From c9275a45efca42f2a53936d4cc1008a1743d3f58 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Thu, 14 Sep 2023 15:32:27 -0400
Subject: [PATCH 1/6] Add script to crop the input image, spinal cord GT, and
 lesion GT around the spinal cord segmentation (based on the dilated spinal
 cord GT)

---
 dataset-conversion/crop_around_sc.sh | 157 +++++++++++++++++++++++++++
 1 file changed, 157 insertions(+)
 create mode 100644 dataset-conversion/crop_around_sc.sh

diff --git a/dataset-conversion/crop_around_sc.sh b/dataset-conversion/crop_around_sc.sh
new file mode 100644
index 00000000..18415e8d
--- /dev/null
+++ b/dataset-conversion/crop_around_sc.sh
@@ -0,0 +1,157 @@
+#!/bin/bash
+#
+# The script crops the input image, spinal cord GT, and lesion GT around the spinal cord segmentation (based on the
+# dilated spinal cord GT)
+#
+# Usage:
+#     sct_run_batch -config config.json
+#
+# Example of config.json:
+# {
+#  "path_data"   : "<PATH_TO_DATASET>",
+#  "path_output" : "<PATH_TO_DATASET>_2023-09-14",
+#  "script"      : "<PATH_TO_REPO>/model_seg_sci/dataset-conversion/crop_around_sc.sh",
+#  "jobs"        : 8
+# }
+#
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+# PATH_DATA_PROCESSED="~/data_processed"
+# PATH_RESULTS="~/results"
+# PATH_LOG="~/log"
+# PATH_QC="~/qc"
+#
+# Author: Jan Valosek, Naga Karthik
+#
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+set -e -o pipefail
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Print retrieved variables from the sct_run_batch script to the log (to allow easier debug)
+echo "Retrieved variables from from the caller sct_run_batch:"
+echo "PATH_DATA: ${PATH_DATA}"
+echo "PATH_DATA_PROCESSED: ${PATH_DATA_PROCESSED}"
+echo "PATH_RESULTS: ${PATH_RESULTS}"
+echo "PATH_LOG: ${PATH_LOG}"
+echo "PATH_QC: ${PATH_QC}"
+
+SUBJECT=$1
+
+echo "SUBJECT: ${SUBJECT}"
+
+
+# CONVENIENCE FUNCTIONS
+# ======================================================================================================================
+# Copy GT spinal cord segmentation
+copy_gt_sc(){
+  local file="$1"
+  # Construct file name to GT segmentation located under derivatives/labels
+  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file}_seg-manual.nii.gz"
+  echo ""
+  echo "Looking for manual segmentation: $FILESEGMANUAL"
+  if [[ -e $FILESEGMANUAL ]]; then
+      echo "Found! Copying ..."
+      rsync -avzh $FILESEGMANUAL ${file}_seg-manual.nii.gz
+  else
+      echo "File ${FILESEGMANUAL}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log
+      echo "ERROR: Manual GT segmentation ${FILESEGMANUAL}.nii.gz does not exist. Exiting."
+      exit 1
+  fi
+}
+
+# Copy GT lesion segmentation
+copy_gt_lesion(){
+  local file="$1"
+  # Construct file name to GT segmentation located under derivatives/labels
+  FILELESIONMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file}_lesion-manual.nii.gz"
+  echo ""
+  echo "Looking for manual segmentation: $FILELESIONMANUAL"
+  if [[ -e $FILELESIONMANUAL ]]; then
+      echo "Found! Copying ..."
+      rsync -avzh $FILELESIONMANUAL ${file}_lesion-manual.nii.gz
+  else
+      echo "File ${FILELESIONMANUAL}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log
+      echo "ERROR: Manual GT segmentation ${FILELESIONMANUAL}.nii.gz does not exist. Exiting."
+      exit 1
+  fi
+}
+
+
+# ------------------------------------------------------------------------------
+# SCRIPT STARTS HERE
+# ------------------------------------------------------------------------------
+# get starting time:
+start=`date +%s`
+
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+# Copy source T2w images
+# Note: we use '/./' in order to include the sub-folder 'ses-0X'
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+if [[ $SUBJECT =~ "sub-zh" ]]; then
+  # for sci-zurich, copy only sagittal T2w to save space
+  rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT//[\/]/_}_*sag_T2w.* .
+else
+  rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT//[\/]/_}_*T2w.* .
+fi
+
+# Go to subject folder for source images
+cd ${SUBJECT}/anat
+
+# ------------------------------------------------------------------------------
+# T2w
+# ------------------------------------------------------------------------------
+# sci-zurich
+if [[ $SUBJECT =~ "sub-zh" ]]; then
+    # We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+    file_t2="${SUBJECT//[\/]/_}"_acq-sag_T2w
+# sci-colorado
+else
+    file_t2="${SUBJECT}"_T2w
+fi
+# ------------------------------------------------------------------------------
+# T2w
+# ------------------------------------------------------------------------------
+
+# Copy GT spinal cord and lesion segmentations
+copy_gt_sc "${file_t2}"
+copy_gt_lesion "${file_t2}"
+
+# Dilate spinal cord mask
+sct_maths -i ${file_t2}_seg.nii.gz -dilate 5 -shape ball -o ${file_sag}_seg-manual_dilate.nii.gz
+
+# Use the dilated mask to crop the original image
+sct_crop_image -i ${file_t2}.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_crop.nii.gz
+
+# Use the dilated mask to crop the spinal cord GT
+sct_crop_image -i ${file_t2}_seg-manual.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_seg-manual_crop.nii.gz
+
+# Use the dilated mask to crop the lesion GT
+sct_crop_image -i ${file_t2}_lesion-manual.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_lesion-manual_crop.nii.gz
+
+# Generate QC to assess the cropping
+sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -p sct_deepseg_sc -qc-subject ${SUBJECT} -qc-dataset ${DATASET}
+
+# ------------------------------------------------------------------------------
+# End
+# ------------------------------------------------------------------------------
+
+# Display results (to easily compare integrity across SCT versions)
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"

From c88c3fb1b424c71965d465750f5ae43ed2a5aef7 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Thu, 14 Sep 2023 16:56:25 -0400
Subject: [PATCH 2/6] Fix typo in filename

---
 dataset-conversion/crop_around_sc.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/dataset-conversion/crop_around_sc.sh b/dataset-conversion/crop_around_sc.sh
index 18415e8d..31b57a59 100644
--- a/dataset-conversion/crop_around_sc.sh
+++ b/dataset-conversion/crop_around_sc.sh
@@ -131,16 +131,17 @@ copy_gt_lesion "${file_t2}"
 sct_maths -i ${file_t2}_seg.nii.gz -dilate 5 -shape ball -o ${file_sag}_seg-manual_dilate.nii.gz
 
 # Use the dilated mask to crop the original image
-sct_crop_image -i ${file_t2}.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_crop.nii.gz
+sct_crop_image -i ${file_t2}.nii.gz -m ${file_t2}_seg-manual_dilate.nii.gz -o ${file_t2}_crop.nii.gz
 
 # Use the dilated mask to crop the spinal cord GT
-sct_crop_image -i ${file_t2}_seg-manual.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_seg-manual_crop.nii.gz
+sct_crop_image -i ${file_t2}_seg-manual.nii.gz -m ${file_t2}_seg-manual_dilate.nii.gz -o ${file_t2}_seg-manual_crop.nii.gz
 
 # Use the dilated mask to crop the lesion GT
-sct_crop_image -i ${file_t2}_lesion-manual.nii.gz -m ${file_sag}_seg-manual_dilate.nii.gz -o ${file_t2}_lesion-manual_crop.nii.gz
+sct_crop_image -i ${file_t2}_lesion-manual.nii.gz -m ${file_t2}_seg-manual_dilate.nii.gz -o ${file_t2}_lesion-manual_crop.nii.gz
 
 # Generate QC to assess the cropping
-sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -p sct_deepseg_sc -qc-subject ${SUBJECT} -qc-dataset ${DATASET}
+sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -d ${file_t2}_seg-manual_crop.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT}
+sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -d ${file_t2}_lesion-manual_crop.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT}
 
 # ------------------------------------------------------------------------------
 # End

From 667e73ed76152a1f3a68fcfb327b124dd200e2f6 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Thu, 14 Sep 2023 16:56:45 -0400
Subject: [PATCH 3/6] Change dilate from 5 to 10

---
 dataset-conversion/crop_around_sc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 mode change 100644 => 100755 dataset-conversion/crop_around_sc.sh

diff --git a/dataset-conversion/crop_around_sc.sh b/dataset-conversion/crop_around_sc.sh
old mode 100644
new mode 100755
index 31b57a59..e6479ede
--- a/dataset-conversion/crop_around_sc.sh
+++ b/dataset-conversion/crop_around_sc.sh
@@ -128,7 +128,7 @@ copy_gt_sc "${file_t2}"
 copy_gt_lesion "${file_t2}"
 
 # Dilate spinal cord mask
-sct_maths -i ${file_t2}_seg.nii.gz -dilate 5 -shape ball -o ${file_sag}_seg-manual_dilate.nii.gz
+sct_maths -i ${file_t2}_seg-manual.nii.gz -dilate 10 -shape ball -o ${file_t2}_seg-manual_dilate.nii.gz
 
 # Use the dilated mask to crop the original image
 sct_crop_image -i ${file_t2}.nii.gz -m ${file_t2}_seg-manual_dilate.nii.gz -o ${file_t2}_crop.nii.gz

From 7ca8aad3823607532c2b2ab956d92674f61a956b Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Thu, 14 Sep 2023 16:59:15 -0400
Subject: [PATCH 4/6] Comment out QC for SC -- only lesion QC is relevant.

---
 dataset-conversion/crop_around_sc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dataset-conversion/crop_around_sc.sh b/dataset-conversion/crop_around_sc.sh
index e6479ede..987d8f74 100755
--- a/dataset-conversion/crop_around_sc.sh
+++ b/dataset-conversion/crop_around_sc.sh
@@ -141,7 +141,7 @@ sct_crop_image -i ${file_t2}_lesion-manual.nii.gz -m ${file_t2}_seg-manual_dilat
 
 # Generate QC to assess the cropping
 sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -d ${file_t2}_seg-manual_crop.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT}
-sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -d ${file_t2}_lesion-manual_crop.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT}
+#sct_qc -i ${file_t2}_crop.nii.gz -s ${file_t2}_seg-manual_crop.nii.gz -d ${file_t2}_lesion-manual_crop.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT}
 
 # ------------------------------------------------------------------------------
 # End

From 6c4be8e78a5ecae6a8eeea48e84d60e98c6d57a6 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Thu, 14 Sep 2023 18:32:00 -0400
Subject: [PATCH 5/6] Add info about cropping to the README.md

---
 dataset-conversion/README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/dataset-conversion/README.md b/dataset-conversion/README.md
index d35c34f8..74785ed9 100644
--- a/dataset-conversion/README.md
+++ b/dataset-conversion/README.md
@@ -71,3 +71,8 @@ This command takes as inputs the list of RPI-reoriented datasets, the output pat
 
 > **Note**
 > This assumes the nnUNet has been successfully installed and the necessary nnUNet-related environment variables have been set. Please refer to the [nnUNet documentation](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/installation_instructions.md) for more details.
+
+#### Cropping around the spinal cord
+
+The cropping of the input images, spinal cord GT, and lesion GT around the spinal cord segmentation can be done using 
+the `crop_around_sc.sh` script. The cropping is done based on the dilated spinal cord GT.
\ No newline at end of file

From c487f9b7f26c21f833c174a9687d9b01e99e10af Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 18 Sep 2023 16:41:35 -0400
Subject: [PATCH 6/6] Update description

---
 dataset-conversion/crop_around_sc.sh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/dataset-conversion/crop_around_sc.sh b/dataset-conversion/crop_around_sc.sh
index 987d8f74..1b538f48 100755
--- a/dataset-conversion/crop_around_sc.sh
+++ b/dataset-conversion/crop_around_sc.sh
@@ -3,6 +3,10 @@
 # The script crops the input image, spinal cord GT, and lesion GT around the spinal cord segmentation (based on the
 # dilated spinal cord GT)
 #
+#
+# Note that the script outputs the cropped images (images, SC GT, lesion GT) in the data_processed folder, which is
+# not BIDS-compatible.
+#
 # Usage:
 #     sct_run_batch -config config.json
 #
@@ -14,6 +18,8 @@
 #  "jobs"        : 8
 # }
 #
+# Note that <PATH_TO_DATASET> has to have both SC and lesion GT in the derivatives/labels folder.
+#
 # The following global variables are retrieved from the caller sct_run_batch
 # but could be overwritten by uncommenting the lines below:
 # PATH_DATA_PROCESSED="~/data_processed"