x320x16 -x spline -o ${file_t2w_seg}.nii.gz;
+sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+sct_image -i ${file_t2w_seg}.nii.gz -setorient AIL;
+
+sct_resample -i ${file_t1w_seg}.nii.gz -vox 320x320x16 -x spline -o ${file_t1w_seg}.nii.gz;
+sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;
+sct_image -i ${file_t1w_seg}.nii.gz -setorient AIL;
+
+path_edema=`pwd`/${file_t1w_edema}.nii.gz
+if [ -f ${path_edema} ]; then
+  sct_resample -i ${file_t2w_edema}.nii.gz -vox 320x320x16 -x linear -o ${file_t2w_edema}.nii.gz;
+  sct_maths -i ${file_t2w_edema}.nii.gz -o ${file_t2w_edema}.nii.gz -bin 0.9;
+  sct_image -i ${file_t2w_edema}.nii.gz -setorient AIL;
+
+  sct_resample -i ${file_t1w_edema}.nii.gz -vox 320x320x16 -x linear -o ${file_t1w_edema}.nii.gz;
+  sct_maths -i ${file_t1w_edema}.nii.gz -o ${file_t1w_edema}.nii.gz -bin 0.9;
+  sct_image -i ${file_t1w_edema}.nii.gz -setorient AIL;
+
+  # Merge labels
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -add ${file_t2w_edema}.nii.gz;
+  sct_maths -i ${file_t1w_edema}.nii.gz -o ${file_t1w_edema}.nii.gz -add ${file_t1w_edema}.nii.gz;
+fi
+
+path_cavity=`pwd`/${file_t1w_cavity}.nii.gz
+if [ -f ${path_cavity} ]; then
+  sct_resample -i ${file_t2w_cavity}.nii.gz -vox 320x320x16 -x linear -o ${file_t2w_cavity}.nii.gz;
+  sct_maths -i ${file_t2w_cavity}.nii.gz -o ${file_t2w_cavity}.nii.gz -bin 0.9;
+  sct_image -i ${file_t2w_cavity}.nii.gz -setorient AIL;
+
+  sct_resample -i ${file_t1w_cavity}.nii.gz -vox 320x320x16 -x linear -o ${file_t1w_cavity}.nii.gz;
+  sct_maths -i ${file_t1w_cavity}.nii.gz -o ${file_t1w_cavity}.nii.gz -bin 0.9;
+  sct_image -i ${file_t1w_cavity}.nii.gz -setorient AIL;
+
+  # Merge labels
+  sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -add ${file_t2w_cavity}.nii.gz;
+  sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -add ${file_t1w_cavity}.nii.gz;
+fi
+
+sct_maths -i ${file_t2w_seg}.nii.gz -o ${file_t2w_seg}.nii.gz -bin 0.9;
+sct_maths -i ${file_t1w_seg}.nii.gz -o ${file_t1w_seg}.nii.gz -bin 0.9;
+
+
+
 

register_data.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+#
+# Pipeline for spinal cord tumor data.
+#
+# Generate sc segmentation, preprocess data before training.
+#
+# Note: All images have .nii extension.
+#
+# Usage:
+#   sct_run_batch <FILEPARAM> process_data.sh
+#
+# Author: Andreanne Lemay
+
+# Uncomment for full verbose
+# set -v
+
+# Immediately exit if error
+set -e
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+FILEPARAM=$2
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# shellcheck disable=SC1090
+source $FILEPARAM
+# Go to results folder, where most of the outputs will be located
+cd $PATH_RESULTS
+# Copy source images and segmentations
+mkdir -p data/derivatives/labels
+cd data
+
+cp -r $PATH_DATA/$SUBJECT .
+cp -r $PATH_DATA/derivatives/labels/$SUBJECT $PATH_RESULTS/data/derivatives/labels
+
+# Go to data folder
+cd $PATH_RESULTS/data/$SUBJECT/anat/
+## Setup file names
+file_t2w=${SUBJECT}_T2w
+file_t1w=${SUBJECT}_T1w
+path_t1w=`pwd`/${file_t1w}.nii.gz
+
+if [ -f ${path_t1w} ]; then
+  sct_register_multimodal -i ${file_t1w}.nii.gz -d ${file_t2w}.nii.gz -x spline
+  mv ${file_t2w}_reg.nii.gz ${file_t2w}.nii.gz
+  mv ${file_t1w}_reg.nii.gz ${file_t1w}.nii.gz
+  warp_T2w2T1w=`pwd`/warp_${file_t2w}2${file_t1w}.nii.gz
+  warp_T1w2T2w=`pwd`/warp_${file_t1w}2${file_t2w}.nii.gz
+fi
+
+cd $PATH_RESULTS/data/derivatives/labels/$SUBJECT/anat/
+
+file_t2w_seg=${SUBJECT}_T2w_seg-tumor
+file_t1w_seg=${SUBJECT}_T1w_seg-tumor
+
+if [ -f ${path_t1w} ]; then
+  sct_apply_transfo -i ${file_t1w_seg}.nii.gz -d ${file_t2w_seg}.nii.gz -w ${warp_T1w2T2w} -o ${file_t1w_seg}.nii.gz -x linear
+  sct_apply_transfo -i ${file_t2w_seg}.nii.gz -d ${file_t1w_seg}.nii.gz -w ${warp_T2w2T1w} -o ${file_t2w_seg}.nii.gz -x linear
+fi