adding preprocessing script

.gitignore

@@ -0,0 +1 @@
+**/.DS_Store

README.md

@@ -14,13 +14,13 @@ git clone https://github.com/ivadomed/model_seg_csf_epi.git
 
 ## Get the data
 
-- [email protected]:datasets/data_gre-epi
+- [email protected]:datasets/mni-bmpd
 
 ### Example calls to get the data
 
 ~~~
-git clone [email protected]:datasets/data_gre-epi
-cd data_gre-epi
+git clone [email protected]:datasets/mni-bmpd
+cd mni-bmpd
 git annex get .
 cd ..
 ~~~

scripts/preprocess.sh

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+#!/bin/bash
+# Functionality: Resizes the images as per the dimensions of the segmentations
+# Usage: preprocess_data.sh
+#
+#
+# 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

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}
+
+