From 7a19fed150d9c188670a345d65aae34580cb6ec2 Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <robana@rosenberg.neuro.polymtl.ca>
Date: Mon, 28 Nov 2022 01:49:11 -0500
Subject: [PATCH 1/6] adding preprocessing script

---
 preprocessing/preprocess.sh | 85 +++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 preprocessing/preprocess.sh

diff --git a/preprocessing/preprocess.sh b/preprocessing/preprocess.sh
new file mode 100644
index 0000000..439113c
--- /dev/null
+++ b/preprocessing/preprocess.sh
@@ -0,0 +1,85 @@
+#!/bin/bash
+#
+# Process data. 
+#     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
+#     
+#     Crop all images.
+#     Generates soft segmentations.
+# Usage:
+#   ./process_data.sh <SUBJECT>
+#
+#
+# Authors: Rohan Banerjee
+
+# 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"
+
+# Uncomment for full verbose
+set -x
+
+# 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 sct_run_batch 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}”
+
+# Retrieve input params
+SUBJECT=$1
+
+# echo SUBJECT
+
+# Save script path
+PATH_SCRIPT=$PWD
+
+get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# 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 list of participants in processed data folder
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+
+if [[ ! -f "participants.json" ]]; then
+  rsync -avzh $PATH_DATA/participants.json .
+fi
+
+if [[ ! -f "README.md" ]]; then
+  rsync -avzh $PATH_DATA/README.md .
+fi
+
+if [[ ! -f "dataset_description.tsv" ]]; then
+  rsync -avzh $PATH_DATA/dataset_description .
+fi
+
+# Copy source images
+rsync -avzh $PATH_DATA/$SUBJECT .
+
+#copy derivatives
+rsync -avzh $PATH_DATA/derivatives .
+
+# Script starts here
+cd ${SUBJECT}/func
+file_bold=${SUBJECT}_task-rest_bold
+file_bold_seg=${PATH_DATA}/derivatives/labels/${SUBJECT}/func/${SUBJECT}_task-rest_bold_seg-manual
+
+sct_register_multimodal -i ${file_bold}.nii.gz -d ${file_bold_seg}.nii.gz -o ${file_bold}_to_${file_bold}_reg.nii.gz -identity 0
+rm warp_${SUBJECT}_task-rest_bold_seg-manual2${SUBJECT}_task-rest_bold.nii.gz warp_${SUBJECT}_task-rest_bold2${SUBJECT}_task-rest_bold_seg-manual.nii.gz ${SUBJECT}_task-rest_bold.nii.gz
+mv ${file_bold}_to_${file_bold}_reg.nii.gz ${file_bold}.nii.gz

From 5a41bf56fb0c94b622b1a5f3fc1765fcd55a70ed Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <banerjee.rohan98@gmail.com>
Date: Fri, 6 Jan 2023 13:07:44 -0500
Subject: [PATCH 2/6] Update preprocess.sh

---
 preprocessing/preprocess.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/preprocessing/preprocess.sh b/preprocessing/preprocess.sh
index 439113c..90089a9 100644
--- a/preprocessing/preprocess.sh
+++ b/preprocessing/preprocess.sh
@@ -1,12 +1,13 @@
 #!/bin/bash
 #
+#!/bin/bash
+#
 # Process data. 
 #     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
 #     
-#     Crop all images.
-#     Generates soft segmentations.
+# Resizes the images as per the corresponding ground truth dimensions
 # Usage:
-#   ./process_data.sh <SUBJECT>
+#   preprocess_data.sh
 #
 #
 # Authors: Rohan Banerjee

From 0f9e0af4757e737d7787f2ccb1f12e4b6f356e20 Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <banerjee.rohan98@gmail.com>
Date: Fri, 6 Jan 2023 13:08:03 -0500
Subject: [PATCH 3/6] Update preprocess.sh

---
 preprocessing/preprocess.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/preprocessing/preprocess.sh b/preprocessing/preprocess.sh
index 90089a9..6ecba52 100644
--- a/preprocessing/preprocess.sh
+++ b/preprocessing/preprocess.sh
@@ -1,9 +1,6 @@
 #!/bin/bash
 #
 #!/bin/bash
-#
-# Process data. 
-#     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
 #     
 # Resizes the images as per the corresponding ground truth dimensions
 # Usage:

From ab343fac765c8735b6117ec2ab0638be90d2140d Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <robana@rosenberg.neuro.polymtl.ca>
Date: Fri, 6 Jan 2023 16:28:04 -0500
Subject: [PATCH 4/6] added qc_generation script

---
 .gitignore                               |  1 +
 {preprocessing => scripts}/preprocess.sh |  8 ++--
 scripts/qc_generation.sh                 | 56 ++++++++++++++++++++++++
 3 files changed, 62 insertions(+), 3 deletions(-)
 create mode 100644 .gitignore
 rename {preprocessing => scripts}/preprocess.sh (92%)
 create mode 100644 scripts/qc_generation.sh

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..79b5594
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+**/.DS_Store
diff --git a/preprocessing/preprocess.sh b/scripts/preprocess.sh
similarity index 92%
rename from preprocessing/preprocess.sh
rename to scripts/preprocess.sh
index 6ecba52..439113c 100644
--- a/preprocessing/preprocess.sh
+++ b/scripts/preprocess.sh
@@ -1,10 +1,12 @@
 #!/bin/bash
 #
-#!/bin/bash
+# Process data. 
+#     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
 #     
-# Resizes the images as per the corresponding ground truth dimensions
+#     Crop all images.
+#     Generates soft segmentations.
 # Usage:
-#   preprocess_data.sh
+#   ./process_data.sh <SUBJECT>
 #
 #
 # Authors: Rohan Banerjee
diff --git a/scripts/qc_generation.sh b/scripts/qc_generation.sh
new file mode 100644
index 0000000..c1fa652
--- /dev/null
+++ b/scripts/qc_generation.sh
@@ -0,0 +1,56 @@
+#!/bin/bash
+#
+#     
+# Functionality: Generates qc reports for already existing images and their corresponding segmentations/labels     
+# Usage:
+#   sct_run_batch -script qc_generation.sh
+# Output: The index.html in the qc folder will have the qc reports for all the subjects in the data.
+#
+# Authors: Rohan Banerjee
+
+# 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"
+
+# Uncomment for full verbose
+set -x
+
+# 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 sct_run_batch 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}”
+
+# Retrieve input params
+SUBJECT=$1
+
+# echo SUBJECT
+
+# Save script path
+PATH_SCRIPT=$PWD
+
+get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+cd ${SUBJECT}/func
+file_bold=${PATH_DATA}/${SUBJECT}/func/${SUBJECT}_task-rest_bold.nii.gz
+file_bold_seg=${PATH_DATA}/derivatives/labels/${SUBJECT}/func/${SUBJECT}_task-rest_bold_seg-manual.nii.gz
+
+echo "file_bold: ${file_bold}"
+
+sct_qc -i ${file_bold} -s ${file_bold_seg} -p sct_propseg -qc qc -qc-subject ${SUBJECT}
+
+

From 08fe1729497806e01f46bce0fa19dad3a62fe98c Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <banerjee.rohan98@gmail.com>
Date: Fri, 6 Jan 2023 16:31:08 -0500
Subject: [PATCH 5/6] updated preprocess.sh

---
 scripts/preprocess.sh | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/scripts/preprocess.sh b/scripts/preprocess.sh
index 439113c..abe5d6c 100644
--- a/scripts/preprocess.sh
+++ b/scripts/preprocess.sh
@@ -1,12 +1,6 @@
 #!/bin/bash
-#
-# Process data. 
-#     For T1 : From raw images, proceeds to resampling and reorientation to RPI.
-#     
-#     Crop all images.
-#     Generates soft segmentations.
-# Usage:
-#   ./process_data.sh <SUBJECT>
+# Functionality: Resizes the images as per the dimensions of the segmentations
+# Usage: preprocess_data.sh
 #
 #
 # Authors: Rohan Banerjee

From 992587da7401e440aed78aeed578b76a509b041e Mon Sep 17 00:00:00 2001
From: Rohan Banerjee <banerjee.rohan98@gmail.com>
Date: Fri, 6 Jan 2023 18:55:02 -0500
Subject: [PATCH 6/6] Update README.md

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 5ecf0ad..c115dd2 100644
--- a/README.md
+++ b/README.md
@@ -14,13 +14,13 @@ git clone https://github.com/ivadomed/model_seg_csf_epi.git
 
 ## Get the data
 
-- git@data.neuro.polymtl.ca:datasets/data_gre-epi
+- git@data.neuro.polymtl.ca:datasets/mni-bmpd
 
 ### Example calls to get the data
 
 ~~~
-git clone git@data.neuro.polymtl.ca:datasets/data_gre-epi
-cd data_gre-epi
+git clone git@data.neuro.polymtl.ca:datasets/mni-bmpd
+cd mni-bmpd
 git annex get .
 cd ..
 ~~~