From 08786fe9777e53dce3ca5b21b9e361ee380463ea Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 10:13:19 -0500
Subject: [PATCH 01/38] Add python script for conversion of INSPIRED dataset to
 BIDS compliant format

---
 scripts/curate_data_inspired.py | 187 ++++++++++++++++++++++++++++++++
 1 file changed, 187 insertions(+)
 create mode 100644 scripts/curate_data_inspired.py

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
new file mode 100644
index 0000000..22fafc0
--- /dev/null
+++ b/scripts/curate_data_inspired.py
@@ -0,0 +1,187 @@
+# Convert the input non-BIDS INSPIRED dataset to the BIDS compliant dataset
+# The INSPIRED dataset contains data from two centers (Toronto, Zurich) across three pathologies (DCM, SCI, HC)
+# Spinal cord MRI data:
+#       - DWI (A-P and P-A phase encoding)
+#       - T1w sag
+#       - T2w sag
+#       - T2w tra
+#       - T2star tra
+# Brain MRI data:
+#       - DWI (A-P and P-A phase encoding)
+#       - MPM (multi-parameter mapping)
+#
+# Authors: Jan Valosek
+
+import os
+import sys
+import shutil
+import json
+import glob
+import argparse
+
+prefix = 'sub-'
+
+# There are two input datasets: `01` and `02`. `01` represents Toronto, `02` represents Zurich
+# Details: https://github.com/neuropoly/data-management/issues/184#issuecomment-1329250514
+centres_conv_dict = {
+    '01': 'toronto',
+    '02': 'zurich'
+    }
+
+pathologies_conv_dict = {
+    'csm': 'DCM',
+    'hc': 'HC',
+    'sci': 'SCI'
+    }
+
+# Dictionary for image filename conversion
+# Note: we use label `bp-cspine` to differentiate spine imaging from brain
+# Details: BIDS BEP025 Proposal (https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4)
+images_spine_conv_dict = {
+    'dwi.nii.gz': 'dir-AP_bp-cspine_dwi.nii.gz',
+    'dwi.bval': 'dir-AP_bp-cspine_dwi.bval',
+    'dwi.bvec': 'dir-AP_bp-cspine_dwi.bvec',
+    'dwi_reversed_blip.nii.gz': 'dir-PA_bp-cspine_dwi.nii.gz',
+    't1_sag.nii.gz': 'bp-cspine_T1w.nii.gz',
+    't2_sag.nii.gz': 'acq-coronal_bp-cspine_T2w.nii.gz',
+    't2_tra.nii.gz': 'acq-axial_bp-cspine_T2w.nii.gz',
+    'pd_medic.nii.gz': 'bp-cspine_T2star.nii.gz'
+    }
+
+# Dictionary for brain image filename conversion
+images_brain_conv_dict = {
+    'dwi.nii.gz': 'dir-AP_dwi.nii.gz',
+    'dwi.bval': 'dir-AP_dwi.bval',
+    'dwi.bvec': 'dir-AP_dwi.bvec',
+    'dwi_reversed_blip.nii.gz': 'dir-PA_dwi.nii.gz',
+    }
+
+
+def copy_file(path_file_in, path_dir_out, file_out):
+    """
+    Copy file from input non-BIDS dataset to BIDS compliant dataset
+    :param path_file_in: path of the input non-BIDS file which will be copied
+    :param path_dir_out: path of the output BIDS directory; for example sub-torontoDCM001/dwi
+    :param file_out: filename of the output BIDS file; for example 'sub-torontoDCM001_bp-cspine_dir-AP_dwi.nii.gz'
+    :return:
+    """
+    # Make sure that the input file exists, if so, copy it
+    if os.path.isfile(path_file_in):
+        # Create dwi or anat folder if does not exist
+        if not os.path.isdir(path_dir_out):
+            os.makedirs(path_dir_out, exist_ok=True)
+        # Construct path to the output file
+        path_file_out = os.path.join(path_dir_out, file_out)
+        print(f'Copying {path_file_in} to {path_file_out}')
+        shutil.copyfile(path_file_in, path_file_out)
+        create_dummy_json_sidecar_if_does_not_exist(path_file_out)
+
+
+# TODO - do we want to create just a empty json sidecar? Or do we want to include some params there?
+def create_dummy_json_sidecar_if_does_not_exist(path_file_out):
+    # Work only with .nii.gz (i.e., ignore .bval and .bvec files)
+    if path_file_out.endswith('.nii.gz'):
+        path_json_sidecar = path_file_out.replace('.nii.gz', '.json')
+        if not os.path.exists(path_json_sidecar):
+            os.system('touch ' + path_json_sidecar)
+
+
+def read_json_file(path_to_file):
+    """
+    Read json file and fetch relevant parameters (SeriesDescription, SeriesDescription, EchoTime) for MPM images
+    :param path_to_file: path to input json file
+    :return:
+    """
+    with open(path_to_file) as p:
+        loaded_json = json.load(p)
+        series_description = loaded_json['acqpar'][0]['SeriesDescription']
+        flip_angle = loaded_json['acqpar'][0]['SeriesDescription']
+        echo_time = loaded_json['acqpar'][0]['EchoTime']
+        return series_description, flip_angle, echo_time
+
+
+def get_parameters():
+    parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
+    parser.add_argument("-i", "--path-input",
+                        help="Path to folder containing the dataset to convert to BIDS",
+                        required=True)
+    parser.add_argument("-o", "--path-output",
+                        help="Path to the output BIDS folder",
+                        required=True,
+                        )
+    arguments = parser.parse_args()
+    return arguments
+
+
+def main(path_input, path_output):
+    # Check if input path is valid
+    if not os.path.isdir(path_input):
+        print(f'ERROR - {path_input} does not exist.')
+        sys.exit()
+    # Remove output folder if already exists and create an empty one again
+    if os.path.isdir(path_output):
+        shutil.rmtree(path_output)
+    os.makedirs(path_output, exist_ok=True)
+
+    # Loop across centers (01, 02)
+    for centre_in, centre_out in centres_conv_dict.items():
+        # Loop across pathologies (hc, csm, sci)
+        for pathology_in, pathology_out in pathologies_conv_dict.items():
+            # Loop across subjects (001, ...)
+            for sub_index, subject_in in enumerate(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*')),
+                                                   start=1):
+                # If the input subject folder is .tar.gz, extract it
+                if subject_in.endswith('.tar.gz'):
+                    os.system("tar -xf " + subject_in + " --directory " + os.path.join(path_input, centre_in, pathology_in))
+                    # TODO - consider what to do with extracted folders once the BIDS conversion is done.
+                    #  Delete them and keep only original .tar.gz files?
+                    # Remove '.tar.gz' from the subject_in variable
+                    subject_in = subject_in.replace('.tar.gz', '')
+                # Loop across regions (brain or cord)
+                for region in ['brain', 'cord']:
+                    if region == 'cord':
+                        # Loop across files
+                        for image_in, image_out in images_spine_conv_dict.items():
+                            # Construct path to the input file
+                            path_file_in = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl', region, image_in)
+                            # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
+                            subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
+                            # Construct output filename, e.g., 'sub-torontoDCM001_bp-cspine_dir-AP_dwi.nii.gz'
+                            file_out = subject_out + '_' + image_out
+                            # Construct path to the output BIDS compliant directory
+                            if 'dwi' in image_in:
+                                path_dir_out = os.path.join(path_output, subject_out, 'dwi')
+                            else:
+                                path_dir_out = os.path.join(path_output, subject_out, 'anat')
+
+                            # Copy file and create a dummy json sidecar if does not exist
+                            copy_file(path_file_in, path_dir_out, file_out)
+                    elif region == 'brain':
+                        # Loop across files
+                        for image_in, image_out in images_brain_conv_dict.items():
+                            # Construct path to the input file
+                            path_file_in = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl', region, image_in)
+                            # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
+                            subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
+                            # Construct output filename, e.g., 'sub-torontoDCM001_dir-AP_dwi.nii.gz'
+                            file_out = subject_out + '_' + image_out
+                            # Construct path to the output BIDS compliant directory
+                            if 'dwi' in image_in:
+                                path_dir_out = os.path.join(path_output, subject_out, 'dwi')
+
+                            # Copy file and create a dummy json sidecar if does not exist
+                            copy_file(path_file_in, path_dir_out, file_out)
+
+                        # Convert raw MPM images
+                        mpm_raw_folder_path = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl',
+                                                           region, 'mpm_raw')
+                        if os.path.isdir(mpm_raw_folder_path):
+                            # Loop across individual MPM files
+                            for mpm_file in glob.glob(os.path.join(mpm_raw_folder_path, '*.nii*')):
+                                series_description, flip_angle, echo_time = read_json_file(mpm_file.replace('.nii', '.json'))
+                                # TODO - finish MPM files conversion
+
+
+if __name__ == "__main__":
+    args = get_parameters()
+    main(args.path_input, args.path_output)

From 37038dc030dac96c2b0fd9f942441deb55f4bd91 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 14:07:55 -0500
Subject: [PATCH 02/38] Implement MPM image BIDSification

---
 scripts/curate_data_inspired.py | 69 ++++++++++++++++++++++++++++-----
 1 file changed, 60 insertions(+), 9 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 22fafc0..6938bba 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -13,6 +13,7 @@
 # Authors: Jan Valosek
 
 import os
+import re
 import sys
 import shutil
 import json
@@ -74,7 +75,9 @@ def copy_file(path_file_in, path_dir_out, file_out):
         path_file_out = os.path.join(path_dir_out, file_out)
         print(f'Copying {path_file_in} to {path_file_out}')
         shutil.copyfile(path_file_in, path_file_out)
-        create_dummy_json_sidecar_if_does_not_exist(path_file_out)
+        # Create a dummy json sidecar for all files except of MPM (for MPM we copy original .json sidecars)
+        if 'MPM' not in file_out:
+            create_dummy_json_sidecar_if_does_not_exist(path_file_out)
 
 
 # TODO - do we want to create just a empty json sidecar? Or do we want to include some params there?
@@ -95,11 +98,54 @@ def read_json_file(path_to_file):
     with open(path_to_file) as p:
         loaded_json = json.load(p)
         series_description = loaded_json['acqpar'][0]['SeriesDescription']
-        flip_angle = loaded_json['acqpar'][0]['SeriesDescription']
+        flip_angle = loaded_json['acqpar'][0]['FlipAngle']
         echo_time = loaded_json['acqpar'][0]['EchoTime']
         return series_description, flip_angle, echo_time
 
 
+def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
+    """
+    Construct BIDS compliant filename for MPM images, e.g. 'acq-T1w_echo-1_flip-1_mt-off_MPM'
+    Then, call function to copy the input non-BIDS MPM file to BIDS compliant MPM file
+    :param mpm_files_dict: dict with SeriesDescription, FlipAngle, and EchoTime across all MPM files
+    :param path_output: path to output BIDS folder
+    :param subject_out: output BIDS subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
+    :return:
+    """
+    mpm_to_bids = dict()
+    # Get unique values
+    unique_SeriesDescription = set([key[0] for key in mpm_files_dict.keys()])
+    unique_FlipAngle = set([key[1] for key in mpm_files_dict.keys()])
+    unique_EchoTime = set([key[2] for key in mpm_files_dict.keys()])
+    # Construct BIDS compliant filename, e.g. 'acq-T1w_echo-1_flip-1_mt-off_MPM'
+    for echo_idx, echo_time in enumerate(unique_EchoTime, start=1):
+        for flip_idx, flip_angle in enumerate(unique_FlipAngle, start=1):
+            for series_description in unique_SeriesDescription:
+                if '_mt_' in series_description:
+                    BIDS_label = 'acq-MTw' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-on_MPM'
+                elif '_pd_' in series_description:
+                    BIDS_label = 'acq-PDw' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-off_MPM'
+                elif '_t1_' in series_description:
+                    BIDS_label = 'acq-T1w' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-off_MPM'
+                # Find original MPM filename
+                if (series_description, flip_angle, echo_time) in mpm_files_dict.keys():
+                    mpm_file = mpm_files_dict[(series_description, flip_angle, echo_time)]
+                    mpm_to_bids[mpm_file] = BIDS_label
+
+    # Construct path to the output BIDS compliant directory
+    path_dir_out = os.path.join(path_output, subject_out, 'anat')
+    # Copy individual mpm raw files to the output BIDS directory
+    for sequence_params, path_file_in in mpm_files_dict.items():
+        label_out = mpm_to_bids[path_file_in]               # e.g., 'acq-MTw_echo-1_flip-1_mt-on_MPM'
+        # Construct output filename, e.g., 'sub-torontoDCM001_acq-MTw_echo-1_flip-1_mt-on_MPM.nii.gz'
+        file_out = subject_out + '_' + label_out + '.nii.gz'
+        # Copy MPM nii file
+        copy_file(path_file_in, path_dir_out, file_out)
+        # Copy MPM json sidecar
+        # Note: re.sub has to be used instead of .replace to match both '.nii' and '.nii.gz'
+        copy_file(re.sub('.nii(.gz)*', '.json', path_file_in), path_dir_out, file_out.replace('.nii.gz', '.json'))
+
+
 def get_parameters():
     parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
     parser.add_argument("-i", "--path-input",
@@ -139,13 +185,13 @@ def main(path_input, path_output):
                     subject_in = subject_in.replace('.tar.gz', '')
                 # Loop across regions (brain or cord)
                 for region in ['brain', 'cord']:
+                    # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
+                    subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
                     if region == 'cord':
                         # Loop across files
                         for image_in, image_out in images_spine_conv_dict.items():
                             # Construct path to the input file
                             path_file_in = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl', region, image_in)
-                            # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
-                            subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
                             # Construct output filename, e.g., 'sub-torontoDCM001_bp-cspine_dir-AP_dwi.nii.gz'
                             file_out = subject_out + '_' + image_out
                             # Construct path to the output BIDS compliant directory
@@ -161,8 +207,6 @@ def main(path_input, path_output):
                         for image_in, image_out in images_brain_conv_dict.items():
                             # Construct path to the input file
                             path_file_in = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl', region, image_in)
-                            # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
-                            subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
                             # Construct output filename, e.g., 'sub-torontoDCM001_dir-AP_dwi.nii.gz'
                             file_out = subject_out + '_' + image_out
                             # Construct path to the output BIDS compliant directory
@@ -172,14 +216,21 @@ def main(path_input, path_output):
                             # Copy file and create a dummy json sidecar if does not exist
                             copy_file(path_file_in, path_dir_out, file_out)
 
-                        # Convert raw MPM images
+                        # Process raw MPM images
                         mpm_raw_folder_path = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl',
                                                            region, 'mpm_raw')
                         if os.path.isdir(mpm_raw_folder_path):
+                            mpm_files_dict = dict()
                             # Loop across individual MPM files
                             for mpm_file in glob.glob(os.path.join(mpm_raw_folder_path, '*.nii*')):
-                                series_description, flip_angle, echo_time = read_json_file(mpm_file.replace('.nii', '.json'))
-                                # TODO - finish MPM files conversion
+                                # Get SeriesDescription, FlipAngle, and EchoTime for each MPM file
+                                # Note: re.sub has to be used instead of .replace to match both '.nii' and '.nii.gz'
+                                series_description, flip_angle, echo_time = read_json_file(re.sub('.nii(.gz)*', '.json', mpm_file))
+                                # Collect SeriesDescription, FlipAngle, and EchoTime across all MPM files
+                                mpm_files_dict[series_description, flip_angle, echo_time] = mpm_file
+
+                            # Construct BIDS compliant filename for MPM images
+                            construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out)
 
 
 if __name__ == "__main__":

From 336ad1082e5eb32878b5adbc5c9a72a3ba7acb9b Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 16:45:32 -0500
Subject: [PATCH 03/38] Make sure that input args have abs path

---
 scripts/curate_data_inspired.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 6938bba..51f4af6 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -160,6 +160,12 @@ def get_parameters():
 
 
 def main(path_input, path_output):
+    # Make sure that input args are absolute paths
+    if os.path.isdir(path_input):
+        path_input = os.path.abspath(path_input)
+    if os.path.isdir(path_output):
+        path_output = os.path.abspath(path_output)
+
     # Check if input path is valid
     if not os.path.isdir(path_input):
         print(f'ERROR - {path_input} does not exist.')

From 3e231d30d30a4e861378335ab049ff8a8010bbf0 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 16:46:11 -0500
Subject: [PATCH 04/38] Match also upper case in MPM json sidecars

---
 scripts/curate_data_inspired.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 51f4af6..cbd6205 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -121,11 +121,11 @@ def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
     for echo_idx, echo_time in enumerate(unique_EchoTime, start=1):
         for flip_idx, flip_angle in enumerate(unique_FlipAngle, start=1):
             for series_description in unique_SeriesDescription:
-                if '_mt_' in series_description:
+                if '_mt_' in series_description or '_MT_' in series_description:
                     BIDS_label = 'acq-MTw' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-on_MPM'
-                elif '_pd_' in series_description:
+                elif '_pd_' in series_description or '_PD_' in series_description:
                     BIDS_label = 'acq-PDw' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-off_MPM'
-                elif '_t1_' in series_description:
+                elif '_t1_' in series_description or '_T1_' in series_description:
                     BIDS_label = 'acq-T1w' + '_echo-' + str(echo_idx) + '_flip-' + str(flip_idx) + '_mt-off_MPM'
                 # Find original MPM filename
                 if (series_description, flip_angle, echo_time) in mpm_files_dict.keys():

From 0df6da572d6711351a0f881a701d8e22dd413aaa Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 16:57:39 -0500
Subject: [PATCH 05/38] Fix condition when there are no json sidecars for MPM
 images

---
 scripts/curate_data_inspired.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index cbd6205..3ad375a 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -231,12 +231,20 @@ def main(path_input, path_output):
                             for mpm_file in glob.glob(os.path.join(mpm_raw_folder_path, '*.nii*')):
                                 # Get SeriesDescription, FlipAngle, and EchoTime for each MPM file
                                 # Note: re.sub has to be used instead of .replace to match both '.nii' and '.nii.gz'
-                                series_description, flip_angle, echo_time = read_json_file(re.sub('.nii(.gz)*', '.json', mpm_file))
-                                # Collect SeriesDescription, FlipAngle, and EchoTime across all MPM files
-                                mpm_files_dict[series_description, flip_angle, echo_time] = mpm_file
+                                json_file = re.sub('.nii(.gz)*', '.json', mpm_file)
+                                # Make sure json sidecar exist
+                                if os.path.isfile(json_file):
+                                    series_description, flip_angle, echo_time = read_json_file(json_file)
+                                    # Collect SeriesDescription, FlipAngle, and EchoTime across all MPM files
+                                    mpm_files_dict[series_description, flip_angle, echo_time] = mpm_file
 
                             # Construct BIDS compliant filename for MPM images
-                            construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out)
+                            if bool(mpm_files_dict):
+                                construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out)
+                            # In some cases, there are no json sidecars for MPM images, thus mpm_files_dict is empty
+                            else:
+                                print(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
+                                      f'Skipping this subject.')
 
 
 if __name__ == "__main__":

From 0c17d8c9d79f09022e04ffcb18f20d338a583795 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Tue, 29 Nov 2022 19:14:50 -0500
Subject: [PATCH 06/38] Save conversion progress to log

---
 scripts/curate_data_inspired.py | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 3ad375a..61c9e90 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -19,6 +19,14 @@
 import json
 import glob
 import argparse
+import logging
+import datetime
+
+# Initialize logging
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)  # default: logging.DEBUG, logging.INFO
+hdlr = logging.StreamHandler(sys.stdout)
+logging.root.addHandler(hdlr)
 
 prefix = 'sub-'
 
@@ -73,7 +81,7 @@ def copy_file(path_file_in, path_dir_out, file_out):
             os.makedirs(path_dir_out, exist_ok=True)
         # Construct path to the output file
         path_file_out = os.path.join(path_dir_out, file_out)
-        print(f'Copying {path_file_in} to {path_file_out}')
+        logger.info(f'Copying {path_file_in} to {path_file_out}')
         shutil.copyfile(path_file_in, path_file_out)
         # Create a dummy json sidecar for all files except of MPM (for MPM we copy original .json sidecars)
         if 'MPM' not in file_out:
@@ -175,6 +183,17 @@ def main(path_input, path_output):
         shutil.rmtree(path_output)
     os.makedirs(path_output, exist_ok=True)
 
+    FNAME_LOG = os.path.join(path_output, 'bids_conversion.log')
+    # Dump log file there
+    if os.path.exists(FNAME_LOG):
+        os.remove(FNAME_LOG)
+    fh = logging.FileHandler(os.path.join(os.path.abspath(os.curdir), FNAME_LOG))
+    logging.root.addHandler(fh)
+    print("INFO: log file will be saved to {}".format(FNAME_LOG))
+
+    # Print current time and date to log file
+    logger.info('\nAnalysis started at {}'.format(datetime.datetime.now()))
+
     # Loop across centers (01, 02)
     for centre_in, centre_out in centres_conv_dict.items():
         # Loop across pathologies (hc, csm, sci)
@@ -184,6 +203,7 @@ def main(path_input, path_output):
                                                    start=1):
                 # If the input subject folder is .tar.gz, extract it
                 if subject_in.endswith('.tar.gz'):
+                    logger.info(f'Unpacking tar archive for {subject_in}...')
                     os.system("tar -xf " + subject_in + " --directory " + os.path.join(path_input, centre_in, pathology_in))
                     # TODO - consider what to do with extracted folders once the BIDS conversion is done.
                     #  Delete them and keep only original .tar.gz files?
@@ -243,8 +263,8 @@ def main(path_input, path_output):
                                 construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out)
                             # In some cases, there are no json sidecars for MPM images, thus mpm_files_dict is empty
                             else:
-                                print(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
-                                      f'Skipping this subject.')
+                                logger.warning(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
+                                               f'Skipping this subject.')
 
 
 if __name__ == "__main__":

From 1814879d2913438bdcfc03246d75616c0fa06c8d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 30 Nov 2022 13:36:52 -0500
Subject: [PATCH 07/38] Write participants.tsv file

---
 scripts/curate_data_inspired.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 61c9e90..acf7f90 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -15,6 +15,7 @@
 import os
 import re
 import sys
+import csv
 import shutil
 import json
 import glob
@@ -154,6 +155,22 @@ def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
         copy_file(re.sub('.nii(.gz)*', '.json', path_file_in), path_dir_out, file_out.replace('.nii.gz', '.json'))
 
 
+def write_participants_tsv(participants_tsv_list, path_output):
+    """
+    Write participants.tsv file
+    :param participants_tsv_list: list containing [subject_out, pathology_out, subject_in, centre_in, centre_out],
+    example:[sub-torontoDCM001, DCM, 001, 01, toronto]
+    :param path_output: path to the output BIDS folder
+    :return:
+    """
+    with open(os.path.join(path_output + '/participants.tsv'), 'w') as tsv_file:
+        tsv_writer = csv.writer(tsv_file, delimiter='\t', lineterminator='\n')
+        tsv_writer.writerow(['participant_id', 'pathology', 'data_id', 'institution_id', 'institution'])
+        for item in participants_tsv_list:
+            tsv_writer.writerow(item)
+        logger.info(f'participants.tsv created in {path_output}')
+
+
 def get_parameters():
     parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
     parser.add_argument("-i", "--path-input",
@@ -194,6 +211,9 @@ def main(path_input, path_output):
     # Print current time and date to log file
     logger.info('\nAnalysis started at {}'.format(datetime.datetime.now()))
 
+    # Initialize list for participants.tsv
+    participants_tsv_list = list()
+
     # Loop across centers (01, 02)
     for centre_in, centre_out in centres_conv_dict.items():
         # Loop across pathologies (hc, csm, sci)
@@ -266,6 +286,10 @@ def main(path_input, path_output):
                                 logger.warning(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
                                                f'Skipping this subject.')
 
+                participants_tsv_list.append([subject_out, pathology_out, subject_in.split(sep='/')[-1], centre_in, centre_out])
+
+    write_participants_tsv(participants_tsv_list, path_output)
+
 
 if __name__ == "__main__":
     args = get_parameters()

From 36a5b8956424c88ee302a000cce2192b91a48aeb Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 30 Nov 2022 13:37:18 -0500
Subject: [PATCH 08/38] Comments clarification

---
 scripts/curate_data_inspired.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index acf7f90..34ac010 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -117,7 +117,7 @@ def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
     Construct BIDS compliant filename for MPM images, e.g. 'acq-T1w_echo-1_flip-1_mt-off_MPM'
     Then, call function to copy the input non-BIDS MPM file to BIDS compliant MPM file
     :param mpm_files_dict: dict with SeriesDescription, FlipAngle, and EchoTime across all MPM files
-    :param path_output: path to output BIDS folder
+    :param path_output: path to the output BIDS folder
     :param subject_out: output BIDS subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
     :return:
     """
@@ -234,6 +234,7 @@ def main(path_input, path_output):
                     # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
                     subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
                     if region == 'cord':
+                        # Process spinal cord anatomical and DWI data
                         # Loop across files
                         for image_in, image_out in images_spine_conv_dict.items():
                             # Construct path to the input file
@@ -249,6 +250,7 @@ def main(path_input, path_output):
                             # Copy file and create a dummy json sidecar if does not exist
                             copy_file(path_file_in, path_dir_out, file_out)
                     elif region == 'brain':
+                        # Process DWI brain files
                         # Loop across files
                         for image_in, image_out in images_brain_conv_dict.items():
                             # Construct path to the input file
@@ -262,7 +264,7 @@ def main(path_input, path_output):
                             # Copy file and create a dummy json sidecar if does not exist
                             copy_file(path_file_in, path_dir_out, file_out)
 
-                        # Process raw MPM images
+                        # Process raw MPM images (located in brain/mpm_raw folder)
                         mpm_raw_folder_path = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl',
                                                            region, 'mpm_raw')
                         if os.path.isdir(mpm_raw_folder_path):

From 6a073739a40f5a00c0a748cc891811e28f82ace4 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Fri, 2 Dec 2022 15:44:53 -0500
Subject: [PATCH 09/38] Create participants.json, dataset_description.json, and
 README files. Copy the script itself to the path_output/code folder.

---
 scripts/curate_data_inspired.py | 90 +++++++++++++++++++++++++++++++--
 1 file changed, 87 insertions(+), 3 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 34ac010..6f84b60 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -155,7 +155,7 @@ def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
         copy_file(re.sub('.nii(.gz)*', '.json', path_file_in), path_dir_out, file_out.replace('.nii.gz', '.json'))
 
 
-def write_participants_tsv(participants_tsv_list, path_output):
+def create_participants_tsv(participants_tsv_list, path_output):
     """
     Write participants.tsv file
     :param participants_tsv_list: list containing [subject_out, pathology_out, subject_in, centre_in, centre_out],
@@ -163,7 +163,7 @@ def write_participants_tsv(participants_tsv_list, path_output):
     :param path_output: path to the output BIDS folder
     :return:
     """
-    with open(os.path.join(path_output + '/participants.tsv'), 'w') as tsv_file:
+    with open(os.path.join(path_output, 'participants.tsv'), 'w') as tsv_file:
         tsv_writer = csv.writer(tsv_file, delimiter='\t', lineterminator='\n')
         tsv_writer.writerow(['participant_id', 'pathology', 'data_id', 'institution_id', 'institution'])
         for item in participants_tsv_list:
@@ -171,6 +171,86 @@ def write_participants_tsv(participants_tsv_list, path_output):
         logger.info(f'participants.tsv created in {path_output}')
 
 
+def create_participants_json(path_output):
+    """
+    Create participants.json file
+    :param path_output: path to the output BIDS folder
+    :return:
+    """
+    # Create participants.json
+    data_json = {
+        "participant_id": {
+            "Description": "Unique Participant ID",
+            "LongName": "Participant ID"
+        },
+        "pathology": {
+            "Description": "Pathology",
+            "LongName": "Pathology name"
+        },
+        "data_id": {
+            "Description": "Subject ID as under duke/mri/",
+            "LongName": "Subject ID"
+        },
+        "institution_id": {
+            "Description": "Institution ID as under duke/mri/",
+            "LongName": "Institution ID"
+        },
+        "institution_": {
+            "Description": "Institution ID after conversion to BIDS",
+            "LongName": "BIDS Institution ID"
+        }
+    }
+    with open(os.path.join(path_output, 'participants.json'), 'w') as json_participants:
+        json.dump(data_json, json_participants, indent=4)
+        logger.info(f'participants.json created in {path_output}')
+
+
+def create_dataset_description(path_output):
+    """
+    Create dataset_description.json file
+    :param path_output: path to the output BIDS folder
+    :return:
+    """
+    dataset_description = {"BIDSVersion": "BIDS 1.8.0",
+                           "Name": "inspired"
+                           }
+    with open(os.path.join(path_output, 'dataset_description.json'), 'w') as json_dataset_description:
+        json.dump(dataset_description, json_dataset_description, indent=4)
+        logger.info(f'dataset_description.json created in {path_output}')
+
+
+def create_README(path_output):
+    """
+    Create README file
+    :param path_output: path to the output BIDS folder
+    :return:
+    """
+    with open(os.path.join(path_output, 'README'), 'w') as readme_file:
+        readme_file.write(f'# INSPIRED\n\nThis is an MRI dataset for the INSPIRED project.\n\n## dataset structure\n\n'
+                          f'The dataset contains data from two centers (Toronto, Zurich) across three pathologies ('
+                          f'DCM, SCI, HC). The following images are included:\n\nSpinal cord MRI data:\n- DWI (A-P and '
+                          f'P-A phase encoding)\n- T1w sag\n- T1w sag\n- T1w sag\n- T2star tra\nBrain MRI data:\n- DWI '
+                          f'(A-P and P-A phase encoding)\n- MPM (multi-parameter mapping)\n\n## naming convention\n\n'
+                          f'sub-<site><pathology>XXX\n\nexample:\nsub-zurichDCM001\n\nNote: the label `bp-cspine` is '
+                          f'used to differentiate spine images from brain.')
+        logger.info(f'README created in {path_output}')
+
+
+def copy_script(path_output):
+    """
+    Copy the script itself to the path_output/code folder
+    :param path_output: path to the output BIDS folder
+    :return:
+    """
+    path_script_in = sys.argv[0]
+    path_code = os.path.join(path_output, 'code')
+    if not os.path.isdir(path_code):
+        os.makedirs(path_code, exist_ok=True)
+    path_script_out = os.path.join(path_code, sys.argv[0].split(sep='/')[-1])
+    logger.info(f'Copying {path_script_in} to {path_script_out}')
+    shutil.copyfile(path_script_in, path_script_out)
+
+
 def get_parameters():
     parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
     parser.add_argument("-i", "--path-input",
@@ -290,7 +370,11 @@ def main(path_input, path_output):
 
                 participants_tsv_list.append([subject_out, pathology_out, subject_in.split(sep='/')[-1], centre_in, centre_out])
 
-    write_participants_tsv(participants_tsv_list, path_output)
+    create_participants_tsv(participants_tsv_list, path_output)
+    create_participants_json(path_output)
+    create_dataset_description(path_output)
+    create_README(path_output)
+    copy_script(path_output)
 
 
 if __name__ == "__main__":

From 1c2d836b8801baa7bf4d23d728e8da2e3391194f Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sun, 4 Dec 2022 14:50:19 -0500
Subject: [PATCH 10/38] Use ISO-8859-1 encoding to open json files

---
 scripts/curate_data_inspired.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 6f84b60..eb3498b 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -104,7 +104,10 @@ def read_json_file(path_to_file):
     :param path_to_file: path to input json file
     :return:
     """
-    with open(path_to_file) as p:
+    # Note: open command returned error for the `02/hc/008/bl/brain/mpm_raw/s837313-0004-00001-000880-05.json` file:
+    #   UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 1340: invalid continuation byte
+    # Thus, `encoding="ISO-8859-1"` has to be used. Source: https://stackoverflow.com/a/19706723
+    with open(path_to_file, encoding="ISO-8859-1") as p:
         loaded_json = json.load(p)
         series_description = loaded_json['acqpar'][0]['SeriesDescription']
         flip_angle = loaded_json['acqpar'][0]['FlipAngle']

From 71c6eb0cb5a8fb33ba2f0077514f243a518b0b0e Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sun, 4 Dec 2022 15:08:38 -0500
Subject: [PATCH 11/38] Sort subjects in participants.tsv; fix typo in
 participants.json

---
 scripts/curate_data_inspired.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index eb3498b..ce1acd5 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -198,7 +198,7 @@ def create_participants_json(path_output):
             "Description": "Institution ID as under duke/mri/",
             "LongName": "Institution ID"
         },
-        "institution_": {
+        "institution": {
             "Description": "Institution ID after conversion to BIDS",
             "LongName": "BIDS Institution ID"
         }
@@ -302,7 +302,7 @@ def main(path_input, path_output):
         # Loop across pathologies (hc, csm, sci)
         for pathology_in, pathology_out in pathologies_conv_dict.items():
             # Loop across subjects (001, ...)
-            for sub_index, subject_in in enumerate(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*')),
+            for sub_index, subject_in in enumerate(sorted(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*'))),
                                                    start=1):
                 # If the input subject folder is .tar.gz, extract it
                 if subject_in.endswith('.tar.gz'):

From 13ecab182bc484d25e60aa3e031953d406d478c5 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sun, 4 Dec 2022 15:32:36 -0500
Subject: [PATCH 12/38] Keep only .tar.gz subjects in the input dataset

---
 scripts/curate_data_inspired.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index ce1acd5..75dfc23 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -372,6 +372,10 @@ def main(path_input, path_output):
                                                f'Skipping this subject.')
 
                 participants_tsv_list.append([subject_out, pathology_out, subject_in.split(sep='/')[-1], centre_in, centre_out])
+                # Remove uncompressed subject dir (i.e., keep only .tar.gz).
+                # (but first, make sure that .tar.gz subject exists)
+                if os.path.isfile(subject_in + '.tar.gz'):
+                    shutil.rmtree(subject_in)
 
     create_participants_tsv(participants_tsv_list, path_output)
     create_participants_json(path_output)

From ad2e6585060098b12c6ef23eebd257e584a3c694 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 5 Dec 2022 09:02:49 -0500
Subject: [PATCH 13/38] Remove solved TODO

---
 scripts/curate_data_inspired.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 75dfc23..cfc02a1 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -306,10 +306,8 @@ def main(path_input, path_output):
                                                    start=1):
                 # If the input subject folder is .tar.gz, extract it
                 if subject_in.endswith('.tar.gz'):
-                    logger.info(f'Unpacking tar archive for {subject_in}...')
+                    logger.info(f'Unpacking tar archive {subject_in}...')
                     os.system("tar -xf " + subject_in + " --directory " + os.path.join(path_input, centre_in, pathology_in))
-                    # TODO - consider what to do with extracted folders once the BIDS conversion is done.
-                    #  Delete them and keep only original .tar.gz files?
                     # Remove '.tar.gz' from the subject_in variable
                     subject_in = subject_in.replace('.tar.gz', '')
                 # Loop across regions (brain or cord)

From 31df28ef8fe2c45059aee2fc1d8cde4e5166b53d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 5 Dec 2022 09:23:07 -0500
Subject: [PATCH 14/38] Add usage example

---
 scripts/curate_data_inspired.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index cfc02a1..8731b16 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -10,6 +10,9 @@
 #       - DWI (A-P and P-A phase encoding)
 #       - MPM (multi-parameter mapping)
 #
+# USAGE:
+#       python3 <PATH_TO_THIS_SCRIPT>/curate_data_inspired.py -i <INPUT_DATASET_PATH>/INSPIRED -o <OUTPUT_DATASET_PATH>/INSPIRED_bids
+#
 # Authors: Jan Valosek
 
 import os

From 581edc0294f3a9916ce7405e25af90e5d5f1d1bc Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 12 Dec 2022 13:49:08 -0500
Subject: [PATCH 15/38] Remove function for automatic README creation.

---
 scripts/curate_data_inspired.py | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 8731b16..e502ddf 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -225,23 +225,6 @@ def create_dataset_description(path_output):
         logger.info(f'dataset_description.json created in {path_output}')
 
 
-def create_README(path_output):
-    """
-    Create README file
-    :param path_output: path to the output BIDS folder
-    :return:
-    """
-    with open(os.path.join(path_output, 'README'), 'w') as readme_file:
-        readme_file.write(f'# INSPIRED\n\nThis is an MRI dataset for the INSPIRED project.\n\n## dataset structure\n\n'
-                          f'The dataset contains data from two centers (Toronto, Zurich) across three pathologies ('
-                          f'DCM, SCI, HC). The following images are included:\n\nSpinal cord MRI data:\n- DWI (A-P and '
-                          f'P-A phase encoding)\n- T1w sag\n- T1w sag\n- T1w sag\n- T2star tra\nBrain MRI data:\n- DWI '
-                          f'(A-P and P-A phase encoding)\n- MPM (multi-parameter mapping)\n\n## naming convention\n\n'
-                          f'sub-<site><pathology>XXX\n\nexample:\nsub-zurichDCM001\n\nNote: the label `bp-cspine` is '
-                          f'used to differentiate spine images from brain.')
-        logger.info(f'README created in {path_output}')
-
-
 def copy_script(path_output):
     """
     Copy the script itself to the path_output/code folder
@@ -381,7 +364,6 @@ def main(path_input, path_output):
     create_participants_tsv(participants_tsv_list, path_output)
     create_participants_json(path_output)
     create_dataset_description(path_output)
-    create_README(path_output)
     copy_script(path_output)
 
 

From 09e12eddafe213b5a3bf1c7dd1ea6abdbcba49e5 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 12 Dec 2022 13:57:28 -0500
Subject: [PATCH 16/38] Keep the original subjectID

---
 scripts/curate_data_inspired.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index e502ddf..871aba8 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -288,8 +288,9 @@ def main(path_input, path_output):
         # Loop across pathologies (hc, csm, sci)
         for pathology_in, pathology_out in pathologies_conv_dict.items():
             # Loop across subjects (001, ...)
-            for sub_index, subject_in in enumerate(sorted(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*'))),
-                                                   start=1):
+            for subject_in in sorted(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*'))):
+                # Get subjectID (e.g., 001)
+                subject_id = subject_in.split(sep='/')[-1]
                 # If the input subject folder is .tar.gz, extract it
                 if subject_in.endswith('.tar.gz'):
                     logger.info(f'Unpacking tar archive {subject_in}...')
@@ -299,7 +300,7 @@ def main(path_input, path_output):
                 # Loop across regions (brain or cord)
                 for region in ['brain', 'cord']:
                     # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'
-                    subject_out = prefix + centre_out + pathology_out + f"{sub_index:03d}"
+                    subject_out = prefix + centre_out + pathology_out + subject_id
                     if region == 'cord':
                         # Process spinal cord anatomical and DWI data
                         # Loop across files
@@ -355,7 +356,7 @@ def main(path_input, path_output):
                                 logger.warning(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
                                                f'Skipping this subject.')
 
-                participants_tsv_list.append([subject_out, pathology_out, subject_in.split(sep='/')[-1], centre_in, centre_out])
+                participants_tsv_list.append([subject_out, pathology_out, subject_id, centre_in, centre_out])
                 # Remove uncompressed subject dir (i.e., keep only .tar.gz).
                 # (but first, make sure that .tar.gz subject exists)
                 if os.path.isfile(subject_in + '.tar.gz'):

From 2ce0afdb54a5bfea31b0af7927ec8f141dfdbf31 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 12 Dec 2022 15:03:08 -0500
Subject: [PATCH 17/38] Create .bidsignore to exclude `bp-cspine` tag from
 bids-validator

---
 scripts/curate_data_inspired.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 871aba8..8d6cc97 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -225,6 +225,21 @@ def create_dataset_description(path_output):
         logger.info(f'dataset_description.json created in {path_output}')
 
 
+def create_bidsignore_file(path_output):
+    """
+    Create .bidsignore file defining files that should be ignored by the bids-validator.
+    We want to exclude files with `bp-cspine` tag since BEP025
+    (https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4/edit#heading=h.4k1noo90gelw)
+    is not merged to  BIDS yet
+    :param path_output:
+    :return:
+    """
+    bidsignore = "*/*/*_bp-cspine*"
+    with open(os.path.join(path_output, '.bidsignore'), 'w') as bidsignore_file:
+        bidsignore_file.write(f'{bidsignore}\n')
+        logger.info(f'.bidsignore created in {path_output}')
+
+
 def copy_script(path_output):
     """
     Copy the script itself to the path_output/code folder
@@ -365,6 +380,7 @@ def main(path_input, path_output):
     create_participants_tsv(participants_tsv_list, path_output)
     create_participants_json(path_output)
     create_dataset_description(path_output)
+    create_bidsignore_file(path_output)
     copy_script(path_output)
 
 

From a2c5bbab87f155b6ba928d5ee120adf87339ec80 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 12 Dec 2022 15:17:56 -0500
Subject: [PATCH 18/38] Fix bug in subject_id variable construction

---
 scripts/curate_data_inspired.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 8d6cc97..465d362 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -304,14 +304,14 @@ def main(path_input, path_output):
         for pathology_in, pathology_out in pathologies_conv_dict.items():
             # Loop across subjects (001, ...)
             for subject_in in sorted(glob.glob(os.path.join(path_input, centre_in, pathology_in, '*'))):
-                # Get subjectID (e.g., 001)
-                subject_id = subject_in.split(sep='/')[-1]
                 # If the input subject folder is .tar.gz, extract it
                 if subject_in.endswith('.tar.gz'):
                     logger.info(f'Unpacking tar archive {subject_in}...')
                     os.system("tar -xf " + subject_in + " --directory " + os.path.join(path_input, centre_in, pathology_in))
                     # Remove '.tar.gz' from the subject_in variable
                     subject_in = subject_in.replace('.tar.gz', '')
+                # Get subjectID (e.g., 001)
+                subject_id = subject_in.split(sep='/')[-1]
                 # Loop across regions (brain or cord)
                 for region in ['brain', 'cord']:
                     # Construct output subjectID containing centre name and pathology, e.g., 'sub-torontoDCM001'

From 8556af9bacf8e137ec2cc2675ebef9634df25fe3 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 12 Dec 2022 15:27:04 -0500
Subject: [PATCH 19/38] Add README for inspired dataset

---
 scripts/README | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 scripts/README

diff --git a/scripts/README b/scripts/README
new file mode 100644
index 0000000..ffcfe43
--- /dev/null
+++ b/scripts/README
@@ -0,0 +1,33 @@
+# INSPIRED
+
+This is an MRI dataset acquired in the context of the INSPIRED project.
+
+https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594
+
+## contact person
+
+Dataset shared by: <NAME AND EMAIL>
+<IF THERE WAS EMAIL COMM>Email communication: <DATE OF EMAIL AND SUBJECT>
+
+## dataset structure
+
+The dataset contains data from two centers (Toronto, Zurich) across three pathologies (DCM, SCI, HC). The following images are included:
+
+Spinal cord MRI data:
+- DWI (A-P and P-A phase encoding)
+- T1w sag
+- T1w sag
+- T1w sag
+- T2star tra
+Brain MRI data:
+- DWI (A-P and P-A phase encoding)
+- MPM (multi-parameter mapping)
+
+## naming convention
+
+sub-<site><pathology>XXX
+
+example:
+sub-zurichDCM001
+
+Note: the label `bp-cspine` is used to differentiate spine images from brain.
\ No newline at end of file

From 30ae9979329ec2fc261abf8be9c5857636af063a Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 21 Dec 2022 15:35:48 -0500
Subject: [PATCH 20/38] Switch from `bp-cspine` to `acq-cspine`

---
 scripts/curate_data_inspired.py | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 465d362..43b3a56 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -48,17 +48,19 @@
     }
 
 # Dictionary for image filename conversion
-# Note: we use label `bp-cspine` to differentiate spine imaging from brain
-# Details: BIDS BEP025 Proposal (https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4)
+# Note: we use label `acq-cspine` to differentiate spine imaging from brain
+# Note: we use label `acq-cspine` over `bp-cspine` since BIDS BEP025 is not merged yet (and thus does not pass bids-validator)
+# BIDS BEP025 Proposal: https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4
+# Discussion `acq-cspine` vs `bp-cspine`: https://github.com/neuropoly/data-management/pull/185#issuecomment-1347421696
 images_spine_conv_dict = {
-    'dwi.nii.gz': 'dir-AP_bp-cspine_dwi.nii.gz',
-    'dwi.bval': 'dir-AP_bp-cspine_dwi.bval',
-    'dwi.bvec': 'dir-AP_bp-cspine_dwi.bvec',
-    'dwi_reversed_blip.nii.gz': 'dir-PA_bp-cspine_dwi.nii.gz',
-    't1_sag.nii.gz': 'bp-cspine_T1w.nii.gz',
-    't2_sag.nii.gz': 'acq-coronal_bp-cspine_T2w.nii.gz',
-    't2_tra.nii.gz': 'acq-axial_bp-cspine_T2w.nii.gz',
-    'pd_medic.nii.gz': 'bp-cspine_T2star.nii.gz'
+    'dwi.nii.gz': 'dir-AP_acq-cspine_dwi.nii.gz',
+    'dwi.bval': 'dir-AP_acq-cspine_dwi.bval',
+    'dwi.bvec': 'dir-AP_acq-cspine_dwi.bvec',
+    'dwi_reversed_blip.nii.gz': 'dir-PA_acq-cspine_dwi.nii.gz',
+    't1_sag.nii.gz': 'acq-cspine_T1w.nii.gz',
+    't2_sag.nii.gz': 'acq-cspineSagittal_T2w.nii.gz',
+    't2_tra.nii.gz': 'acq-cspineAxial_T2w.nii.gz',
+    'pd_medic.nii.gz': 'acq-cspine_T2star.nii.gz'
     }
 
 # Dictionary for brain image filename conversion
@@ -75,7 +77,7 @@ def copy_file(path_file_in, path_dir_out, file_out):
     Copy file from input non-BIDS dataset to BIDS compliant dataset
     :param path_file_in: path of the input non-BIDS file which will be copied
     :param path_dir_out: path of the output BIDS directory; for example sub-torontoDCM001/dwi
-    :param file_out: filename of the output BIDS file; for example 'sub-torontoDCM001_bp-cspine_dir-AP_dwi.nii.gz'
+    :param file_out: filename of the output BIDS file; for example 'sub-torontoDCM001_dir-AP_acq-cspine_dwi.nii.gz'
     :return:
     """
     # Make sure that the input file exists, if so, copy it
@@ -228,7 +230,7 @@ def create_dataset_description(path_output):
 def create_bidsignore_file(path_output):
     """
     Create .bidsignore file defining files that should be ignored by the bids-validator.
-    We want to exclude files with `bp-cspine` tag since BEP025
+    We want to exclude files with `acq-cspine` tag since BEP025
     (https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4/edit#heading=h.4k1noo90gelw)
     is not merged to  BIDS yet
     :param path_output:
@@ -322,7 +324,7 @@ def main(path_input, path_output):
                         for image_in, image_out in images_spine_conv_dict.items():
                             # Construct path to the input file
                             path_file_in = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl', region, image_in)
-                            # Construct output filename, e.g., 'sub-torontoDCM001_bp-cspine_dir-AP_dwi.nii.gz'
+                            # Construct output filename, e.g., 'sub-torontoDCM001_dir-AP_acq-cspine_dwi.nii.gz'
                             file_out = subject_out + '_' + image_out
                             # Construct path to the output BIDS compliant directory
                             if 'dwi' in image_in:
@@ -380,7 +382,7 @@ def main(path_input, path_output):
     create_participants_tsv(participants_tsv_list, path_output)
     create_participants_json(path_output)
     create_dataset_description(path_output)
-    create_bidsignore_file(path_output)
+    #create_bidsignore_file(path_output)
     copy_script(path_output)
 
 

From b364bf51acf960157f2a62cbe03ad9819ca46804 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 21 Dec 2022 15:36:30 -0500
Subject: [PATCH 21/38] Deal with SC derivatives

---
 scripts/curate_data_inspired.py | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 43b3a56..6a51b32 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -63,6 +63,14 @@
     'pd_medic.nii.gz': 'acq-cspine_T2star.nii.gz'
     }
 
+# TODO - include also DWI derivatives
+derivatives_spine_conv_dict = {
+    't2_seg.nii.gz': 'acq-cspineAxial_T2w_seg.nii.gz',
+    # TODO - check which suffix is used for BIDS gm-seg and wm-seg derivatives
+    'gm_seg.nii.gz': 'acq-cspine_T2star_gm-seg.nii.gz',
+    'wm_seg.nii.gz': 'acq-cspine_T2star_wm-seg.nii.gz'
+}
+
 # Dictionary for brain image filename conversion
 images_brain_conv_dict = {
     'dwi.nii.gz': 'dir-AP_dwi.nii.gz',
@@ -286,6 +294,10 @@ def main(path_input, path_output):
         shutil.rmtree(path_output)
     os.makedirs(path_output, exist_ok=True)
 
+    # Construct path to derivatives/labels
+    path_derivatives = os.path.join(path_output, 'derivatives', 'labels')
+    os.makedirs(path_derivatives, exist_ok=True)
+
     FNAME_LOG = os.path.join(path_output, 'bids_conversion.log')
     # Dump log file there
     if os.path.exists(FNAME_LOG):
@@ -334,6 +346,22 @@ def main(path_input, path_output):
 
                             # Copy file and create a dummy json sidecar if does not exist
                             copy_file(path_file_in, path_dir_out, file_out)
+                        # Deal with derivatives (i.e., spinal cord segmentation) located in `sct_processing` folder
+                        path_sct_processing = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl',
+                                                           region, 'sct_processing')
+                        if os.path.isdir(path_sct_processing):
+                            for image_in, image_out in derivatives_spine_conv_dict.items():
+                                if 't2' in image_in:
+                                    contrast = 't2'
+                                else:
+                                    contrast = 't2s'
+                                # Construct path to the input file
+                                path_file_in = os.path.join(path_sct_processing, contrast, image_in)
+                                # Construct output filename, e.g., 'sub-torontoDCM001_acq-cspineAxial_T2w_seg.nii.gz'
+                                file_out = subject_out + '_' + image_out
+                                # Construct path to the output BIDS compliant derivatives directory
+                                path_dir_out = os.path.join(path_derivatives, subject_out, 'anat')
+                                copy_file(path_file_in, path_dir_out, file_out)
                     elif region == 'brain':
                         # Process DWI brain files
                         # Loop across files

From cf6079007ec3c83260cd03a91d3707ce596dc17d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 08:33:16 -0500
Subject: [PATCH 22/38] Use label-SC_mask, label-WM_mask, and label-GM_mask

---
 scripts/curate_data_inspired.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 6a51b32..b8d5210 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -65,10 +65,9 @@
 
 # TODO - include also DWI derivatives
 derivatives_spine_conv_dict = {
-    't2_seg.nii.gz': 'acq-cspineAxial_T2w_seg.nii.gz',
-    # TODO - check which suffix is used for BIDS gm-seg and wm-seg derivatives
-    'gm_seg.nii.gz': 'acq-cspine_T2star_gm-seg.nii.gz',
-    'wm_seg.nii.gz': 'acq-cspine_T2star_wm-seg.nii.gz'
+    't2_seg.nii.gz': 'acq-cspineAxial_T2w_label-SC_mask.nii.gz',
+    'gm_seg.nii.gz': 'acq-cspine_T2star_label-GM_mask.nii.gz',
+    'wm_seg.nii.gz': 'acq-cspine_T2star_label-WM_mask.nii.gz'
 }
 
 # Dictionary for brain image filename conversion
@@ -357,7 +356,7 @@ def main(path_input, path_output):
                                     contrast = 't2s'
                                 # Construct path to the input file
                                 path_file_in = os.path.join(path_sct_processing, contrast, image_in)
-                                # Construct output filename, e.g., 'sub-torontoDCM001_acq-cspineAxial_T2w_seg.nii.gz'
+                                # Construct output filename, e.g., 'sub-torontoDCM001_acq-cspineAxial_T2w_label-SC_mask.nii.gz'
                                 file_out = subject_out + '_' + image_out
                                 # Construct path to the output BIDS compliant derivatives directory
                                 path_dir_out = os.path.join(path_derivatives, subject_out, 'anat')

From 0d135cc4e60dff40f374165da255a8ac4397e7cb Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 08:35:26 -0500
Subject: [PATCH 23/38] Include DatasetType (raw or derivative) to
 dataset_description.json. Add write_json function.

---
 scripts/curate_data_inspired.py | 52 ++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index b8d5210..19612c5 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -170,6 +170,20 @@ def construct_mpm_bids_filename(mpm_files_dict, path_output, subject_out):
         copy_file(re.sub('.nii(.gz)*', '.json', path_file_in), path_dir_out, file_out.replace('.nii.gz', '.json'))
 
 
+def write_json(path_output, json_filename, data_json):
+    """
+    :param path_output: path to the output BIDS folder
+    :param json_filename: json filename, for example: participants.json
+    :param data_json: JSON formatted content
+    :return:
+    """
+    with open(os.path.join(path_output, json_filename), 'w') as json_file:
+        json.dump(data_json, json_file, indent=4)
+        # Add last newline
+        json_file.write("\n")
+        logger.info(f'{json_filename} created in {path_output}')
+
+
 def create_participants_tsv(participants_tsv_list, path_output):
     """
     Write participants.tsv file
@@ -215,38 +229,22 @@ def create_participants_json(path_output):
             "LongName": "BIDS Institution ID"
         }
     }
-    with open(os.path.join(path_output, 'participants.json'), 'w') as json_participants:
-        json.dump(data_json, json_participants, indent=4)
-        logger.info(f'participants.json created in {path_output}')
+    write_json(path_output, 'participants.json', data_json)
 
 
-def create_dataset_description(path_output):
+def create_dataset_description(path_output, datasettype):
     """
     Create dataset_description.json file
     :param path_output: path to the output BIDS folder
+    :param datasettype: raw or derivative (https://bids-specification.readthedocs.io/en/stable/glossary.html#datasettype-metadata)
     :return:
     """
-    dataset_description = {"BIDSVersion": "BIDS 1.8.0",
-                           "Name": "inspired"
-                           }
-    with open(os.path.join(path_output, 'dataset_description.json'), 'w') as json_dataset_description:
-        json.dump(dataset_description, json_dataset_description, indent=4)
-        logger.info(f'dataset_description.json created in {path_output}')
-
-
-def create_bidsignore_file(path_output):
-    """
-    Create .bidsignore file defining files that should be ignored by the bids-validator.
-    We want to exclude files with `acq-cspine` tag since BEP025
-    (https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4/edit#heading=h.4k1noo90gelw)
-    is not merged to  BIDS yet
-    :param path_output:
-    :return:
-    """
-    bidsignore = "*/*/*_bp-cspine*"
-    with open(os.path.join(path_output, '.bidsignore'), 'w') as bidsignore_file:
-        bidsignore_file.write(f'{bidsignore}\n')
-        logger.info(f'.bidsignore created in {path_output}')
+    data_json = {
+        "BIDSVersion": "BIDS 1.8.0",
+        "Name": "inspired",
+        "DatasetType": datasettype,
+    }
+    write_json(path_output, 'dataset_description.json', data_json)
 
 
 def copy_script(path_output):
@@ -408,8 +406,8 @@ def main(path_input, path_output):
 
     create_participants_tsv(participants_tsv_list, path_output)
     create_participants_json(path_output)
-    create_dataset_description(path_output)
-    #create_bidsignore_file(path_output)
+    create_dataset_description(path_output, 'raw')
+    create_dataset_description(os.path.join(path_output, 'derivatives'), 'derivative')
     copy_script(path_output)
 
 

From 1b528670fc99504263a1191eecc74336a1bd5416 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 08:36:05 -0500
Subject: [PATCH 24/38] Update participants.tsv and participants.json

---
 scripts/curate_data_inspired.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 19612c5..11adcac 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -194,7 +194,7 @@ def create_participants_tsv(participants_tsv_list, path_output):
     """
     with open(os.path.join(path_output, 'participants.tsv'), 'w') as tsv_file:
         tsv_writer = csv.writer(tsv_file, delimiter='\t', lineterminator='\n')
-        tsv_writer.writerow(['participant_id', 'pathology', 'data_id', 'institution_id', 'institution'])
+        tsv_writer.writerow(['participant_id', 'source_id', 'pathology', 'institution_id', 'institution'])
         for item in participants_tsv_list:
             tsv_writer.writerow(item)
         logger.info(f'participants.tsv created in {path_output}')
@@ -212,20 +212,20 @@ def create_participants_json(path_output):
             "Description": "Unique Participant ID",
             "LongName": "Participant ID"
         },
+        "source_id": {
+            "Description": "Subject ID in the unprocessed data",
+            "LongName": "Subject ID in the unprocessed data"
+        },
         "pathology": {
             "Description": "Pathology",
             "LongName": "Pathology name"
         },
-        "data_id": {
-            "Description": "Subject ID as under duke/mri/",
-            "LongName": "Subject ID"
-        },
         "institution_id": {
-            "Description": "Institution ID as under duke/mri/",
-            "LongName": "Institution ID"
+            "Description": "Institution ID in the unprocessed data",
+            "LongName": "Institution ID in the unprocessed data"
         },
         "institution": {
-            "Description": "Institution ID after conversion to BIDS",
+            "Description": "Human-friendly institution name",
             "LongName": "BIDS Institution ID"
         }
     }
@@ -398,7 +398,7 @@ def main(path_input, path_output):
                                 logger.warning(f'WARNING: There are no json sidecars in {mpm_raw_folder_path}. '
                                                f'Skipping this subject.')
 
-                participants_tsv_list.append([subject_out, pathology_out, subject_id, centre_in, centre_out])
+                participants_tsv_list.append([subject_out, subject_id, pathology_out, centre_in, centre_out])
                 # Remove uncompressed subject dir (i.e., keep only .tar.gz).
                 # (but first, make sure that .tar.gz subject exists)
                 if os.path.isfile(subject_in + '.tar.gz'):

From 65e56e1d9a7022b56c3cdff2fe7573c88e2e1160 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 10:58:00 -0500
Subject: [PATCH 25/38] Add script for merge of participants.tsv and table with
 clinical DCM data

---
 ...erge_clinical_table_to_participants_tsv.py | 127 ++++++++++++++++++
 1 file changed, 127 insertions(+)
 create mode 100644 scripts/inspired_merge_clinical_table_to_participants_tsv.py

diff --git a/scripts/inspired_merge_clinical_table_to_participants_tsv.py b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
new file mode 100644
index 0000000..ae841b5
--- /dev/null
+++ b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
@@ -0,0 +1,127 @@
+#
+# Merge table with clinical data for DCM patients (provided Patrick Freund, Balgrist) with INSPIRED participants.tsv
+#
+# Note - pandas.read_excel requires openpyxl library (pip install openpyxl or conda install openpyxl)
+#
+# Authors: Jan Valosek
+#
+
+import os
+import argparse
+import shutil
+
+import pandas as pd
+
+# For zurich site, subjectIDs match between clinical table and participants.tsv (i.e., ID 1 in clinical table
+# corresponds to sub-zurichDCM001 in participants.tsv, ID 2 corresponds to sub-zurichDCM002, etc.)
+# But for toronto site, subjectIDs do not match (i.e., ID 25 in clinical table corresponds to sub-torontoDCM001 in
+# participants.tsv, ID 26 corresponds to sub-torontoDCM005, etc.)
+# This dict thus allows the merge of both tables.
+#   - keys are subject ID from clinical table
+#   - values are subject ID for DCM patients from participants.tsv
+subject_ID_dict = {
+    1: 1,
+    2: 2,
+    3: 3,
+    4: 4,
+    5: 5,
+    6: 6,
+    7: 7,
+    8: 8,
+    9: 9,
+    10: 10,
+    11: 11,
+    12: 12,
+    13: 13,
+    14: 14,
+    15: 15,
+    16: 16,
+    17: 17,
+    18: 18,
+    19: 19,
+    20: 20,
+    21: 21,
+    22: 22,
+    23: 23,
+    24: 24,
+    25: 1,
+    26: 5,
+    27: 6,
+    28: 7,
+    29: 8,
+    30: 9,
+    31: 10,
+    32: 15,
+    33: 17,
+    34: 18,
+    35: 19,
+    36: 21,
+    37: 22,
+    38: 23,
+    }
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
+    parser.add_argument("-participants-file",
+                        help="INSPIRED participants.tsv file",
+                        required=True)
+    parser.add_argument("-clinical-file",
+                        help="Excel table (.xlsx) with clinical data for DCM patients.",
+                        required=True,
+                        )
+    return parser
+
+
+def main():
+    # Parse the command line arguments
+    parser = get_parser()
+    args = parser.parse_args()
+
+    # Read input .tsv and .xlsx tables as Pandas DataFrames
+    if os.path.isfile(args.participants_file):
+        print('Reading: {}'.format(args.participants_file))
+        participants_df = pd.read_csv(args.participants_file, sep='\t', header=0)
+    else:
+        raise FileNotFoundError(f'{args.participants_file} not found')
+    if os.path.isfile(args.clinical_file):
+        print('Reading: {}'.format(args.clinical_file))
+        # skip first two rows because they contain legend
+        clinical_df = pd.read_excel(args.clinical_file, skiprows=[0, 1])
+    else:
+        raise FileNotFoundError(f'{args.clinical_file} not found')
+
+    # Insert list of DCM subjectIDs from participants.tsv into clinical table to allow merge
+    # Note: 'data_id' is used to match with column in participants.tsv
+    clinical_df.insert(1, 'data_id', list(subject_ID_dict.values()))
+    # Insert a new column with institutions in lower case (toronto, zurich) into clinical table to allow merge
+    # Note: 'institution' is used to match with column in participants.tsv
+    clinical_df['institution'] = [x.lower() for x in clinical_df['Site']]
+
+    # First, merge clinical table to participants.tsv
+    # Note: we work here only with DCM since there is overlap in 'data_id' with other pathologies
+    temp_df = pd.merge(participants_df[participants_df['pathology'] == 'DCM'], clinical_df,
+                       on=['institution', 'data_id'])
+    # Drop columns from 'temp_df' (they are already included in the participants.tsv)
+    temp_df = temp_df.drop(['pathology', 'data_id', 'institution_id', 'institution', 'ID', 'Site'], axis=1)
+    # Now, merge 'temp_df' back to the participants.tsv
+    final_df = pd.merge(participants_df, temp_df, on='participant_id', how='outer')
+
+    # Convert pd column names to lowercase
+    final_df = final_df.rename(columns=str.lower)
+    # Replace spaces in pd column names by '_'
+    final_df.columns = final_df.columns.str.replace(' ', '_')
+
+    # Rename female to F and male to M
+    final_df = final_df.replace({"sex": {'female': 'F', 'male': 'M'}})
+
+    # Backup original participants.tsv
+    shutil.move(args.participants_file, args.participants_file.replace('.tsv', '_backup.tsv'))
+
+    # Save merged pd as .tsv
+    print('Saving: {}'.format(args.participants_file))
+    final_df.to_csv(args.participants_file, sep="\t")
+
+
+if __name__ == "__main__":
+    main()

From 5a39c77766a3b4eb135612aac923642244273687 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 11:22:10 -0500
Subject: [PATCH 26/38] Rename data_id to source_id to be compatible with
 participants.tsv

---
 ...nspired_merge_clinical_table_to_participants_tsv.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/inspired_merge_clinical_table_to_participants_tsv.py b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
index ae841b5..4a7fe39 100644
--- a/scripts/inspired_merge_clinical_table_to_participants_tsv.py
+++ b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
@@ -92,18 +92,18 @@ def main():
         raise FileNotFoundError(f'{args.clinical_file} not found')
 
     # Insert list of DCM subjectIDs from participants.tsv into clinical table to allow merge
-    # Note: 'data_id' is used to match with column in participants.tsv
-    clinical_df.insert(1, 'data_id', list(subject_ID_dict.values()))
+    # Note: 'source_id' is used to match with column in participants.tsv
+    clinical_df.insert(1, 'source_id', list(subject_ID_dict.values()))
     # Insert a new column with institutions in lower case (toronto, zurich) into clinical table to allow merge
     # Note: 'institution' is used to match with column in participants.tsv
     clinical_df['institution'] = [x.lower() for x in clinical_df['Site']]
 
     # First, merge clinical table to participants.tsv
-    # Note: we work here only with DCM since there is overlap in 'data_id' with other pathologies
+    # Note: we work here only with DCM since there is overlap in 'source_id' with other pathologies
     temp_df = pd.merge(participants_df[participants_df['pathology'] == 'DCM'], clinical_df,
-                       on=['institution', 'data_id'])
+                       on=['institution', 'source_id'])
     # Drop columns from 'temp_df' (they are already included in the participants.tsv)
-    temp_df = temp_df.drop(['pathology', 'data_id', 'institution_id', 'institution', 'ID', 'Site'], axis=1)
+    temp_df = temp_df.drop(['pathology', 'source_id', 'institution_id', 'institution', 'ID', 'Site'], axis=1)
     # Now, merge 'temp_df' back to the participants.tsv
     final_df = pd.merge(participants_df, temp_df, on='participant_id', how='outer')
 

From 1151061c47a63aa35365b918658cdf48a827c5c9 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 11:25:12 -0500
Subject: [PATCH 27/38] Use n/a for empty cells

---
 scripts/inspired_merge_clinical_table_to_participants_tsv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/inspired_merge_clinical_table_to_participants_tsv.py b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
index 4a7fe39..662cab8 100644
--- a/scripts/inspired_merge_clinical_table_to_participants_tsv.py
+++ b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
@@ -120,7 +120,7 @@ def main():
 
     # Save merged pd as .tsv
     print('Saving: {}'.format(args.participants_file))
-    final_df.to_csv(args.participants_file, sep="\t")
+    final_df.to_csv(args.participants_file, sep='\t', na_rep='n/a')
 
 
 if __name__ == "__main__":

From 374876a753cbedddc95ec7cda8685fdfde388bb5 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 11:34:32 -0500
Subject: [PATCH 28/38] Add leading zeros to source_id and institution_id (to
 match with the original participants.tsv)

---
 scripts/inspired_merge_clinical_table_to_participants_tsv.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/inspired_merge_clinical_table_to_participants_tsv.py b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
index 662cab8..204700b 100644
--- a/scripts/inspired_merge_clinical_table_to_participants_tsv.py
+++ b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
@@ -114,6 +114,9 @@ def main():
 
     # Rename female to F and male to M
     final_df = final_df.replace({"sex": {'female': 'F', 'male': 'M'}})
+    # Add leading zeros to source_id and institution_id (to match with the original participants.tsv)
+    final_df['source_id'] = final_df['source_id'].astype(str).str.zfill(3)
+    final_df['institution_id'] = final_df['institution_id'].astype(str).str.zfill(2)
 
     # Backup original participants.tsv
     shutil.move(args.participants_file, args.participants_file.replace('.tsv', '_backup.tsv'))

From 8959d2c7a68643aed45744a72a0ee5dc3f08d99b Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Wed, 4 Jan 2023 11:46:15 -0500
Subject: [PATCH 29/38] Clarify script description

---
 ...pired_merge_clinical_table_to_participants_tsv.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/inspired_merge_clinical_table_to_participants_tsv.py b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
index 204700b..ee56375 100644
--- a/scripts/inspired_merge_clinical_table_to_participants_tsv.py
+++ b/scripts/inspired_merge_clinical_table_to_participants_tsv.py
@@ -1,7 +1,7 @@
 #
-# Merge table with clinical data for DCM patients (provided Patrick Freund, Balgrist) with INSPIRED participants.tsv
+# Merge the .xlsx table with DCM clinical data (provided by Patrick Freund, Balgrist) with the INSPIRED participants.tsv
 #
-# Note - pandas.read_excel requires openpyxl library (pip install openpyxl or conda install openpyxl)
+# Note: pandas.read_excel requires openpyxl library (pip install openpyxl or conda install openpyxl)
 #
 # Authors: Jan Valosek
 #
@@ -13,12 +13,12 @@
 import pandas as pd
 
 # For zurich site, subjectIDs match between clinical table and participants.tsv (i.e., ID 1 in clinical table
-# corresponds to sub-zurichDCM001 in participants.tsv, ID 2 corresponds to sub-zurichDCM002, etc.)
+# corresponds to sub-zurichDCM001 in participants.tsv, ID 2 corresponds to sub-zurichDCM002, etc.).
 # But for toronto site, subjectIDs do not match (i.e., ID 25 in clinical table corresponds to sub-torontoDCM001 in
-# participants.tsv, ID 26 corresponds to sub-torontoDCM005, etc.)
+# participants.tsv, ID 26 corresponds to sub-torontoDCM005, etc.).
 # This dict thus allows the merge of both tables.
-#   - keys are subject ID from clinical table
-#   - values are subject ID for DCM patients from participants.tsv
+#   - keys are subjectIDs from the clinical table
+#   - values are subjectIDs for DCM patients from the participants.tsv
 subject_ID_dict = {
     1: 1,
     2: 2,

From 6d3a956b22f82e8ce53423d638b8ebb260889dd1 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Fri, 6 Jan 2023 12:35:10 -0500
Subject: [PATCH 30/38] Rename derivatives/labels to derivatives/manual_labels

---
 scripts/curate_data_inspired.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 11adcac..e9adc0a 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -292,7 +292,7 @@ def main(path_input, path_output):
     os.makedirs(path_output, exist_ok=True)
 
     # Construct path to derivatives/labels
-    path_derivatives = os.path.join(path_output, 'derivatives', 'labels')
+    path_derivatives = os.path.join(path_output, 'derivatives', 'manual_labels')
     os.makedirs(path_derivatives, exist_ok=True)
 
     FNAME_LOG = os.path.join(path_output, 'bids_conversion.log')

From a81a8efd8afa8a54ce36d629b2c3032ecbc8e958 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Fri, 20 Jan 2023 18:20:52 -0500
Subject: [PATCH 31/38] Copy qform to sform

To address https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3991#issuecomment-1378765661
---
 scripts/curate_data_inspired.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index e9adc0a..29b824b 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -101,6 +101,19 @@ def copy_file(path_file_in, path_dir_out, file_out):
             create_dummy_json_sidecar_if_does_not_exist(path_file_out)
 
 
+def copy_qform_to_sform(path_dir_out, file_out):
+    """
+    Copy qform to sform for to address https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3991#issuecomment-1378765661
+    :param path_dir_out:
+    :param file_out:
+    :return:
+    """
+    path_file = os.path.join(path_dir_out, file_out)
+    # Make sure that the input file exists, if so, copy it
+    if os.path.isfile(path_file):
+        os.system('sct_image -i ' + path_file + ' -set-qform-to-sform')
+
+
 # TODO - do we want to create just a empty json sidecar? Or do we want to include some params there?
 def create_dummy_json_sidecar_if_does_not_exist(path_file_out):
     # Work only with .nii.gz (i.e., ignore .bval and .bvec files)
@@ -343,6 +356,9 @@ def main(path_input, path_output):
 
                             # Copy file and create a dummy json sidecar if does not exist
                             copy_file(path_file_in, path_dir_out, file_out)
+                            # Copy qform to sform to address https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3991#issuecomment-1378765661
+                            if file_out.endswith('.nii.gz'):
+                                copy_qform_to_sform(path_dir_out, file_out)
                         # Deal with derivatives (i.e., spinal cord segmentation) located in `sct_processing` folder
                         path_sct_processing = os.path.join(path_input, centre_in, pathology_in, subject_in, 'bl',
                                                            region, 'sct_processing')

From 4fbc4bfbb92f88c7973cfe57ced72d6f5861a5e0 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sat, 21 Jan 2023 08:44:27 -0500
Subject: [PATCH 32/38] Swap 'dir-AP_acq-cspine' to 'acq-cspine_dir-AP' to pass
 bids-validator

---
 scripts/curate_data_inspired.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 29b824b..ca74413 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -53,10 +53,10 @@
 # BIDS BEP025 Proposal: https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4
 # Discussion `acq-cspine` vs `bp-cspine`: https://github.com/neuropoly/data-management/pull/185#issuecomment-1347421696
 images_spine_conv_dict = {
-    'dwi.nii.gz': 'dir-AP_acq-cspine_dwi.nii.gz',
-    'dwi.bval': 'dir-AP_acq-cspine_dwi.bval',
-    'dwi.bvec': 'dir-AP_acq-cspine_dwi.bvec',
-    'dwi_reversed_blip.nii.gz': 'dir-PA_acq-cspine_dwi.nii.gz',
+    'dwi.nii.gz': 'acq-cspine_dir-AP_dwi.nii.gz',
+    'dwi.bval': 'acq-cspine_dir-AP_dwi.bval',
+    'dwi.bvec': 'acq-cspine_dir-AP_dwi.bvec',
+    'dwi_reversed_blip.nii.gz': 'acq-cspine_dir-PA_dwi.nii.gz',
     't1_sag.nii.gz': 'acq-cspine_T1w.nii.gz',
     't2_sag.nii.gz': 'acq-cspineSagittal_T2w.nii.gz',
     't2_tra.nii.gz': 'acq-cspineAxial_T2w.nii.gz',

From f529249a0c1877c7b954cdb85649c27f76ce016d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sat, 21 Jan 2023 08:45:14 -0500
Subject: [PATCH 33/38] Change '_mask' to '_seg'

---
 scripts/curate_data_inspired.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index ca74413..7401fd7 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -65,9 +65,9 @@
 
 # TODO - include also DWI derivatives
 derivatives_spine_conv_dict = {
-    't2_seg.nii.gz': 'acq-cspineAxial_T2w_label-SC_mask.nii.gz',
-    'gm_seg.nii.gz': 'acq-cspine_T2star_label-GM_mask.nii.gz',
-    'wm_seg.nii.gz': 'acq-cspine_T2star_label-WM_mask.nii.gz'
+    't2_seg.nii.gz': 'acq-cspineAxial_T2w_label-SC_seg.nii.gz',
+    'gm_seg.nii.gz': 'acq-cspine_T2star_label-GM_seg.nii.gz',
+    'wm_seg.nii.gz': 'acq-cspine_T2star_label-WM_seg.nii.gz'
 }
 
 # Dictionary for brain image filename conversion

From b5a7b5fa75b34e802f1fab22afa77bf99c2144d0 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sat, 21 Jan 2023 10:01:25 -0500
Subject: [PATCH 34/38] Rename README to README.md and update it.

---
 scripts/README    | 33 ---------------------------------
 scripts/README.md | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 33 deletions(-)
 delete mode 100644 scripts/README
 create mode 100644 scripts/README.md

diff --git a/scripts/README b/scripts/README
deleted file mode 100644
index ffcfe43..0000000
--- a/scripts/README
+++ /dev/null
@@ -1,33 +0,0 @@
-# INSPIRED
-
-This is an MRI dataset acquired in the context of the INSPIRED project.
-
-https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594
-
-## contact person
-
-Dataset shared by: <NAME AND EMAIL>
-<IF THERE WAS EMAIL COMM>Email communication: <DATE OF EMAIL AND SUBJECT>
-
-## dataset structure
-
-The dataset contains data from two centers (Toronto, Zurich) across three pathologies (DCM, SCI, HC). The following images are included:
-
-Spinal cord MRI data:
-- DWI (A-P and P-A phase encoding)
-- T1w sag
-- T1w sag
-- T1w sag
-- T2star tra
-Brain MRI data:
-- DWI (A-P and P-A phase encoding)
-- MPM (multi-parameter mapping)
-
-## naming convention
-
-sub-<site><pathology>XXX
-
-example:
-sub-zurichDCM001
-
-Note: the label `bp-cspine` is used to differentiate spine images from brain.
\ No newline at end of file
diff --git a/scripts/README.md b/scripts/README.md
new file mode 100644
index 0000000..b38e4bf
--- /dev/null
+++ b/scripts/README.md
@@ -0,0 +1,34 @@
+# INSPIRED
+
+This is an MRI dataset acquired in the context of the INSPIRED project.
+
+It contains brain and spinal cord data acquired at two sites centers (Toronto, Zurich) from healthy controls (HC) and two pathologies:
+- degenerative cervical myelopathy (DCM)
+- spinal cord injury (SCI)
+
+It also contains spinal cord, gray matter and white matter segmentations for T2w axial images.
+
+## Dataset structure
+
+Spinal cord MRI data:
+- T1w
+- T2w axial
+- T2w sagittal
+- T2star
+- DWI (A-P and P-A phase encoding)
+
+Brain MRI data:
+- MPM (multi-parameter mapping)
+- DWI (A-P and P-A phase encoding)
+
+## Naming convention
+
+sub-<site><pathology>XXX
+
+Note: BIDS label `acq-cspine` is used to differentiate spine images from brain. For details, see https://github.com/neuropoly/data-management/pull/185#issuecomment-1362069079.
+
+Note: 01 corresponds to Toronto site, 02 to Zurich site. For details, see https://github.com/neuropoly/data-management/issues/184#issuecomment-1329250514.
+
+## Details
+
+https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594
\ No newline at end of file

From 33f440a17047d77665e0c0206e598b9499099860 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sat, 21 Jan 2023 10:05:33 -0500
Subject: [PATCH 35/38] Update 'participants.json' according to
 https://intranet.neuro.polymtl.ca/data/dataset-curation.html#participants-json

---
 scripts/curate_data_inspired.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/scripts/curate_data_inspired.py b/scripts/curate_data_inspired.py
index 7401fd7..a2789bd 100644
--- a/scripts/curate_data_inspired.py
+++ b/scripts/curate_data_inspired.py
@@ -230,8 +230,13 @@ def create_participants_json(path_output):
             "LongName": "Subject ID in the unprocessed data"
         },
         "pathology": {
-            "Description": "Pathology",
-            "LongName": "Pathology name"
+            "Description": "The diagnosis of pathology of the participant",
+            "LongName": "Pathology name",
+            "Levels": {
+                "HC": "Healthy Control",
+                "DCM": "Degenerative Cervical Myelopathy",
+                "SCI": "Traumatic Spinal Cord Injury"
+            }
         },
         "institution_id": {
             "Description": "Institution ID in the unprocessed data",

From e17ed2c72fdf127664ef2dba0e7eefb0ca28478d Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Sat, 21 Jan 2023 10:13:53 -0500
Subject: [PATCH 36/38] README.md update

---
 scripts/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/README.md b/scripts/README.md
index b38e4bf..8c97410 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -6,7 +6,7 @@ It contains brain and spinal cord data acquired at two sites centers (Toronto, Z
 - degenerative cervical myelopathy (DCM)
 - spinal cord injury (SCI)
 
-It also contains spinal cord, gray matter and white matter segmentations for T2w axial images.
+It also contains spinal cord segmentation for T2w axial images and gray matter and white matter segmentations for T2star images.
 
 ## Dataset structure
 

From 9941af1811b4bf2553d9f3821ac46c4cc4a0fd1b Mon Sep 17 00:00:00 2001
From: Jan Valosek <39456460+valosekj@users.noreply.github.com>
Date: Tue, 24 Jan 2023 11:22:15 -0500
Subject: [PATCH 37/38] Move infolink

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>
---
 scripts/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/README.md b/scripts/README.md
index 8c97410..e3345e9 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,6 +1,6 @@
 # INSPIRED
 
-This is an MRI dataset acquired in the context of the INSPIRED project.
+This is an MRI dataset acquired in the context of the INSPIRED project (https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594).
 
 It contains brain and spinal cord data acquired at two sites centers (Toronto, Zurich) from healthy controls (HC) and two pathologies:
 - degenerative cervical myelopathy (DCM)

From 7d9783667086b12dacfebd524a130d91ec483030 Mon Sep 17 00:00:00 2001
From: Jan Valosek <39456460+valosekj@users.noreply.github.com>
Date: Tue, 24 Jan 2023 11:22:34 -0500
Subject: [PATCH 38/38] Add Contact Person section

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>
---
 scripts/README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/README.md b/scripts/README.md
index e3345e9..2246e30 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -29,6 +29,7 @@ Note: BIDS label `acq-cspine` is used to differentiate spine images from brain.
 
 Note: 01 corresponds to Toronto site, 02 to Zurich site. For details, see https://github.com/neuropoly/data-management/issues/184#issuecomment-1329250514.
 
-## Details
+## Contact Person
 
-https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594
\ No newline at end of file
+Main PI of the project: Claudia Wheeler Kingshott
+Contact person: Julien Cohen-Adad
\ No newline at end of file