From be63ca02fa6bf64bd099c8626ebe763289eb4641 Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 14:11:28 -0400
Subject: [PATCH 01/18] remove unused train.sh script

---
 scripts/train.sh | 74 ------------------------------------------------
 1 file changed, 74 deletions(-)
 delete mode 100644 scripts/train.sh

diff --git a/scripts/train.sh b/scripts/train.sh
deleted file mode 100644
index 9a44b17c..00000000
--- a/scripts/train.sh
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/bin/bash
-# 
-# This script does the following:
-# 1. Creates a virtual environment `venv_monai` and installs the required dependencies
-# 2. Generates a MSD-style datalist containing image/label pairs for training
-# 3. Trains the contrast-agnostic soft segmentation model
-# 4. Evaluates the model on the test set
-# 
-# Usage:
-# bash train.sh <path_to_preprocessed_data> <contrast> <label_type> <path_to_train_yaml>
-# 
-# Examples:
-# 1. Train a model on 'T1w' contrast with 'hard' labels
-#       bash train.sh /path/to/spine-generic-processed/ t1w hard train.yaml
-# 2. Train a model on 'all' contrasts with 'soft' labels
-#       bash train.sh /path/to/spine-generic-processed/ all soft train.yaml
-#
-#
-
-
-# Uncomment for full verbose
-# set -x
-
-# Immediately exit if error
-set -e -o pipefail
-
-# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
-trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
-
-# Set the following variables to the desired values
-# Path to the pre-processed spine-generic dataset
-PATH_DATA=$1
-CONTRAST=$2     # options: ["t1w", "t2w", "t2star", "mton", "mtoff", "dwi", "all"]
-LABEL_TYPE=$3   # options: ["hard", "soft", "soft_bin"]
-PATH_TRAIN_YAML=$4  # path to the yaml file containing the training configuration
-
-PATH_DATALIST_OUT="../datalists/spine-generic/temp/seed15/"
-# create folder if doesn't exist
-if [ ! -d $PATH_DATALIST_OUT ]; then
-  mkdir -p $PATH_DATALIST_OUT
-fi
-
-MODEL="nnunet"
-
-# # Create virtual environment
-# conda create -n venv_monai python=3.9 -y
-
-# NOTE: running conda activate <env_name> errors out requesting conda init to be run, 
-# the eval expression here makes it work without conda init.
-# source: https://stackoverflow.com/questions/34534513/calling-conda-source-activate-from-bash-script
-eval "$(conda shell.bash hook)"
-conda activate venv_monai
-
-# # Install dependencies quietly
-# pip install -r monai/requirements.txt --quiet
-
-# Run the script to generate the datalist JSON file
-python monai/create_msd_data.py \
-  --path-data $PATH_DATA \
-  --path-out $PATH_DATALIST_OUT \
-  --path-joblib "monai/split_datasets_all_seed=15.joblib" \
-  --contrast $CONTRAST \
-  --label-type $LABEL_TYPE \
-  --seed 15
-
-echo "----------------------------------------"
-echo "Training contrast-agnostic '$MODEL' model on '$CONTRAST' contrasts with '$LABEL_TYPE' labels"
-echo "----------------------------------------"
-
-# Train the model
-python monai/main.py --model $MODEL --config $PATH_TRAIN_YAML --debug
-
-# Deactivate the virtual environment
-conda deactivate

From 525322641dc4d98df92ac02eabe0f7984afb778e Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 14:24:06 -0400
Subject: [PATCH 02/18] add docstring for creating msd datalist json

---
 nnUnet/02_create_msd_data.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nnUnet/02_create_msd_data.py b/nnUnet/02_create_msd_data.py
index 374b8e56..aa569938 100644
--- a/nnUnet/02_create_msd_data.py
+++ b/nnUnet/02_create_msd_data.py
@@ -1,3 +1,11 @@
+"""
+This script takes as input the path to the original BIDS dataset and outputs a datalist json file
+    containing the train/val/test splits. To reproduce contrast-agnostic v3.0 training, the script
+    uses pre-defined splits by default (they can be found under the folder <path-to-repo/datasetplits>.)
+
+Authors: Naga Karthik
+"""
+
 import os
 import re
 import json

From a44d300f11b6680fe931b2d9727660e04d8a543d Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 14:26:28 -0400
Subject: [PATCH 03/18] minor update readme

---
 scripts/train_contrast_agnostic.sh | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/scripts/train_contrast_agnostic.sh b/scripts/train_contrast_agnostic.sh
index bcb83501..9edc48df 100644
--- a/scripts/train_contrast_agnostic.sh
+++ b/scripts/train_contrast_agnostic.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# This script is used for reproducing contrast-agnostic v3.1 training and also provides the option to extend the 
+# This script is used for reproducing contrast-agnostic v3.0 training and also provides the option to extend the 
 # contrast-agnostic spinal cord segmentation model with new datasets. It achieves the following:
 # 1. Clones the datasets from NeuroPoly's git-annex server. 
 # 2. Creates datalists (i.e. json files with image/label pairs) based on pre-defined or random dataset splits 
@@ -20,22 +20,23 @@ PATH_REPO="/home/GRAMES.POLYMTL.CA/u114716/contrast-agnostic/contrast-agnostic-s
 SEED=50
 
 # List of datasets to train on
-# NOTE 1: the following datasets were used for training the contrast-agnostic v3.1 model
-# https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/tag/v3.1 
-# NOTE 2: training on praxis acute SCI data requires special access to spineimage.ca. Because this is different from
+# NOTE 1: the following datasets were used for training the contrast-agnostic v3.0 model
+# https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/tag/v3.0
+# NOTE 2: training on praxis acute SCI data requires special access to `spineimage.ca`. Because this is different from
 # the usual downloading from git-annex, this script does not support downloading praxis data. To train contrast-agnostic model 
 # download the dataset manually and store it in PATH_DATA_BASE (see below)
 
-DATASETS=("data-multi-subject" "basel-mp2rage" "canproco" \
-            "lumbar-epfl" "lumbar-vanderbilt" "dcm-brno" "dcm-zurich" "dcm-zurich-lesions" "dcm-zurich-lesions-20231115" \
-            "sci-paris" "sci-zurich" "sci-colorado" "sct-testing-large" \
-            "site_006" "site_007"
-            )
-DATASETS=("site_006")
+# DATASETS=("data-multi-subject" "basel-mp2rage" "canproco" \
+#             "lumbar-epfl" "lumbar-vanderbilt" "dcm-brno" "dcm-zurich" "dcm-zurich-lesions" "dcm-zurich-lesions-20231115" \
+#             "sci-paris" "sci-zurich" "sci-colorado" "sct-testing-large" \
+#             "site_006" "site_007"
+#             )
+# for debugging purposes, test the script on 1 dataset from the above list
+DATASETS=("lumbar-vanderbilt")
 
 # Path to the folder where the datasets will be downloaded
-# PATH_DATA_BASE="/home/GRAMES.POLYMTL.CA/u114716/datasets"
-PATH_DATA_BASE="/scratch/naga/contrast_agnostic/datasets"
+PATH_DATA_BASE="/home/GRAMES.POLYMTL.CA/<your-grames-id>/datasets"
+# PATH_DATA_BASE="/scratch/naga/contrast_agnostic/datasets"
 
 # Path to the output folder where the dataset in MSD-style format will be saved as json files with image/label pairs
 # and other dataset-related statistics. To keep track of the experiments, date is also appended as a prefix or suffix

From ca36cec3bdc0397bd3c76881286451bd224e31a1 Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 14:34:32 -0400
Subject: [PATCH 04/18] pin package versions

---
 nnUnet/requirements.txt | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/nnUnet/requirements.txt b/nnUnet/requirements.txt
index d3d5f5a0..9db781cc 100644
--- a/nnUnet/requirements.txt
+++ b/nnUnet/requirements.txt
@@ -1,9 +1,9 @@
-nibabel
-seaborn
-matplotlib
-pandas
-numpy
+nibabel==5.1.0
+seaborn==0.13.2
+matplotlib==3.7.1
+pandas==2.0.1
+numpy<2.0.0
 tqdm
-pyyaml
+pyyaml==6.0
 loguru
-scikit-learn
\ No newline at end of file
+scikit-learn==1.2.2
\ No newline at end of file

From 784b34bbe6ca8bc108afe9318a08acafdc9761fd Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 14:38:52 -0400
Subject: [PATCH 05/18] update training instructions

---
 README.md | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index d6ed5f46..66708f63 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,7 @@ note = {Shared authorship -- authors contributed equally}
 
 1. Create a conda environment with the following command:
 ```bash
-conda create -n contrast_agnostic python=3.9
+conda create -n contrast_agnostic python=3.9.16
 ```
 
 2. Activate the environment with the following command:
@@ -64,8 +64,8 @@ git clone https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord.g
 
 3. Install the required packages with the following command:
 ```bash
-cd contrast-agnostic-softseg-spinalcord/nnUnet
-pip install -r requirements.txt
+cd contrast-agnostic-softseg-spinalcord
+pip install -r nnUnet/requirements.txt
 ```
 
 > **Note**
@@ -74,11 +74,16 @@ pip install -r requirements.txt
 
 ### Step 2: Train the model
 
-The script `scripts/train_contrast_agnostic.sh` downloads the datasets from git-annex, creates datalists, converts them into nnUNet-specific format, and trains the model. More instructions about what variables to set and which datasets to use can be found in the script itself. Once these variables are set, the script can be run simply as follows:
+The script `scripts/train_contrast_agnostic.sh` downloads the datasets from git-annex, creates datalists, converts them into nnUNet-specific format, and trains the model. More instructions about what variables to set and which datasets to use can be found in the script itself. Once these variables are set, run:
 
 ```bash
 bash scripts/train_contrast_agnostic.sh
 ```
+
+> [!IMPORTANT]  
+> The script `train_contrast_agnostic.sh` will NOT run out-of-the-box. User-specific variables such as the path to download datasets and nnUnet repository need to be set. Info about which varibles to set can be found in the script itself.
+
+
 <!-- 
 TODO: move to csa_qc_evaluation folder
 ## 5. Computing morphometric measures (CSA)

From 05c984fc7629ff6bffa6a9f5f57052f8073f3db4 Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 15:53:30 -0400
Subject: [PATCH 06/18] remove previous version of data-multi-subject; store
 dataset_name and commit also in datasplit.yml

---
 nnUnet/02_create_msd_data.py | 38 +++++++++++++-----------------------
 1 file changed, 14 insertions(+), 24 deletions(-)

diff --git a/nnUnet/02_create_msd_data.py b/nnUnet/02_create_msd_data.py
index aa569938..13671d14 100644
--- a/nnUnet/02_create_msd_data.py
+++ b/nnUnet/02_create_msd_data.py
@@ -119,13 +119,9 @@ def fetch_subject_nifti_details(filename_path):
     orientation = re.search('acq-(.*?)[_/]', filename_path)     # [_/] means either underscore or slash
     orientationID = orientation.group(0)[:-1] if orientation else ""    # [:-1] removes the last underscore or slash
 
-    if 'data-multi-subject' in filename_path:
-        # NOTE: the preprocessed spine-generic dataset have a weird BIDS naming convention (due to how they were preprocessed)
-        contrast_pattern =  r'.*_(space-other_T1w|space-other_T2w|space-other_T2star|flip-1_mt-on_space-other_MTS|flip-2_mt-off_space-other_MTS|rec-average_dwi).*'
-    else:
-        # TODO: add more contrasts as needed
-        # contrast_pattern =  r'.*_(T1w|T2w|T2star|PSIR|STIR|UNIT1|acq-MTon_MTR|acq-dwiMean_dwi|acq-b0Mean_dwi|acq-T1w_MTR).*'
-        contrast_pattern =  r'.*_(T1w|T2w|acq-sagthor_T2w|acq-sagcerv_T2w|acq-sagstir_T2w|acq-ax_T2w|T2star|PSIR|STIR|UNIT1|acq-MTon_MTR|acq-dwiMean_dwi|acq-T1w_MTR).*'
+    # TODO: add more contrasts as needed
+    # contrast_pattern =  r'.*_(T1w|T2w|T2star|PSIR|STIR|UNIT1|acq-MTon_MTR|acq-dwiMean_dwi|acq-b0Mean_dwi|acq-T1w_MTR).*'
+    contrast_pattern =  r'.*_(T1w|T2w|acq-sagthor_T2w|acq-sagcerv_T2w|acq-sagstir_T2w|acq-ax_T2w|T2star|PSIR|STIR|UNIT1|flip-1_mt-on_MTS|flip-2_mt-off_MTS|acq-MTon_MTR|acq-dwiMean_dwi|rec-average_dwi|acq-T1w_MTR).*'
     contrast = re.search(contrast_pattern, filename_path)
     contrastID = contrast.group(1) if contrast else ""
 
@@ -147,11 +143,7 @@ def create_df(args, dataset_path):
     labels_folder = FILESEG_SUFFIXES[dataset_name][0]
     labels_suffix = FILESEG_SUFFIXES[dataset_name][1]
 
-    if dataset_name == 'data-multi-subject':
-        # get only the (preprocessed) subject files, which are in the `derivatives` folder
-        path_files = os.path.join(dataset_path, 'derivatives', 'data_preprocessed', 'sub-*', '**', f'*.nii.gz')
-    
-    elif dataset_name == 'sct-testing-large':
+    if dataset_name == 'sct-testing-large':
         path_files = os.path.join(dataset_path, 'derivatives', labels_folder, 'sub-*', '**', f'*_{labels_suffix}.nii.gz')
 
         df_participants = pd.read_csv(os.path.join(dataset_path, 'participants.tsv'), sep='\t')
@@ -294,7 +286,7 @@ def create_df(args, dataset_path):
 
     # NOTE: Datasets might have lot of images might not have labels (and hence need not be downloaded to save space)
     # Get only those images which have labels and are present in the dataframe (and belong to the pathology)
-    for file in df['filename']:            
+    for file in df['filename']:
         fname_label = file
         gitannex_cmd_label = f'cd {dataset_path}; git annex get {fname_label}'
         
@@ -412,16 +404,9 @@ def main():
                 for idx in range(num_files_per_subject):
                 
                     temp_data = {}
-                    # if the subject belongs to a data-multi-subject dataset, then the filename is different
-                    if df['datasetName'].values[0] == 'data-multi-subject':
-                        # NOTE: for spine-generic subjects, we're pulling the data from image filename
-                        fname_image = df[df['subjectID'] == subject]['filename'].values[idx]
-                        fname_label = fname_image.replace('data_preprocessed', labels_folder).replace('.nii.gz', f'_{labels_suffix}.nii.gz')
-                    
-                    else: 
-                        # NOTE: but for other datasets, we are getting them from the lesion filenames
-                        fname_label = df[df['subjectID'] == subject]['filename'].values[idx]
-                        fname_image = fname_label.replace(f'/derivatives/{labels_folder}', '').replace(f'_{labels_suffix}.nii.gz', '.nii.gz')
+
+                    fname_label = df[df['subjectID'] == subject]['filename'].values[idx]
+                    fname_image = fname_label.replace(f'/derivatives/{labels_folder}', '').replace(f'_{labels_suffix}.nii.gz', '.nii.gz')
 
                     # # use when creating a balanced dataset
                     # temp_data["image"] = df[(df['subjectID'] == subject) & (df['split'] == name)].iloc[idx]['fname_image']
@@ -483,7 +468,12 @@ def main():
 
     # dump train/val/test splits into a yaml file
     with open(f"datasplits/datasplit_{dataset_name}_seed{args.seed}.yaml", 'w') as file:
-        yaml.dump({'train': sorted(train_subs_all), 'val': sorted(val_subs_all), 'test': sorted(test_subs_all)}, file, indent=2, sort_keys=True)
+        yaml.dump({
+            'dataset_name': dataset_name,
+            'dataset_version_commit': commit,
+            'train': sorted(train_subs_all), 
+            'val': sorted(val_subs_all), 
+            'test': sorted(test_subs_all)}, file, indent=2, sort_keys=True)
 
     # save the dataframe to a csv file
     # df.drop(columns=['filename'], inplace=True)     # drop the filename column

From 500f1a3c23dd75ca3ae4e302e5b604a31b6afb25 Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 16:00:43 -0400
Subject: [PATCH 07/18] add path-datasplits as arg so that dataset commit can
 be retrieved for subsequent dataset downloading

---
 nnUnet/01_clone_dataset.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/nnUnet/01_clone_dataset.py b/nnUnet/01_clone_dataset.py
index bf7fc23b..ff530a09 100644
--- a/nnUnet/01_clone_dataset.py
+++ b/nnUnet/01_clone_dataset.py
@@ -14,6 +14,7 @@
 import sys
 import subprocess
 import argparse
+import yaml
 
 # Add the parent directory of the script to the Python path
 SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
@@ -24,10 +25,16 @@
 # from utils.utils import SITES_DICT, get_git_branch_and_commit
 
 
-def download_dataset(dataset_name):
+def download_dataset(dataset_name, dataset_commit):
     # Clone the dataset
     subprocess.run(["git", "clone", f"git@data.neuro.polymtl.ca:datasets/{dataset_name}"])
     os.chdir(dataset_name)
+    
+    # Checkout the specific commit
+    subprocess.run(["git", "checkout", f"{dataset_commit}"])
+    
+    # Get the git-annex files
+    subprocess.run(["git", "annex", "init"])
     subprocess.run(["git", "annex", "dead", "here"])
 
     # Get the git commit ID of the dataset
@@ -53,10 +60,17 @@ def download_dataset(dataset_name):
                         required=True,
                         type=str,
                         help="Name of the dataset to be cloned")
+    parser.add_argument('--path-datasplits', type=str, default=None,
+                        help='Path to the datasplits folder containing predefined datasplits (used to fetch dataset commit)')
     args = parser.parse_args()
 
     PATH_DATA = os.path.abspath(os.path.expanduser(args.ofolder))
     os.chdir(PATH_DATA)
 
+    # get commit of the dataset
+    with open(os.path.join(args.path_datasplits, f"datasplit_{args.dataset}_seed50.yaml"), 'r') as file:
+        datasplits = yaml.safe_load(file)
+        dataset_commit = datasplits['dataset_version_commit']
+
     # for site, dataset_name in SITES_DICT.items():
-    download_dataset(args.dataset)
\ No newline at end of file
+    download_dataset(args.dataset, dataset_commit)
\ No newline at end of file

From a68591b8c3492f88ff311061c7d90af84e9afb8f Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 16:31:00 -0400
Subject: [PATCH 08/18] add dataset name and commit to the file

---
 datasplits/datasplit_data-multi-subject_seed50.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/datasplits/datasplit_data-multi-subject_seed50.yaml b/datasplits/datasplit_data-multi-subject_seed50.yaml
index d5eb5ab0..63641a0e 100644
--- a/datasplits/datasplit_data-multi-subject_seed50.yaml
+++ b/datasplits/datasplit_data-multi-subject_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: data-multi-subject
+dataset_version_commit: a0738046538232df8e09eba8d98899eada9c11d5
 test:
 - sub-barcelona06
 - sub-beijingPrisma01

From 5f26005b67a14329de9790ff8894dff1c360bba1 Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 16:31:35 -0400
Subject: [PATCH 09/18] update training script

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

diff --git a/scripts/train_contrast_agnostic.sh b/scripts/train_contrast_agnostic.sh
index a59ac663..f03fa84c 100644
--- a/scripts/train_contrast_agnostic.sh
+++ b/scripts/train_contrast_agnostic.sh
@@ -32,10 +32,10 @@ SEED=50
 #             "site_006" "site_007"
 #             )
 # for debugging purposes, test the script on 1 dataset from the above list
-DATASETS=("lumbar-vanderbilt")
+DATASETS=("data-multi-subject")
 
 # Path to the folder where the datasets will be downloaded
-PATH_DATA_BASE="/home/GRAMES.POLYMTL.CA/<your-grames-id>/datasets"
+PATH_DATA_BASE="/home/GRAMES.POLYMTL.CA/u114716/datasets"
 # PATH_DATA_BASE="/scratch/naga/contrast_agnostic/datasets"
 
 # Path to the output folder where the dataset in MSD-style format will be saved as json files with image/label pairs
@@ -73,7 +73,7 @@ NNUNET_TRAINER="nnUNetTrainer_5epochs"
 NNUNET_PLANS_FILE="nnUNetPlans"
 
 # Type/Kernel of the model. for 2D training, use "2d"; for 3D training, use "3d_fullres"
-# configurations=("2d" "3d_fullres")                        
+# configurations=("2d" "3d_fullres")
 configurations=("3d_fullres")
 
 # Number of cross-validation folds to run the model on. nnUNet by default allows training on 5 folds
@@ -106,7 +106,8 @@ for dataset in ${DATASETS[@]}; do
         echo "-----------------------------------"
         python ${PATH_REPO}/nnUnet/01_clone_dataset.py \
             --ofolder ${PATH_DATA_BASE} \
-            --dataset ${dataset} 
+            --dataset ${dataset} \
+            --path-datasplits ${PATH_REPO}/datasplits
     
     fi
 

From c428442930c18bc83706b065c49fa8cdbfc07a0e Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 7 Apr 2025 21:06:41 -0400
Subject: [PATCH 10/18] add dataset name and commit for all datasets

---
 datasplits/datasplit_basel-mp2rage_seed50.yaml               | 2 ++
 datasplits/datasplit_canproco_seed50.yaml                    | 2 ++
 datasplits/datasplit_dcm-brno_seed50.yaml                    | 2 ++
 datasplits/datasplit_dcm-zurich-lesions-20231115_seed50.yaml | 2 ++
 datasplits/datasplit_dcm-zurich-lesions_seed50.yaml          | 2 ++
 datasplits/datasplit_dcm-zurich_seed50.yaml                  | 2 ++
 datasplits/datasplit_lumbar-epfl_seed50.yaml                 | 2 ++
 datasplits/datasplit_lumbar-vanderbilt_seed50.yaml           | 2 ++
 datasplits/datasplit_sci-colorado_seed50.yaml                | 2 ++
 datasplits/datasplit_sci-paris_seed50.yaml                   | 2 ++
 datasplits/datasplit_sci-zurich_seed50.yaml                  | 2 ++
 datasplits/datasplit_sct-testing-large_seed50.yaml           | 2 ++
 datasplits/datasplit_site_006_seed50.yaml                    | 2 ++
 datasplits/datasplit_site_007_seed50.yaml                    | 2 ++
 14 files changed, 28 insertions(+)

diff --git a/datasplits/datasplit_basel-mp2rage_seed50.yaml b/datasplits/datasplit_basel-mp2rage_seed50.yaml
index 4db1ca44..68231006 100644
--- a/datasplits/datasplit_basel-mp2rage_seed50.yaml
+++ b/datasplits/datasplit_basel-mp2rage_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: basel-mp2rage
+dataset_version_commit: 1efa01bc306292bc043f9f6a6ea8c6ed4d6c44fd
 test:
 - sub-C069
 - sub-C090
diff --git a/datasplits/datasplit_canproco_seed50.yaml b/datasplits/datasplit_canproco_seed50.yaml
index 218bcb15..e0879167 100644
--- a/datasplits/datasplit_canproco_seed50.yaml
+++ b/datasplits/datasplit_canproco_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: canproco
+dataset_version_commit: a04d89739c769dc03f23fcda183df62c62f586a9
 test:
 - sub-cal080
 - sub-cal085
diff --git a/datasplits/datasplit_dcm-brno_seed50.yaml b/datasplits/datasplit_dcm-brno_seed50.yaml
index ca256f44..c3763de6 100644
--- a/datasplits/datasplit_dcm-brno_seed50.yaml
+++ b/datasplits/datasplit_dcm-brno_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: dcm-brno
+dataset_version_commit: 3dacde7ee16f0dfc27508fe0bf8f1919cfc7eb4d
 test:
 - sub-1860B6472B
 - sub-2295B4676B
diff --git a/datasplits/datasplit_dcm-zurich-lesions-20231115_seed50.yaml b/datasplits/datasplit_dcm-zurich-lesions-20231115_seed50.yaml
index f5cc1f5f..d7497bdd 100644
--- a/datasplits/datasplit_dcm-zurich-lesions-20231115_seed50.yaml
+++ b/datasplits/datasplit_dcm-zurich-lesions-20231115_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: dcm-zurich-lesions-20231115
+dataset_version_commit: 
 test:
 - sub-11
 - sub-12
diff --git a/datasplits/datasplit_dcm-zurich-lesions_seed50.yaml b/datasplits/datasplit_dcm-zurich-lesions_seed50.yaml
index 0bf5ddba..e009e254 100644
--- a/datasplits/datasplit_dcm-zurich-lesions_seed50.yaml
+++ b/datasplits/datasplit_dcm-zurich-lesions_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: dcm-zurich-lesions
+dataset_version_commit: d214e0603fcd3879317fe0a0b4cd634ee2a92f1d
 test:
 - sub-09
 - sub-16
diff --git a/datasplits/datasplit_dcm-zurich_seed50.yaml b/datasplits/datasplit_dcm-zurich_seed50.yaml
index 6cfa4588..b84ad25f 100644
--- a/datasplits/datasplit_dcm-zurich_seed50.yaml
+++ b/datasplits/datasplit_dcm-zurich_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: dcm-zurich
+dataset_version_commit: 83dab50d8138bbc1f8e4f18672e651e988d1e000
 test:
 - sub-260155
 - sub-296085
diff --git a/datasplits/datasplit_lumbar-epfl_seed50.yaml b/datasplits/datasplit_lumbar-epfl_seed50.yaml
index 6c92f1eb..3bd202a9 100644
--- a/datasplits/datasplit_lumbar-epfl_seed50.yaml
+++ b/datasplits/datasplit_lumbar-epfl_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: lumbar-epfl
+dataset_version_commit: c6685fc4762daea3ec6f184b128b7fe19acad2b8
 test:
 - sub-05
 - sub-11
diff --git a/datasplits/datasplit_lumbar-vanderbilt_seed50.yaml b/datasplits/datasplit_lumbar-vanderbilt_seed50.yaml
index b74f6214..7b704f43 100644
--- a/datasplits/datasplit_lumbar-vanderbilt_seed50.yaml
+++ b/datasplits/datasplit_lumbar-vanderbilt_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: lumbar-vanderbilt
+dataset_version_commit: 81fc970a6515ec27d90c0dda5935b5179a10305e
 test:
 - sub-140549
 - sub-242142
diff --git a/datasplits/datasplit_sci-colorado_seed50.yaml b/datasplits/datasplit_sci-colorado_seed50.yaml
index 4d5db4e3..8b736d25 100644
--- a/datasplits/datasplit_sci-colorado_seed50.yaml
+++ b/datasplits/datasplit_sci-colorado_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: sci-colorado
+dataset_version_commit: 1518ecd184b8a89bc1a1197eb5ae4caf5c608fb9
 test:
 - sub-5575
 - sub-5629
diff --git a/datasplits/datasplit_sci-paris_seed50.yaml b/datasplits/datasplit_sci-paris_seed50.yaml
index 0aeac2d8..31aeec2a 100644
--- a/datasplits/datasplit_sci-paris_seed50.yaml
+++ b/datasplits/datasplit_sci-paris_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: sci-paris
+dataset_version_commit: 0a0d252c95e2400038f86e80bde85ffba0ffff0e 
 test:
 - sub-045
 - sub-049
diff --git a/datasplits/datasplit_sci-zurich_seed50.yaml b/datasplits/datasplit_sci-zurich_seed50.yaml
index 760e2365..61bd2d77 100644
--- a/datasplits/datasplit_sci-zurich_seed50.yaml
+++ b/datasplits/datasplit_sci-zurich_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: sci-zurich
+dataset_version_commit: ac1e679a91e5befac1bcd09ba451daddf2a25d1b
 test:
 - sub-zh117
 - sub-zh119
diff --git a/datasplits/datasplit_sct-testing-large_seed50.yaml b/datasplits/datasplit_sct-testing-large_seed50.yaml
index c245a28a..983eff9f 100644
--- a/datasplits/datasplit_sct-testing-large_seed50.yaml
+++ b/datasplits/datasplit_sct-testing-large_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: sct-testing-large
+dataset_version_commit: c26a5d690e2ced34bd5dea61cab66a7cb0eaebed
 test:
 - sub-milanFilippi003
 - sub-milanFilippi005
diff --git a/datasplits/datasplit_site_006_seed50.yaml b/datasplits/datasplit_site_006_seed50.yaml
index 3763ecf1..a24dc61f 100644
--- a/datasplits/datasplit_site_006_seed50.yaml
+++ b/datasplits/datasplit_site_006_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: site_006
+dataset_version_commit: 
 test:
 - sub-mon111
 train:
diff --git a/datasplits/datasplit_site_007_seed50.yaml b/datasplits/datasplit_site_007_seed50.yaml
index 928517e3..5947fa01 100644
--- a/datasplits/datasplit_site_007_seed50.yaml
+++ b/datasplits/datasplit_site_007_seed50.yaml
@@ -1,3 +1,5 @@
+dataset_name: site_007
+dataset_version_commit: 
 test:
 - sub-007473
 train:

From 41cac3d26d50d2519336e357179ebc85cb08ade2 Mon Sep 17 00:00:00 2001
From: valosekj <jan.valosek@upol.cz>
Date: Mon, 14 Apr 2025 07:51:42 -0400
Subject: [PATCH 11/18] clarify 'sct_register_multimodal -identity 1'

---
 nnUnet/03_convert_msd_to_nnunet_reorient.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nnUnet/03_convert_msd_to_nnunet_reorient.py b/nnUnet/03_convert_msd_to_nnunet_reorient.py
index 544597d6..cc9908e5 100644
--- a/nnUnet/03_convert_msd_to_nnunet_reorient.py
+++ b/nnUnet/03_convert_msd_to_nnunet_reorient.py
@@ -46,7 +46,8 @@ def process_single_image(args):
     # Reorient label to RPI
     assert os.system(f"sct_image -i {img_dict['label']} -setorient RPI -o {label_file_nnunet}") == 0
     
-    # Register label to image
+    # Put label to image to match dimension, resolution and orientation
+    # '-identity 1': registration optimization (e.g. translations, rotations, deformations) is skipped
     assert os.system(f"sct_register_multimodal -i {str(label_file_nnunet)} -d {str(image_file_nnunet)} "
                     f"-identity 1 -o {str(label_file_nnunet)} -owarp file_to_delete_{counter}.nii.gz "
                     f"-owarpinv file_to_delete_2_{counter}.nii.gz") == 0

From 69c6d0a8aefa87182065262935ac05ee2a4ab3ad Mon Sep 17 00:00:00 2001
From: Naga Karthik Enamundram <53445351+naga-karthik@users.noreply.github.com>
Date: Mon, 14 Apr 2025 08:40:59 -0400
Subject: [PATCH 12/18] add a note for running on tmux

Co-authored-by: Jan Valosek <39456460+valosekj@users.noreply.github.com>
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 66708f63..4143e177 100644
--- a/README.md
+++ b/README.md
@@ -83,7 +83,8 @@ bash scripts/train_contrast_agnostic.sh
 > [!IMPORTANT]  
 > The script `train_contrast_agnostic.sh` will NOT run out-of-the-box. User-specific variables such as the path to download datasets and nnUnet repository need to be set. Info about which varibles to set can be found in the script itself.
 
-
+> [!IMPORTANT]  
+ > You might need to run the `train_contrast_agnostic.sh` script in a virtual terminal such as `tmux` or `screen`.
 <!-- 
 TODO: move to csa_qc_evaluation folder
 ## 5. Computing morphometric measures (CSA)

From 4525309b58cb87620283c08b9f8fb55f9f2cb86a Mon Sep 17 00:00:00 2001
From: Naga Karthik <emvnagakarthik@gmail.com>
Date: Mon, 14 Apr 2025 08:45:20 -0400
Subject: [PATCH 13/18] add condition for data-multi to not download from gitea

---
 nnUnet/01_clone_dataset.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nnUnet/01_clone_dataset.py b/nnUnet/01_clone_dataset.py
index ff530a09..974818e9 100644
--- a/nnUnet/01_clone_dataset.py
+++ b/nnUnet/01_clone_dataset.py
@@ -27,7 +27,10 @@
 
 def download_dataset(dataset_name, dataset_commit):
     # Clone the dataset
-    subprocess.run(["git", "clone", f"git@data.neuro.polymtl.ca:datasets/{dataset_name}"])
+    if dataset_name == 'data-multi-subject':
+        subprocess.run(["git", "clone", f"https://github.com/spine-generic/{dataset_name}"])
+    else:
+        subprocess.run(["git", "clone", f"git@data.neuro.polymtl.ca:datasets/{dataset_name}"])
     os.chdir(dataset_name)
     
     # Checkout the specific commit

From 214fa3901816a232d901f9c882aed0368252cca3 Mon Sep 17 00:00:00 2001
From: Naga Karthik Enamundram <53445351+naga-karthik@users.noreply.github.com>
Date: Mon, 14 Apr 2025 09:14:57 -0400
Subject: [PATCH 14/18] add lifelong learning figure

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 4143e177..6abe4589 100644
--- a/README.md
+++ b/README.md
@@ -7,6 +7,9 @@ Official repository for contrast-agnostic segmentation of the spinal cord.
 This repo contains all the code for training the contrast-agnostic model. The code for training is based on the [nnUNetv2 framework](https://github.com/MIC-DKFZ/nnUNet). The segmentation model is available as part of [Spinal Cord Toolbox (SCT)](https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/spinalcord.html) via the `sct_deepseg` functionality.
 
 
+<img width="1540" alt="lifelong_ca_final" src="https://github.com/user-attachments/assets/c35d445c-d2ec-4bca-9995-e16371972cbf" />
+
+
 ### Citation Information
 
 If you find this work and/or code useful for your research, please cite our paper:
@@ -26,8 +29,6 @@ note = {Shared authorship -- authors contributed equally}
 }
 ```
 
-**TODO**: add lifelong learning figure
-
 
 ## Table of contents
 * [Training the model ](#training-the-model)

From 6aca11a3a10462c2f3b2ea2253c12332353292a0 Mon Sep 17 00:00:00 2001
From: Naga <emvnagakarthik@gmail.com>
Date: Thu, 16 Oct 2025 23:36:03 -0400
Subject: [PATCH 15/18] add function to compute statistical tests

---
 csa_generate_figures/analyse_csa_across.py | 147 ++++++++++++++++++++-
 1 file changed, 145 insertions(+), 2 deletions(-)

diff --git a/csa_generate_figures/analyse_csa_across.py b/csa_generate_figures/analyse_csa_across.py
index 252e31b0..9f11aa93 100644
--- a/csa_generate_figures/analyse_csa_across.py
+++ b/csa_generate_figures/analyse_csa_across.py
@@ -12,6 +12,9 @@
 import seaborn as sns
 import numpy as np
 import matplotlib.pyplot as plt
+from scipy.stats import friedmanchisquare, normaltest, wilcoxon
+import scikit_posthocs as sp
+from loguru import logger
 
 # Setting the hue order as specified
 HUE_ORDER = ["softseg_bin", "deepseg_2d", "v20", "nnunet-AllRandInit3D_bin"]
@@ -33,6 +36,36 @@
         'nnunet-AllRandInit3D_bin': '#a6d854',
     }
 
+def format_pvalue(p_value, decimal_places=3, include_space=False, include_equal=True):
+    """
+    Format p-value.
+    If the p-value is lower than alpha, format it to "<0.001", otherwise, round it to three decimals
+
+    :param p_value: input p-value as a float
+    :param decimal_places: number of decimal places the p-value will be rounded
+    :param include_space: include space or not (e.g., ' = 0.06')
+    :param include_equal: include equal sign ('=') to the p-value (e.g., '=0.06') or not (e.g., '0.06')
+    :return: p_value: the formatted p-value (e.g., '<0.05') as a str
+    """
+    if include_space:
+        space = ' '
+    else:
+        space = ''
+
+    # If the p-value is lower than alpha, return '<alpha' (e.g., <0.001)
+    for alpha in [0.001, 0.01, 0.05]:
+        if p_value < alpha:
+            p_value = space + "<" + space + str(alpha)
+            break
+    # If the p-value is greater than 0.05, round it number of decimals specified by decimal_places
+    else:
+        if include_equal:
+            p_value = space + '=' + space + str(round(p_value, decimal_places))
+        else:
+            p_value = space + str(round(p_value, decimal_places))
+
+    return p_value
+
 
 def save_figure(file_path, save_fname):
     plt.tight_layout()
@@ -97,7 +130,6 @@ def extract_contrast_and_details(filename, across="Method"):
         raise ValueError(f'Unknown analysis type: {across}. Choices: [Method, Resolution, Threshold].')
     
 
-
 def generate_figure_std(data, file_path, across="Method", metric="csa", hue_order=HUE_ORDER):
     """
     Generate violinplot showing STD across participants for each method
@@ -334,7 +366,6 @@ def generate_figure_csa(file_path, data, method=None, threshold=None):
     save_figure(file_path, save_fname)
 
 
-
 def generate_figure_csa_all_methods(file_path, data):
     """
     Generate a single violinplot showing CSA for each contrast across all methods
@@ -464,10 +495,117 @@ def generate_figure_csa_all_methods(file_path, data):
     plt.show()
 
 
+def compute_statistical_tests(df_avg_csa, exp_type='default'):
+    """
+    Compute statistical tests to compare the STD of CSA across methods.
+    """
+    # Compute mean and std across contrasts for each method
+    # contains columns: 'Method', 'Participant', 'mean', 'std'
+    df = df_avg_csa.groupby(['Method', 'Participant'])['MEAN(area)'].agg(['mean', 'std']).reset_index()
+    # drop method 'softseg_bin'
+    df = df[df['Method'] != 'softseg_bin']  # we don't want pair-wise comparisons with GT (only methods)
+    
+    # create df for each method
+    method_dfs = {}
+    for method in df['Method'].unique():
+        method_dfs[method] = df[df['Method'] == method][['Participant', 'std']].set_index('Participant')
+    
+    # check the length of each method dataframe
+    lengths = [len(method_dfs[method]) for method in method_dfs]
+    if len(set(lengths)) != 1:
+        logger.info("Error: Not all methods have the same number of participants. Cannot perform Friedman test.")
+        return
+    
+    # for method in df['Method'].unique():
+    #     if method == 'v20':
+    #         # just a sanity check to see if average of std values matches what we have on STD CSA plot
+    #         # print mean and std of the 'std' column
+    #         mean_std = method_dfs[method]['std'].mean()
+    #         std_std = method_dfs[method]['std'].std()
+    #         print(f'Method: {method}, Mean of STD: {mean_std:.3f}, Std of STD: {std_std:.3f}')
+
+    # Check normality of the data for each method using D'Agostino and Pearson's test
+    for method in method_dfs:
+        stat, p_value = normaltest(method_dfs[method]['std'])
+        logger.info(f'Normality test for method {method}: stat={stat}, p-value (formatted): {format_pvalue(p_value)}, p-value: {p_value}')
+        if p_value < 0.05:
+            logger.info(f"The data for method {method} is not normally distributed (reject H0). Consider using a non-parametric test.\n")
+        else:
+            logger.info(f"The data for method {method} is normally distributed (fail to reject H0)")
+
+    if exp_type == 'ablation':
+
+        # check if nnunet-AllInferred3D_bin|nnunet-AllRandInit3D_bin are in method_dfs
+        methods_to_compare = ['nnunet-AllInferred3D_bin', 'nnunet-AllRandInit3D_bin']
+        for method in methods_to_compare:
+            if method not in method_dfs:
+                logger.info(f"Error: Method {method} not found in the data. Cannot perform Wilcoxon signed-rank test.")
+                return
+
+        # NOTE: because we only have 2 related samples (i.e., methods): original model and one trained with recursive GT.
+        # we use Wilcoxon signed-rank test
+        stat, p_value = wilcoxon(method_dfs['nnunet-AllInferred3D_bin']['std'], method_dfs['nnunet-AllRandInit3D_bin']['std'])
+        logger.info(f'Wilcoxon signed-rank test statistic: {stat}, p-value (formatted): {format_pvalue(p_value)}, p-value: {p_value}')
+        if p_value < 0.05:
+            logger.info("There is a significant difference between the two methods (reject H0).\n")
+
+    else:
+        # NOTE: Why Friedman? Because we have more than 2 related samples (i.e., methods) and we want to compare their distributions.
+        # Related (paired) samples because the same participants (i.e. test set) are used for each method.
+        stat, p_value = friedmanchisquare(*[method_dfs[method]['std'] for method in method_dfs])
+        logger.info(f'Friedman test statistic: {stat}, p-value (formatted): {format_pvalue(p_value)}, p-value: {p_value}')
+        if p_value < 0.05:
+            logger.info("There is a significant difference between the methods (reject H0). Perform post-hoc test to identify which pairs are different.\n")
+
+            # reframe the df to have all methods in a column and the metric values in another column
+            df_friedman = pd.DataFrame()
+            for method in method_dfs:
+                temp_df = method_dfs[method].reset_index()
+                temp_df['Method'] = method
+                df_friedman = pd.concat([df_friedman, temp_df])
+            df_friedman = df_friedman.rename(columns={'std': 'Metric'})
+
+            # NOTE: As per https://scikit-posthocs.readthedocs.io/en/latest/generated/scikit_posthocs.posthoc_dunn.html
+            # Dunn's test is suitable after Kruskall-Wallis test
+            # # Perform post-hoc test using Dunn's test with Holm correction
+            # p_posthoc = sp.posthoc_dunn(df_friedman, val_col='Metric', group_col='Method', p_adjust='holm')
+            # logger.info("Post-hoc Dunn's test p-values (Holm corrected):")
+            # logger.info(f"\n{p_posthoc}")
+
+            # NOTE: As per https://scikit-posthocs.readthedocs.io/en/latest/generated/scikit_posthocs.posthoc_nemenyi_friedman.html
+            # there exists a post-hoc test specifically for Friedman test, which is the Nemenyi test
+            # Perform post-hoc test using nemenyi test
+            # get a non-melted version of df_friedman (can be used with default setting of scikit-posthocs)
+            df_wide = df_friedman.pivot(index='Participant', columns='Method', values='Metric')
+            
+            p_posthoc = sp.posthoc_nemenyi_friedman(df_wide)
+            logger.info("Post-hoc Nemenyi test p-values:")
+            logger.info(f"\n{p_posthoc}")
+
+            # check if p_posthoc is symmetric
+            assert (p_posthoc.values == p_posthoc.values.T).all(), "Post-hoc p-value matrix is not symmetric"
+
+            # p_posthoc is a square matrix with the p-values for each pair of methods. The diagonal is always 1 
+            # (i.e., method compared to itself). So, the matrix is symmetric (i.e., p-value for method A vs B is the same as B vs A)
+            # we only need to print the upper triangle of the matrix
+            logger.info("Significant differences (p < 0.05) between methods:")
+            for i in range(len(p_posthoc)):
+                for j in range(i+1, len(p_posthoc)):
+                    method1 = p_posthoc.index[i]
+                    method2 = p_posthoc.columns[j]
+                    p_val = p_posthoc.iloc[i, j]
+                    if p_val < 0.05:
+                        logger.info(f"\t{method1} vs {method2}: p-value (formatted): {format_pvalue(p_val)}, p-value: {p_val}")
+        else:
+            logger.info("No significant difference between the methods (fail to reject H0)")
+
+
 def main(args, analysis_type="methods"):
     # Load the CSV file containing averaged (across slices) C2-C3 CSA 
     data_avg_csa = pd.read_csv(args.i)
 
+    logger.add(os.path.join(os.path.dirname(args.i), 'log.txt'), rotation='10 MB', level='INFO')
+
     # Apply the function to extract participant ID
     data_avg_csa['Participant'] = data_avg_csa['Filename'].apply(fetch_participant_id)
 
@@ -483,6 +621,9 @@ def main(args, analysis_type="methods"):
         # Generate violinplot showing STD across participants for each method
         generate_figure_std(data_avg_csa, file_path=args.i, metric="csa")
 
+        # Compute statistical tests
+        compute_statistical_tests(data_avg_csa, exp_type='ablation' if args.ablation else 'default')
+
         if args.i_dice is not None:
             # Generate violinplot showing average slicewise Dice scores across participants for each method
 
@@ -532,5 +673,7 @@ def main(args, analysis_type="methods"):
                         help="Path to the CSV file containing averaged slice-wise Dice scores for each contrast, method, and subjects")
     parser.add_argument('-a', type=str, default="methods", 
                         help='Options to analyse CSA across. Choices: [methods, resolutions]')
+    parser.add_argument('--ablation', action='store_true',
+                        help='If set, perform generate std, stats results for recursive/ablation experiments.')
     args = parser.parse_args()
     main(args, analysis_type=args.a)
\ No newline at end of file

From 3e1453cb0f5efb6802e1676f73a2ee7509d4936d Mon Sep 17 00:00:00 2001
From: Naga <emvnagakarthik@gmail.com>
Date: Mon, 20 Oct 2025 17:01:44 -0400
Subject: [PATCH 16/18] update script to get sequence params for frozen spine
 generic test set

---
 scripts/fetch_sequence_parameters.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/scripts/fetch_sequence_parameters.py b/scripts/fetch_sequence_parameters.py
index 1bc714b3..bf99cfe3 100644
--- a/scripts/fetch_sequence_parameters.py
+++ b/scripts/fetch_sequence_parameters.py
@@ -137,7 +137,8 @@ def fetch_participant_details(input_string):
 
     if 'data-multi-subject' in input_string:
         # NOTE: the preprocessed spine-generic dataset have a weird BIDS naming convention (due to how they were preprocessed)
-        contrast_pattern =  r'.*_(space-other_T1w|space-other_T2w|space-other_T2star|flip-1_mt-on_space-other_MTS|flip-2_mt-off_space-other_MTS|rec-average_dwi).*'
+        # contrast_pattern =  r'.*_(space-other_T1w|space-other_T2w|space-other_T2star|flip-1_mt-on_space-other_MTS|flip-2_mt-off_space-other_MTS|rec-average_dwi).*'
+        contrast_pattern =  r'.*_(T1w|T2w|T2star|flip-1_mt-on_MTS|flip-2_mt-off_MTS|rec-average_dwi).*'
     else:
         # TODO: add more contrasts as needed
         # contrast_pattern =  r'.*_(T1w|T2w|T2star|PSIR|STIR|UNIT1|acq-MTon_MTR|acq-dwiMean_dwi|acq-b0Mean_dwi|acq-T1w_MTR).*'
@@ -173,7 +174,8 @@ def main():
             data = json.load(f)
         
         list_of_files = []
-        for split in ['train', 'validation', 'test']:
+        # for split in ['train', 'validation', 'test']:
+        for split in ['test']:
             for idx in range(len(data[split])):
                 list_of_files.append(data[split][idx]["image"])
 
@@ -206,6 +208,15 @@ def main():
 
         logger.info(f"Dataset: {dataset_name}")
 
+        contrasts = df['Contrast'].unique()
+        # contrasts = ['DWI', 'MToff', 'MTon', 'T1w', 'T2star', 'T2w']
+        for contrast in contrasts:
+            df_contrast = df[df['Contrast'] == contrast]
+            logger.info(f"\nContrast: {contrast}")
+            logger.info(f"Number of files: {len(df_contrast)}")
+            logger.info(f"PixDim (min, max): {df_contrast['PixDim'].agg(['min', 'max']).to_dict()}")
+            logger.info(f"SliceThickness (min, max): {df_contrast['SliceThickness'].agg(['min', 'max']).to_dict()}")
+
         # Remove rows with n/a values for MagneticFieldStrength
         df = df[df['MagneticFieldStrength'] != 'n/a']
 
@@ -215,8 +226,8 @@ def main():
         # Print the min and max values of the MagneticFieldStrength, PixDim, and SliceThickness
         logger.info(f"\n{df[['MagneticFieldStrength', 'PixDim', 'SliceThickness']].agg(['min', 'max'])}")
 
-        # Print unique values of the Manufacturer and ManufacturerModelName
-        logger.info(f"\n{df[['Manufacturer', 'ManufacturerModelName']].drop_duplicates()}")
+        # # Print unique values of the Manufacturer and ManufacturerModelName
+        # logger.info(f"\n{df[['Manufacturer', 'ManufacturerModelName']].drop_duplicates()}")
         # # Print number of filenames for unique values of the Manufacturer
         # print(df.groupby('Manufacturer')['filename'].nunique())
         # # Print number of filenames for unique values of the MagneticFieldStrength

From 4e5ad8b3145c2ab0f2911c97e44380069e30b672 Mon Sep 17 00:00:00 2001
From: Naga <emvnagakarthik@gmail.com>
Date: Mon, 20 Oct 2025 17:02:19 -0400
Subject: [PATCH 17/18] add weights_only argument

---
 monai/run_inference_single_image.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/run_inference_single_image.py b/monai/run_inference_single_image.py
index 81a383c3..ee3bef57 100644
--- a/monai/run_inference_single_image.py
+++ b/monai/run_inference_single_image.py
@@ -316,7 +316,7 @@ def main():
             test_input = batch["image"].to(DEVICE)
             
             # this loop only takes about 0.2s on average on a CPU
-            checkpoint = torch.load(chkp_path, map_location=torch.device(DEVICE))["state_dict"]
+            checkpoint = torch.load(chkp_path, map_location=torch.device(DEVICE), weights_only=False)["state_dict"]
             # NOTE: remove the 'net.' prefix from the keys because of how the model was initialized in lightning
             # https://discuss.pytorch.org/t/missing-keys-unexpected-keys-in-state-dict-when-loading-self-trained-model/22379/14
             for key in list(checkpoint.keys()):

From f33c62c7e382e46807c5141b2a75d712a8e4b189 Mon Sep 17 00:00:00 2001
From: Naga <emvnagakarthik@gmail.com>
Date: Mon, 20 Oct 2025 17:03:56 -0400
Subject: [PATCH 18/18] update script to add Jaccard, HD metrics; add support
 to compute metrics based on existing xml files

---
 .../compute_anima_metrics_spine_generic.py    | 26 ++++++++++++-------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/anima_metrics/compute_anima_metrics_spine_generic.py b/anima_metrics/compute_anima_metrics_spine_generic.py
index b9a1f3d6..f4265de7 100644
--- a/anima_metrics/compute_anima_metrics_spine_generic.py
+++ b/anima_metrics/compute_anima_metrics_spine_generic.py
@@ -102,11 +102,13 @@ def get_parser():
                         help='Path to the folder containing nifti images of test predictions AND GTs'
                         ' when method == monai, else path to the xml files containing the pre-computed'
                         ' ANIMA metrics when method == [deepseg*, propseg]')
+    parser.add_argument('--out-folder', required=False, type=str, default=None,
+                        help='Path to the folder containing the output xml files containing the ANIMA metrics.')
     parser.add_argument('-dname', '--dataset-name', required=True, type=str, choices=STANDARD_DATASETS,
                         help='Dataset name used for storing on git-annex. For region-based metrics, '
                              'append "-region" to the dataset name. Default: spine-generic')
     parser.add_argument('--method', required=True, type=str, default='monai', 
-                        choices=['monai', 'synthseg', 'deepseg2d', 'deepseg3d', 'propseg', 'v20', 'v30'],
+                        choices=['monai', 'synthseg', 'deepseg2d', 'deepseg3d', 'propseg', 'v20', 'v30', 'scisegv2'],
                         help='Segmentation method to compute metrics for. Default: monai')
 
     return parser
@@ -120,10 +122,13 @@ def get_test_metrics_by_dataset(pred_folder, output_folder, anima_binaries_path,
     if method == 'v20':
         pred_suffix = 'seg_v20' # '_pred.nii.gz'
     elif method == 'v30':
-        pred_suffix = 'seg_nnunet-AllRandInit3D_bin'
+        # pred_suffix = 'seg_nnunet-AllRandInit3D_bin'
+        pred_suffix = 'seg_nnunet-AllRandInit3D'
     elif method == 'deepseg2d':
         pred_suffix = 'seg_deepseg_2d'
-    gt_suffix = 'softseg_bin' # '_softseg_gt.nii.gz'
+    elif method == 'scisegv2':
+        pred_suffix = 'seg_scisegv2'
+    gt_suffix = "label-SC_seg" #'seg-manual' # 'softseg_bin'
     if data_set in STANDARD_DATASETS:
         # glob all the predictions and GTs and get the last three digits of the filename
         pred_files = sorted(glob.glob(f"{pred_folder}/**/**/*_{pred_suffix}.nii.gz"))
@@ -202,9 +207,13 @@ def main():
     print(f"Saving ANIMA performance metrics to {output_folder}")
 
     # Get all XML filepaths where ANIMA performance metrics are saved for each hold-out subject
-    if method in ['monai', 'synthseg', 'v20', 'deepseg2d', 'v30']:
-        subject_filepaths = get_test_metrics_by_dataset(pred_folder, output_folder, anima_binaries_path, 
-                                                        data_set=dataset_name, method=method)
+    if method in ['monai', 'synthseg', 'v20', 'deepseg2d', 'v30', 'scisegv2']:
+        if args.out_folder:
+            subject_filepaths = [os.path.join(output_folder, f) for f in os.listdir(output_folder) if f.endswith('.xml')]
+        else:
+            print("Computing ANIMA metrics from scratch as no output folder is provided!")
+            subject_filepaths = get_test_metrics_by_dataset(pred_folder, output_folder, anima_binaries_path, 
+                                                            data_set=dataset_name, method=method)
     elif method in ['deepseg3d', 'propseg']:
         subject_filepaths = sorted(glob.glob(f"{pred_folder}/*.xml"))
     else:
@@ -216,7 +225,7 @@ def main():
     # Update the test metrics dictionary by iterating over all subjects
     for subject_filepath in subject_filepaths:
         subject = os.path.split(subject_filepath)[-1].split('_')[0]
-        contrast = os.path.split(subject_filepath)[-1].split('_')[1]
+        contrast = 'T2' #os.path.split(subject_filepath)[-1].split('_')[1] # T2w
         root_node = ET.parse(source=subject_filepath).getroot()
 
         # create a dictionary to store the metrics for each subject
@@ -252,8 +261,7 @@ def main():
     # get the list of contrasts
     contrasts = sorted(list(test_metrics[list(test_metrics.keys())[0]].keys()))
     print(f"Contrasts: {contrasts}")
-    metrics = ['Dice', 'RelativeVolumeError', 'SurfaceDistance', 'HausdorffDistance']
-
+    metrics = ['Jaccard', 'Dice', 'RelativeVolumeError', 'SurfaceDistance', 'HausdorffDistance']
     metrics_per_contrast = {}
     metrics_avg_all = {}