diff --git a/compass-nd/10_connectome_slurm_array_missing.bash b/compass-nd/10_connectome_slurm_array_missing.bash
new file mode 100644
index 0000000..87b7985
--- /dev/null
+++ b/compass-nd/10_connectome_slurm_array_missing.bash
@@ -0,0 +1,45 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --cpus-per-task=1
+
+GIGA_CONNECTOME_VERSION=0.4.1
+GIGA_CONNECTOME=/home/${USER}/projects/rrg-pbellec/containers/giga_connectome-${GIGA_CONNECTOME_VERSION}.simg
+FMRIPREP_DIR=/lustre04/scratch/${USER}/compass-nd_fmriprep-20.2.7lts/bids_release_7/fmriprep-20.2.7lts
+CONNECTOME_OUTPUT=/lustre04/scratch/${USER}/compass-nd_connectome-${GIGA_CONNECTOME_VERSION}
+WORKINGDIR="${CONNECTOME_OUTPUT}/working_directory"
+
+module load apptainer
+
+mkdir -p $WORKINGDIR
+
+PARTICIPANT_LABEL=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ${participant_labels})
+PARTICIPANT_OUTPUT="${CONNECTOME_OUTPUT}/${PARTICIPANT_LABEL}"
+
+echo "${FMRIPREP_DIR}"
+if [ -d "${FMRIPREP_DIR}" ]; then
+    mkdir -p ${WORKINGDIR}
+        mkdir -p ${SLURM_TMPDIR}
+        mkdir -p ${PARTICIPANT_OUTPUT}
+        echo "Running ${PARTICIPANT_LABEL} connectomes"
+        echo "=========${STRATEGY}========="
+        echo "${ATLAS}"
+        apptainer run \
+                --bind ${FMRIPREP_DIR}:/data/input \
+                --bind ${SLURM_TMPDIR}:/data/output \
+                --bind ${WORKINGDIR}:/data/working \
+                ${GIGA_CONNECTOME} \
+                -w /data/working \
+                --atlas ${ATLAS} \
+                --denoise-strategy ${STRATEGY} \
+                ${INTRANETWORK_FLAG} \
+                /data/input \
+                /data/output \
+                participant \
+        --participant_label ${PARTICIPANT_LABEL}
+        exitcode=$?  # catch exit code
+        if [ $exitcode -eq 0 ] ; then rsync -rltv --info=progress2 ${SLURM_TMPDIR}/*.h5 ${PARTICIPANT_OUTPUT} ; fi
+else
+    echo "no preprocessed data for ${DATASET}"
+fi
\ No newline at end of file
diff --git a/compass-nd/10_submit_connectome_array_missing.sh b/compass-nd/10_submit_connectome_array_missing.sh
new file mode 100644
index 0000000..930ece2
--- /dev/null
+++ b/compass-nd/10_submit_connectome_array_missing.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+
+DATASET="compass-nd"
+CONNECTOME_OUTPUT=/lustre04/scratch/${USER}/compass-nd_connectome-0.4.1
+
+STRATEGIES=("simple" "simple+gsr" "scrubbing.2" "scrubbing.2+gsr" "scrubbing.5" "scrubbing.5+gsr" "acompcor50")
+ATLASES=("DiFuMo" "Schaefer20187Networks" "MIST")
+
+for strategy in "${STRATEGIES[@]}"; do
+    for atlas in "${ATLASES[@]}"; do
+            mem=8G
+            time="00:15:00"
+            INTRANETWORK_FLAG="--calculate-intranetwork-average-correlation"
+
+            if [ "${atlas}" == "DiFuMo" ]; then
+                time="00:25:00"
+                mem=12G
+                INTRANETWORK_FLAG=""
+            fi
+
+            # Generate the participant_labels file based on the missing file information
+            missing_file="missing_atlas-${atlas}_desc-${strategy}.h5.txt"
+            participant_labels="/lustre03/project/rrg-pbellec/nclarke/giga_preprocess2/compass-nd/${missing_file}"
+            echo "participant_labels: ${participant_labels}"
+
+            # Determine the array size based on the number of directories missing
+            array_size=$(wc -l < "$participant_labels")
+            echo "ARRAY_SIZE: ${array_size}"
+
+            echo "Submitting ${atlas} ${strategy}"
+            sbatch \
+                --time=${time} --mem-per-cpu=${mem} --array=1-${array_size}\
+                --job-name=${DATASET}_${atlas}_${strategy} \
+                --export=DATASET=${DATASET},ATLAS=${atlas},STRATEGY=${strategy},participant_labels=${participant_labels}\
+                ./connectome_slurm_array_missing.bash
+    done
+done
diff --git a/compass-nd/11_archive_connectome.sh b/compass-nd/11_archive_connectome.sh
new file mode 100644
index 0000000..c9cc0e2
--- /dev/null
+++ b/compass-nd/11_archive_connectome.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --account=rrg-pbellec
+#SBATCH --job-name=conn_archive
+#SBATCH --output=/lustre04/scratch/nclarke/logs/compass-nd_conn_archive.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/compass-nd_conn_archive.err
+#SBATCH --time=10:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=8G
+
+
+CONNECTOME_PATH="/lustre04/scratch/${USER}/compass-nd_connectome-0.4.1"
+DATASET_NAME=`basename $CONNECTOME_PATH`
+
+ARCHIVE_PATH="/lustre03/nearline/6035398/giga_preprocessing_2/compass-nd_fmriprep-20.2.7lts"
+
+cd ${CONNECTOME_PATH}
+echo $PWD
+tar -vcf ${ARCHIVE_PATH}/${DATASET_NAME}.tar.gz .
diff --git a/compass-nd/1_create_dataset_description.py b/compass-nd/1_create_dataset_description.py
new file mode 100644
index 0000000..327848e
--- /dev/null
+++ b/compass-nd/1_create_dataset_description.py
@@ -0,0 +1,16 @@
+import json
+
+# Path to directory where dataset_description.json will be created
+path = "/home/nclarke/scratch/compass-nd/bids_release_7/"
+
+# JSON file content
+json_content = {"Name": "COMPASS-ND", "BIDSVersion": "1.9.0"}
+
+# Serialize JSON
+json_object = json.dumps(json_content, indent=2)
+
+# Write to dataset_description.json
+with open(path + "dataset_description.json", "w") as file:
+    file.write(json_object)
+
+print(f"dataset_description.json created at'{path}'")
diff --git a/compass-nd/2_create_task-rest_bold.py b/compass-nd/2_create_task-rest_bold.py
new file mode 100644
index 0000000..072f170
--- /dev/null
+++ b/compass-nd/2_create_task-rest_bold.py
@@ -0,0 +1,16 @@
+import json
+
+# Path to directory where task-rest_bold.json will be created
+path = "/home/nclarke/scratch/compass-nd/bids_release_7/"
+
+# JSON file content
+json_content = {"TaskName": "rest"}
+
+# Serialize JSON
+json_object = json.dumps(json_content, indent=2)
+
+# Write to dataset_description.json
+with open(path + "task-rest_bold.json", "w") as file:
+    file.write(json_object)
+
+print(f"task-rest_bold.json created at'{path}'")
diff --git a/compass-nd/3_create_bidsignore.sh b/compass-nd/3_create_bidsignore.sh
new file mode 100644
index 0000000..d456ea6
--- /dev/null
+++ b/compass-nd/3_create_bidsignore.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+cd /home/nclarke/scratch/compass-nd/bids_release_7
+
+cat <<EOF > .bidsignore
+fmap/
+dwi/
+*FLAIR*
+*PD*
+
+EOF
+
+echo 'Done!'
diff --git a/compass-nd/4_generate_slurm_script.sh b/compass-nd/4_generate_slurm_script.sh
new file mode 100644
index 0000000..ba56f1d
--- /dev/null
+++ b/compass-nd/4_generate_slurm_script.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+#SBATCH --mem-per-cpu=12288
+#SBATCH --time=02:00:00
+
+CONTAINER_PATH="/lustre03/project/6003287/containers"
+VERSION="20.2.7"
+EMAIL=${SLACK_EMAIL_BOT}
+
+module load singularity/3.8
+echo "Create fmriprep-slurm scripts for COMPASS-ND"
+
+DATASET_PATH="/lustre04/scratch/${USER}/compass-nd/bids_release_7"
+echo $DATASET_PATH
+time=`date +%s`
+OUTPUT_PATH="/lustre04/scratch/nclarke/compass-nd_fmriprep-${VERSION}lts"
+
+mkdir -p $OUTPUT_PATH
+
+# run BIDS validator on the dataset
+# you only need this done once
+singularity exec -B ${DATASET_PATH}:/DATA \
+    ${CONTAINER_PATH}/fmriprep-${VERSION}lts.sif bids-validator /DATA \
+    > ${OUTPUT_PATH}/bids_validator.log
+
+# running the script from the current directory, reference
+# fmriprep_slurm_singularity_run.bash from one level up
+bash ../scripts/fmriprep_slurm_singularity_run.bash \
+    ${OUTPUT_PATH} \
+    ${DATASET_PATH} \
+    fmriprep-${VERSION}lts \
+    --fmriprep-args=\"--ignore slicetiming fieldmaps\" \
+    --email=${EMAIL} \
+    --time=24:00:00 \
+    --mem-per-cpu=12288 \
+    --cpus=1 \
+    --container fmriprep-${VERSION}lts
diff --git a/compass-nd/5_archive_fmriprep.sh b/compass-nd/5_archive_fmriprep.sh
new file mode 100644
index 0000000..8248519
--- /dev/null
+++ b/compass-nd/5_archive_fmriprep.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH --account=rrg-pbellec
+#SBATCH --job-name=fmriprep_archive
+#SBATCH --output=/home/nclarke/scratch/logs/compass-nd_fmriprep_archive.out
+#SBATCH --error=/home/nclarke/scratch/logs/compass-nd_fmriprep_archive.err
+#SBATCH --time=72:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=8G
+
+
+FMRIPREP_PATH="/lustre04/scratch/${USER}/compass-nd_fmriprep-20.2.7lts"
+DATASET_NAME=`basename $FMRIPREP_PATH`
+
+ARCHIVE_PATH="/lustre03/nearline/6035398/giga_preprocessing_2/${DATASET_NAME}"
+
+mkdir -p $ARCHIVE_PATH
+
+cd ${FMRIPREP_PATH}
+echo $PWD
+tar -vcf ${ARCHIVE_PATH}/${DATASET_NAME}.tar.gz .
diff --git a/compass-nd/6_submit_qc_participant.sh b/compass-nd/6_submit_qc_participant.sh
new file mode 100644
index 0000000..7e7383d
--- /dev/null
+++ b/compass-nd/6_submit_qc_participant.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --job-name=compass-nd_qc
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --time=00:10:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=5G
+#SBATCH --array=1-784
+
+module load apptainer
+
+GIGA_QC_VERSION=0.3.3
+FMRIPREP_DIR=/lustre04/scratch/${USER}/compass-nd_fmriprep-20.2.7lts/bids_release_7/fmriprep-20.2.7lts
+GIGA_AUTO_QC_CONTAINER=/lustre03/project/rrg-pbellec/${USER}/giga_preprocess2/giga_auto_qc-${GIGA_QC_VERSION}.simg
+QC_OUTPUT=/lustre04/scratch/${USER}/compass-nd_giga_auto_qc-${GIGA_QC_VERSION}
+participant_labels=/home/${USER}/projects/rrg-pbellec/nclarke/giga_preprocess2/compass-nd/participant_labels.txt # One subject number per line
+
+mkdir -p $QC_OUTPUT
+
+PARTICIPANT_LABEL=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ${participant_labels})
+
+# Create a directory for participant
+PARTICIPANT_OUTPUT="${QC_OUTPUT}/${PARTICIPANT_LABEL}"
+mkdir -p $PARTICIPANT_OUTPUT
+
+echo "Running ${PARTICIPANT_LABEL} QC"
+
+apptainer run --cleanenv -B ${FMRIPREP_DIR}:/inputs -B ${PARTICIPANT_OUTPUT}:/outputs ${GIGA_AUTO_QC_CONTAINER} /inputs /outputs participant --participant_label ${PARTICIPANT_LABEL}
diff --git a/compass-nd/7_archive_qc.sh b/compass-nd/7_archive_qc.sh
new file mode 100644
index 0000000..6c1bf41
--- /dev/null
+++ b/compass-nd/7_archive_qc.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --job-name=qc_archive
+#SBATCH --output=/lustre04/scratch/nclarke/logs/compass-nd_qc_archive.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/compass-nd_qc_archive.err
+#SBATCH --time=01:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=8G
+
+
+RAW_PATH="/lustre04/scratch/nclarke/compass-nd_giga_auto_qc-0.3.3"
+DATASET_NAME=`basename $RAW_PATH`
+
+ARCHIVE_PATH="/lustre03/nearline/6035398/giga_preprocessing_2/compass-nd_fmriprep-20.2.7lts"
+
+mkdir -p $ARCHIVE_PATH
+
+cd ${RAW_PATH}
+echo $PWD
+tar -vcf ${ARCHIVE_PATH}/${DATASET_NAME}.tar.gz .
diff --git a/compass-nd/8_submit_connectome.sh b/compass-nd/8_submit_connectome.sh
new file mode 100644
index 0000000..6e80d03
--- /dev/null
+++ b/compass-nd/8_submit_connectome.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --cpus-per-task=1
+#SBATCH --time=02:30:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=12G
+#SBATCH --array=1-784
+
+GIGA_CONNECTOME_VERSION=0.4.1
+GIGA_CONNECTOME=/home/${USER}/projects/rrg-pbellec/containers/giga_connectome-${GIGA_CONNECTOME_VERSION}.simg
+FMRIPREP_DIR=/lustre04/scratch/${USER}/compass-nd_fmriprep-20.2.7lts/bids_release_7/fmriprep-20.2.7lts
+CONNECTOME_OUTPUT=/lustre04/scratch/${USER}/compass-nd_connectome-${GIGA_CONNECTOME_VERSION}
+WORKINGDIR=${CONNECTOME_OUTPUT}/working_directory
+participant_labels=/home/${USER}/projects/rrg-pbellec/nclarke/giga_preprocess2/compass-nd/participant_labels.txt # One subject number per line
+
+module load apptainer
+
+PARTICIPANT_LABEL=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ${participant_labels})
+PARTICIPANT_OUTPUT="${CONNECTOME_OUTPUT}/${PARTICIPANT_LABEL}"
+
+mkdir -p $WORKINGDIR
+
+# Create participant-specific directory
+mkdir -p ${PARTICIPANT_OUTPUT}
+
+# Define strategies and atlases
+STRATEGIES=("acompcor50" "simple" "simple+gsr" "scrubbing.2" "scrubbing.2+gsr" "scrubbing.5" "scrubbing.5+gsr")
+ATLASES=("Schaefer20187Networks" "MIST" "DiFuMo")
+
+# Loop through each strategy and atlas
+for STRATEGY in "${STRATEGIES[@]}"; do
+    for ATLAS in "${ATLASES[@]}"; do
+        # Set AFC flag based on atlas
+        if [[ "$ATLAS" == "DiFuMo" ]]; then
+            INTRANETWORK_FLAG=""
+        else
+            INTRANETWORK_FLAG="--calculate-intranetwork-average-correlation"
+        fi
+        echo "Running ${PARTICIPANT_LABEL} with ${ATLAS} ${STRATEGY}"
+        	apptainer run \
+            --bind ${FMRIPREP_DIR}:/data/input \
+            --bind ${SLURM_TMPDIR}:/data/output \
+            --bind ${WORKINGDIR}:/data/working \
+            ${GIGA_CONNECTOME} \
+            -w /data/working \
+            --atlas ${ATLAS} \
+            --denoise-strategy ${STRATEGY} \
+            ${INTRANETWORK_FLAG} \
+            /data/input \
+            /data/output \
+            participant \
+            --participant_label ${PARTICIPANT_LABEL}
+        exitcode=$?  # catch exit code
+        if [ $exitcode -eq 0 ] ; then rsync -rltv --info=progress2 ${SLURM_TMPDIR}/*.h5 ${PARTICIPANT_OUTPUT} ; fi
+    done
+done
diff --git a/compass-nd/9_check_participant_missing_h5.py b/compass-nd/9_check_participant_missing_h5.py
new file mode 100644
index 0000000..f06f255
--- /dev/null
+++ b/compass-nd/9_check_participant_missing_h5.py
@@ -0,0 +1,55 @@
+import os
+
+# Directory containing sub-directories
+main_directory = "/home/nclarke/scratch/compass-nd_connectome-0.4.1"
+
+# List of file endings to check for
+file_endings_to_check = [
+    "atlas-DiFuMo_desc-acompcor50.h5",
+    "atlas-MIST_desc-scrubbing.5.h5",
+    "atlas-DiFuMo_desc-scrubbing.2+gsr.h5",
+    "atlas-MIST_desc-simple+gsr.h5",
+    "atlas-DiFuMo_desc-scrubbing.2.h5",
+    "atlas-MIST_desc-simple.h5",
+    "atlas-DiFuMo_desc-scrubbing.5+gsr.h5",
+    "atlas-Schaefer20187Networks_desc-acompcor50.h5",
+    "atlas-DiFuMo_desc-scrubbing.5.h5",
+    "atlas-Schaefer20187Networks_desc-scrubbing.2+gsr.h5",
+    "atlas-DiFuMo_desc-simple+gsr.h5",
+    "atlas-Schaefer20187Networks_desc-scrubbing.2.h5",
+    "atlas-DiFuMo_desc-simple.h5",
+    "atlas-Schaefer20187Networks_desc-scrubbing.5+gsr.h5",
+    "atlas-MIST_desc-acompcor50.h5",
+    "atlas-Schaefer20187Networks_desc-scrubbing.5.h5",
+    "atlas-MIST_desc-scrubbing.2+gsr.h5",
+    "atlas-Schaefer20187Networks_desc-simple+gsr.h5",
+    "atlas-MIST_desc-scrubbing.2.h5",
+]
+
+
+# Directories to exclude
+excluded_directories = {"working_directory"}
+
+
+# Create a dictionary to store missing directories for each file ending
+missing_directories_dict = {}
+
+# Loop over sub-directories and check for files
+for directory in os.listdir(main_directory):
+    if directory not in excluded_directories:
+        sub_directory = os.path.join(main_directory, directory)
+        if os.path.isdir(sub_directory):
+            for ending in file_endings_to_check:
+                if not any(f.endswith(ending) for f in os.listdir(sub_directory)):
+                    if ending not in missing_directories_dict:
+                        missing_directories_dict[ending] = []
+                    missing_directories_dict[ending].append(directory)
+
+# Create a separate file for each file ending listing the missing directories
+for ending, missing_directories in missing_directories_dict.items():
+    output_file = f"missing_{ending}.txt"
+    with open(output_file, "w") as f:
+        for directory in missing_directories:
+            f.write(directory + "\n")
+    print(f"Missing file: {ending}")
+    print(f"Number of directories missing it: {len(missing_directories)}")
diff --git a/compass-nd/README.md b/compass-nd/README.md
new file mode 100644
index 0000000..3540b9e
--- /dev/null
+++ b/compass-nd/README.md
@@ -0,0 +1,33 @@
+# COMPASS-ND-fmriprep-slurm
+Scripts for preprocessing the Comprehensive Assessment of Neurodegeneration and Dementia (COMPASS-ND) Study with fMRIPrep2.2.7lts.
+## Dependency
+- [fmriprep-slurm](https://simexp-documentation.readthedocs.io/en/latest/giga_preprocessing/preprocessing.html)
+- Python
+## Retrieving data
+Data was downloaded from [here](https://ccna.loris.ca/) after submitting a data access request and receiving approval.
+
+## BIDS validation fixes
+- `1_create_dataset_description.py`
+    -  creates `dataset_description.json` at the root directory with minimal information
+    -  BIDS version used is unknown, so specified latest version (same as adni, see [discussion]( https://neurostars.org/t/what-bids-version-to-use-for-legacy-dataset/25619)).
+- `2_create_task-rest_bold.py`
+    - creates `task-rest_bold.json` at the root directory, detailing bold task
+- `3_create_bids_ignore.sh`
+    - creates `.bidsignore` at the root and adds relevant lines
+
+## Run fMRIPrep
+- `4_generate_slurm_script.sh`
+- `5_archive_fmriprep.sh`
+
+## Run QC
+- `6_submit_qc_participant.sh`
+    - Run once first with one participant only and `--reindex-bids` flag.
+- `7_archive_qc.sh`
+
+## Generate connectomes
+- `8_submit_connectome.sh` loops through each participant and generates connectomes for each atlas and strategy pair.
+    - Run once first with one participant only and `--reindex-bids` flag.
+    - Do `ls -d sub-* | grep -v '\.html$' | sed 's/sub-//' > /home/${USER}/participant_labels.txt`.
+- `9_check_participant_missing_h5.py` checks which subjects failed in the previous step.
+- `10_connectome_slurm_array_missing.bash` and `10_submit_connectome_array_missing.sh` submit any failed atlas/strategy pairs one by one. Use the portal to check if jobs are timed out/ OOM and adjust accordingly, but if they failed after that will be due to no frames left after scrubbing.
+- `11_archive_connectome.sh`
\ No newline at end of file
diff --git a/compass-nd/submit_qc_scrub5.sh b/compass-nd/submit_qc_scrub5.sh
new file mode 100644
index 0000000..5deb892
--- /dev/null
+++ b/compass-nd/submit_qc_scrub5.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --job-name=qc
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --time=00:15:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=4G
+#SBATCH --array=1-784
+
+module load apptainer
+
+FMRIPREP_DIR=/lustre04/scratch/${USER}/compass-nd_fmriprep-20.2.7lts/bids_release_7/fmriprep-20.2.7lts
+GIGA_AUTO_QC_CONTAINER=/lustre03/project/rrg-pbellec/${USER}/giga_preprocess2/giga_auto_qc-0.3.3.simg
+QC_OUTPUT=/lustre04/scratch/${USER}/compass-nd_giga_auto_qc-0.3.3_scrub.5
+QC_PARAMS=/lustre03/project/rrg-pbellec/${USER}/giga_preprocess2/qc_params_scrub5.json
+participant_labels=/lustre03/project/rrg-pbellec/${USER}/giga_preprocess2/compass-nd/participant_labels.txt # One subject number per line
+
+mkdir -p $QC_OUTPUT
+
+PARTICIPANT_LABEL=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ${participant_labels})
+
+# Create a directory for participant
+PARTICIPANT_OUTPUT="${QC_OUTPUT}/${PARTICIPANT_LABEL}"
+mkdir -p $PARTICIPANT_OUTPUT
+
+echo "Running ${PARTICIPANT_LABEL} QC"
+
+apptainer run --cleanenv -B ${QC_PARAMS} -B ${FMRIPREP_DIR}:/inputs -B ${PARTICIPANT_OUTPUT}:/outputs ${GIGA_AUTO_QC_CONTAINER} /inputs /outputs --quality_control_parameters ${QC_PARAMS} participant --participant_label ${PARTICIPANT_LABEL}
diff --git a/prisme/ColeAnticevic12.json b/prisme/ColeAnticevic12.json
new file mode 100644
index 0000000..44d7844
--- /dev/null
+++ b/prisme/ColeAnticevic12.json
@@ -0,0 +1,11 @@
+{
+    "name": "coleanticevic",
+    "parameters": {
+        "atlas": "coleanticevic",
+        "template": "MNI152NLin2009cAsym",
+        "resolution": "1",
+        "suffix": "dseg"
+    },
+    "desc":"12parcels",
+    "templateflow_dir": null
+}
diff --git a/prisme/README.md b/prisme/README.md
new file mode 100644
index 0000000..1787e3a
--- /dev/null
+++ b/prisme/README.md
@@ -0,0 +1,21 @@
+# PRISME QC and connectome generation
+
+For more info on connectome workflow see the giga-connectome [docs](https://giga-connectome.readthedocs.io/en/latest/usage.html).
+
+1. Run QC (see [repo](https://github.com/SIMEXP/giga_auto_qc))
+- `submit_qc.sh`
+
+2. Organise atlases according to TemplateFlow convention
+- `ColeAnticevic12.json` & `brainnetome.json`: config files
+- `copy_rename_CABNP.py` & `copy_rename_BA.py`: copy atlas files and rename.
+
+3. Submit connectome generation scripts on Beluga
+- `submit_connectome_CABNP.sh` & `submit_connectome_BA.sh`
+
+4. Generate a .tsv connectome per participant from the .h5 file
+- `h5_to_tsv_prisme.py`: uses [this repo](https://github.com/SIMEXP/rs-autoregression-prediction).
+
+5. Copy data to Elm `/data/orban/data/prisme-connectomes`
+
+6. Archive on Beluga nearline - TO DO
+
diff --git a/prisme/brainnetome.json b/prisme/brainnetome.json
new file mode 100644
index 0000000..704c969
--- /dev/null
+++ b/prisme/brainnetome.json
@@ -0,0 +1,11 @@
+{
+    "name": "brainnetome",
+    "parameters": {
+        "atlas": "brainnetome",
+        "template": "MNI152NLin2009cAsym",
+        "resolution": "02",
+        "suffix": "dseg"
+    },
+    "desc":"246parcels",
+    "templateflow_dir": null
+}
diff --git a/prisme/copy_rename_BA.py b/prisme/copy_rename_BA.py
new file mode 100644
index 0000000..10c28c3
--- /dev/null
+++ b/prisme/copy_rename_BA.py
@@ -0,0 +1,29 @@
+import json
+import shutil
+from pathlib import Path
+
+root_p = Path("/home/neuromod/prisme/BA")
+json_file_p = "brainnetome.json"
+nifti_file_p = "BN_Atlas_246_2mm.nii.gz"
+output_dir = root_p
+output_dir.mkdir(parents=True, exist_ok=True)
+
+with open(json_file_p, "r") as f:
+    config = json.load(f)
+
+# Extract parameters
+template = config["parameters"]["template"]
+resolution = config["parameters"]["resolution"]
+atlas = config["parameters"]["atlas"]
+suffix = config["parameters"]["suffix"]
+desc = config["desc"]
+
+# Construct new filename
+new_filename = (
+    f"tpl-{template}_res-{resolution}_atlas-{atlas}_desc-{desc}_{suffix}.nii.gz"
+)
+
+# Copy and rename the atlas
+output_file_path = output_dir / new_filename
+shutil.copy(nifti_file_p, output_file_path)
+print(f"Copied and renamed file to: {output_file_path}")
diff --git a/prisme/copy_rename_CABNP.py b/prisme/copy_rename_CABNP.py
new file mode 100644
index 0000000..87a6103
--- /dev/null
+++ b/prisme/copy_rename_CABNP.py
@@ -0,0 +1,30 @@
+import json
+import shutil
+from pathlib import Path
+
+root_p = Path("/home/neuromod/prisme/CAB-NP")
+json_file_p = "ColeAnticevic12.json"
+nifti_file_p = "CAB-NP_volumetric_liberal_reordered.nii.gz"
+output_dir = root_p
+output_dir.mkdir(parents=True, exist_ok=True)
+
+with open(json_file_p, "r") as f:
+    config = json.load(f)
+
+# Extract parameters
+template = config["parameters"]["template"]
+resolution = config["parameters"]["resolution"]
+atlas = config["parameters"]["atlas"]
+suffix = config["parameters"]["suffix"]
+desc = config["desc"]
+
+# Construct new filename
+new_filename = (
+    f"tpl-{template}_res-{resolution}_atlas-{atlas}_desc-{desc}_{suffix}.nii.gz"
+)
+output_file_p = output_dir / new_filename
+
+# Copy (no need to compress)
+shutil.copy(nifti_file_p, output_file_p)
+
+print(f"Renamed file to: {output_file_p}")
diff --git a/prisme/h5_to_tsv_prisme.py b/prisme/h5_to_tsv_prisme.py
new file mode 100644
index 0000000..0bb82ac
--- /dev/null
+++ b/prisme/h5_to_tsv_prisme.py
@@ -0,0 +1,78 @@
+import sys
+import pandas as pd
+
+sys.path.append("/home/neuromod/rs-autoregression-prediction/src")
+from data.load_data import load_data, load_h5_data_path
+from pathlib import Path
+
+
+def label_connectome(connectome_df, labels_p, atlas):
+    if atlas == "CAB-NP":
+        labels_df = pd.read_csv(labels_p, delimiter=";")
+        labels_df.sort_values(by=["index"], inplace=True)
+        region_labels = labels_df["name"].tolist()
+    elif atlas == "BA":
+        labels_df = pd.read_csv(labels_p)
+        labels_df.sort_values(by=["Label"], inplace=True)
+        region_labels = labels_df["region"].tolist()
+    else:
+        raise ValueError(f"Unknown atlas: {atlas}")
+
+    connectome_df.columns = region_labels
+    connectome_df.index = region_labels
+    return connectome_df
+
+
+def save_connectome_to_tsv(connectome, path, output_p):
+    filename = f"{Path(path).stem}.tsv"
+    filepath = output_p / filename
+    output_p.mkdir(parents=True, exist_ok=True)
+    connectome.to_csv(filepath, sep="\t")
+    print(f"Saved: {filepath}")
+
+
+def process_connectomes(atlas, root_p):
+    if atlas == "CAB-NP":
+        h5_file = (
+            root_p
+            / "prisme-connectomes/CAB-NP/prisme_connectome_CABNP-0.4.1_20250110/atlas-coleanticevic_desc-simple+gsr.h5"
+        )
+        labels_p = root_p / "prisme/CAB-NP/CAB-NP_labels_reordered.csv"
+        output_p = (
+            root_p
+            / "prisme-connectomes/CAB-NP/tsv_files_atlas-coleanticevic_desc-simple+gsr_20250110"
+        )
+    elif atlas == "BA":
+        h5_file = (
+            root_p
+            / "prisme-connectomes/BA/prisme_connectome-0.4.1_BA_20241218/atlas-brainnetome_desc-simple+gsr.h5"
+        )
+        labels_p = root_p / "prisme/BA/subregion_func_network_Yeo_updated.csv"
+        output_p = (
+            root_p
+            / "prisme-connectomes/BA/tsv_files_atlas-BA_desc-simple+gsr_20241218"
+        )
+    else:
+        raise ValueError(f"Unknown atlas: {atlas}")
+
+    # Load data
+    dset_paths = load_h5_data_path(
+        path=h5_file, data_filter="connectome", shuffle=False
+    )
+    data = load_data(
+        path=h5_file, h5dset_path=dset_paths, standardize=False, dtype="data"
+    )
+
+    # Process each connectome
+    for connectome, path in zip(data, dset_paths):
+        connectome_df = pd.DataFrame(connectome)
+        connectome_df = label_connectome(connectome_df, labels_p, atlas)
+        save_connectome_to_tsv(connectome_df, path, output_p)
+
+    print(f"Connectomes processed and saved to {output_p}")
+
+
+if __name__ == "__main__":
+    root_p = Path("/home/neuromod")
+    for atlas in ["CAB-NP"]:  # ["BA", "CAB-NP"]
+        process_connectomes(atlas, root_p)
diff --git a/prisme/submit_connectome_BA.sh b/prisme/submit_connectome_BA.sh
new file mode 100644
index 0000000..f15500e
--- /dev/null
+++ b/prisme/submit_connectome_BA.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+#SBATCH --account=rrg-pbellec
+#SBATCH --job-name=prisme_BA_conn
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.err
+#SBATCH --cpus-per-task=1
+#SBATCH --time=22:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=36G
+
+GIGA_CONNECTOME_VERSION=0.4.1
+GIGA_CONNECTOME=/lustre03/project/6003287/containers/giga_connectome-${GIGA_CONNECTOME_VERSION}.simg
+FMRIPREP_DIR=/lustre03/project/6003287/${USER}/prisme.fmriprep
+CONNECTOME_OUTPUT=/lustre04/scratch/${USER}/prisme_connectome-${GIGA_CONNECTOME_VERSION}_BA_20241218
+WORKINGDIR=${CONNECTOME_OUTPUT}/working_directory
+ATLAS_CONFIG=/lustre03/project/6003287/${USER}/giga_preprocess2/prisme/brainnetome.json
+ATLAS_PATH=/home/${USER}/.cache/templateflow
+export APPTAINERENV_TEMPLATEFLOW_HOME=/templateflow
+
+module load apptainer
+
+mkdir -p ${WORKINGDIR}
+
+echo "${FMRIPREP_DIR}"
+if [ -d "${FMRIPREP_DIR}" ]; then
+    mkdir -p ${WORKINGDIR}
+	mkdir -p ${SLURM_TMPDIR}
+	mkdir -p ${CONNECTOME_OUTPUT}/
+	echo "=========${STRATEGY}========="
+	apptainer run \
+	    --bind ${FMRIPREP_DIR}:/data/input \
+	    --bind ${SLURM_TMPDIR}:/data/output \
+	    --bind ${WORKINGDIR}:/data/working \
+	    --bind ${ATLAS_CONFIG}:/data/brainnetome.json \
+	    --bind ${ATLAS_PATH}:/templateflow \
+	    -B /lustre03:/lustre03 \
+	    ${GIGA_CONNECTOME} \
+	    --reindex-bids \
+	    -w /data/working \
+       	--atlas /data/brainnetome.json \
+	    --denoise-strategy simple+gsr \
+        /data/input \
+	    /data/output \
+	    group
+	exitcode=$?  # catch exit code
+	if [ $exitcode -eq 0 ] ; then rsync -rltv --info=progress2 ${SLURM_TMPDIR}/*.h5 ${CONNECTOME_OUTPUT} ; fi
+else
+    echo "no preprocessed data for ${FMRIPREP_DIR}"
+fi
diff --git a/prisme/submit_connectome_CABNP.sh b/prisme/submit_connectome_CABNP.sh
new file mode 100644
index 0000000..ea66fee
--- /dev/null
+++ b/prisme/submit_connectome_CABNP.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+#SBATCH --account=rrg-pbellec
+#SBATCH --job-name=prisme_CABNP_conn
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.err
+#SBATCH --cpus-per-task=1
+#SBATCH --time=22:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=34G
+
+GIGA_CONNECTOME_VERSION=0.4.1
+GIGA_CONNECTOME=/lustre03/project/6003287/containers/giga_connectome-${GIGA_CONNECTOME_VERSION}.simg
+FMRIPREP_DIR=/lustre03/project/6003287/${USER}/prisme.fmriprep
+CONNECTOME_OUTPUT=/lustre04/scratch/${USER}/prisme_connectome_CABNP-${GIGA_CONNECTOME_VERSION}_20250110
+WORKINGDIR=${CONNECTOME_OUTPUT}/working_directory
+ATLAS_CONFIG=/lustre03/project/6003287/${USER}/giga_preprocess2/prisme/ColeAnticevic12.json
+ATLAS_PATH=/home/${USER}/.cache/templateflow
+export APPTAINERENV_TEMPLATEFLOW_HOME=/templateflow
+
+module load apptainer
+
+mkdir -p ${WORKINGDIR}
+
+echo "${FMRIPREP_DIR}"
+if [ -d "${FMRIPREP_DIR}" ]; then
+    mkdir -p ${WORKINGDIR}
+	mkdir -p ${SLURM_TMPDIR}
+	mkdir -p ${CONNECTOME_OUTPUT}/
+	echo "=========${STRATEGY}========="
+	apptainer run \
+	    --bind ${FMRIPREP_DIR}:/data/input \
+	    --bind ${SLURM_TMPDIR}:/data/output \
+	    --bind ${WORKINGDIR}:/data/working \
+	    --bind ${ATLAS_CONFIG}:/data/ColeAnticevic12.json \
+	    --bind ${ATLAS_PATH}:/templateflow \
+	    -B /lustre03:/lustre03 \
+	    ${GIGA_CONNECTOME} \
+	    --reindex-bids \
+	    -w /data/working \
+       	--atlas /data/ColeAnticevic12.json \
+	    --denoise-strategy simple+gsr \
+        /data/input \
+	    /data/output \
+	    group
+	exitcode=$?  # catch exit code
+	if [ $exitcode -eq 0 ] ; then rsync -rltv --info=progress2 ${SLURM_TMPDIR}/*.h5 ${CONNECTOME_OUTPUT} ; fi
+else
+    echo "no preprocessed data for ${FMRIPREP_DIR}"
+fi
diff --git a/prisme/submit_qc.sh b/prisme/submit_qc.sh
new file mode 100644
index 0000000..3ee7a4f
--- /dev/null
+++ b/prisme/submit_qc.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --job-name=prisme_qc
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --time=10:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=6G 
+
+module load apptainer
+
+GIGA_QC_VERSION=0.3.4
+FMRIPREP_DIR=/lustre03/project/6003287/${USER}/prisme.fmriprep
+GIGA_AUTO_QC_CONTAINER=/lustre03/project/6003287/containers/giga_auto_qc_unstable_update.simg
+QC_OUTPUT=/lustre04/scratch/${USER}/prisme_giga_auto_qc-${GIGA_QC_VERSION}_20241029 
+
+mkdir -p $QC_OUTPUT
+
+echo "Running QC"
+
+apptainer run --cleanenv -B ${FMRIPREP_DIR}:/inputs -B ${QC_OUTPUT}:/outputs -B /lustre03:/lustre03 ${GIGA_AUTO_QC_CONTAINER} --reindex-bids /inputs /outputs  group
diff --git a/prisme/submit_qc_scrub5.sh b/prisme/submit_qc_scrub5.sh
new file mode 100644
index 0000000..31acd8b
--- /dev/null
+++ b/prisme/submit_qc_scrub5.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH --account=def-pbellec
+#SBATCH --job-name=prisme_qc
+#SBATCH --output=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --error=/lustre04/scratch/nclarke/logs/%x_%A.out
+#SBATCH --time=10:00:00
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=6G 
+
+module load apptainer
+
+GIGA_QC_VERSION=0.3.4
+FMRIPREP_DIR=/lustre04/scratch/${USER}/prisme.fmriprep
+GIGA_AUTO_QC_CONTAINER=/lustre03/project/6003287/containers/giga_auto_qc_unstable_update.simg
+QC_OUTPUT=/lustre04/scratch/${USER}/prisme_giga_auto_qc-${GIGA_QC_VERSION}_scrub5
+QC_PARAMS=/lustre03/project/rrg-pbellec/${USER}/giga_preprocess2/qc_params_scrub5.json 
+
+mkdir -p $QC_OUTPUT
+
+echo "Running QC"
+
+apptainer run --cleanenv -B ${QC_PARAMS}:/tmp/qc_params_scrub5.json -B ${FMRIPREP_DIR}:/inputs -B ${QC_OUTPUT}:/outputs -B /lustre03:/lustre03 ${GIGA_AUTO_QC_CONTAINER} --reindex-bids /inputs /outputs --quality_control_parameters ${QC_PARAMS} group