diff --git a/fmriprep/README.md b/fmriprep/README.md
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index 0000000..f07e303
--- /dev/null
+++ b/fmriprep/README.md
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+# fmriprep processing 
+
+## Notes
+- Goal: Process 40k UKB subjects with fmriprep pipeline
+- fmriprep version: 20.2.0
+- Currently processing subset of ~3k subjects which have ses-2 and ses-3 timepoints
+- Currently processing only anatomical stream
+
+## Known issues
+- BIDS sql indexing: fmriprep gets stuck while processing even a single subject when squashFS is used as an overlay. Current guess is that it tries to index all ~40k subjects from the participants.tsv which takes for ever.
+  - Workaround: copy UKB subsets in scratch and mount that on singularity
+- fmriprep 20.2.7 crashes with this [error](https://github.com/nipreps/fmriprep/issues/2683). Error goes away if you remove --resource-monitor flag from CLI. 
+
+## Organization
+- Metadata: contains list of subjects for various tests and runs. 
+  - ukbb_long_subject_list.txt: All subjects with two timepoints
+  - ukbb_subject_ids_run1.txt: First processed subset
+  - ukbb_subject_ids_run2.txt: Second processed subset
+  - and so on... 
+
+- Scripts: contains scripts to prepare data and run the pipeline
+  - unsquash_data.sh and copy_ukb_data.sh: scripts to copy data from squashFS into local scratch
+    e.g. ./unsquash_data.sh neurohub_ukbb_t1_ses2_0_bids.squashfs /scratch/nikhil/ukbb_processing/fmriprep/test_BIDS_DIR ukbb_long_subject_list_100.txt
+  - fmriprep_anat_sub_regular.sh: script to run fmriprep in a regular setup with BIDS dataset in local FS
+    e.g. ./fmriprep_anat_sub_regular.sh /home/nikhil/scratch/ukbb_processing/fmriprep/test_WD/ 1000011
+  - fmriprep_anat_sub_squashfs.sh: script to run fmriprep with squashFS setup with BIDS dataset in local FS (*DOES NOT WORK WITH LARGE DATASETS*) 
+  - fmriprep_anat_slurm.sh: script to submit fmriprep_anat_sub_regular.sh to slurm. This uses a list of subjects from metadata (e.g. ukbb_subject_ids_run1.txt)
+    e.g. sbatch fmriprep_anat_slurm.sh /home/nikhil/scratch/ukbb_processing/fmriprep/UKB_WD
diff --git a/fmriprep/metadata/ukbb_long_subject_list.txt b/fmriprep/metadata/ukbb_long_subject_list.txt
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+++ b/fmriprep/metadata/ukbb_long_subject_list.txt
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diff --git a/fmriprep/metadata/ukbb_long_subject_list_100.txt b/fmriprep/metadata/ukbb_long_subject_list_100.txt
new file mode 100644
index 0000000..8e1d727
--- /dev/null
+++ b/fmriprep/metadata/ukbb_long_subject_list_100.txt
@@ -0,0 +1,100 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_long_run_1.txt b/fmriprep/metadata/ukbb_subject_ids_long_run_1.txt
new file mode 100644
index 0000000..8eb8d45
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_long_run_1.txt
@@ -0,0 +1,300 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_long_run_2.txt b/fmriprep/metadata/ukbb_subject_ids_long_run_2.txt
new file mode 100644
index 0000000..9df1516
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_long_run_2.txt
@@ -0,0 +1,300 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_long_run_3.txt b/fmriprep/metadata/ukbb_subject_ids_long_run_3.txt
new file mode 100644
index 0000000..51d3aff
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_long_run_3.txt
@@ -0,0 +1,300 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_long_run_4.txt b/fmriprep/metadata/ukbb_subject_ids_long_run_4.txt
new file mode 100644
index 0000000..17fd8ef
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_long_run_4.txt
@@ -0,0 +1,300 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_long_run_5.txt b/fmriprep/metadata/ukbb_subject_ids_long_run_5.txt
new file mode 100644
index 0000000..18c6526
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_long_run_5.txt
@@ -0,0 +1,227 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_run1.txt b/fmriprep/metadata/ukbb_subject_ids_run1.txt
new file mode 100644
index 0000000..5adbdc5
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_run1.txt
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diff --git a/fmriprep/metadata/ukbb_subject_ids_run_long.txt b/fmriprep/metadata/ukbb_subject_ids_run_long.txt
new file mode 100644
index 0000000..696fae0
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_run_long.txt
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diff --git a/fmriprep/metadata/ukbb_subject_ids_run_long_1.txt b/fmriprep/metadata/ukbb_subject_ids_run_long_1.txt
new file mode 100644
index 0000000..f6100d9
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_run_long_1.txt
@@ -0,0 +1,1000 @@
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diff --git a/fmriprep/metadata/ukbb_subject_ids_run_long_2.txt b/fmriprep/metadata/ukbb_subject_ids_run_long_2.txt
new file mode 100644
index 0000000..86c02d6
--- /dev/null
+++ b/fmriprep/metadata/ukbb_subject_ids_run_long_2.txt
@@ -0,0 +1,427 @@
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diff --git a/fmriprep/scripts/copy_ukb_data.sh b/fmriprep/scripts/copy_ukb_data.sh
new file mode 100755
index 0000000..a73196c
--- /dev/null
+++ b/fmriprep/scripts/copy_ukb_data.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+SUBJECT_LIST=$1
+
+for i in `cat $SUBJECT_LIST`; do 
+    cp -r /neurohub/ukbb/imaging/sub-${i} /output/; 
+done
+
+cp /neurohub/ukbb/imaging/{participants.tsv,dataset_description.json} /output/
diff --git a/fmriprep/scripts/find_run_outcome.sh b/fmriprep/scripts/find_run_outcome.sh
new file mode 100755
index 0000000..3ecbe95
--- /dev/null
+++ b/fmriprep/scripts/find_run_outcome.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+LOG_DIR=$1
+for i in $LOG_DIR/*.out; do echo `cat $i | head -2 | tail -1 | cut -d " " -f3` `cat $i | grep "fMRIPrep finished successfully!" | wc -l`; done > slurm_run_outcomes.txt
+
+echo "Saved run outcome in ./slurm_run_outcomes.txt (1 implies successful run)" 
diff --git a/fmriprep/scripts/fmriprep_anat_sub_regular.sh b/fmriprep/scripts/fmriprep_anat_sub_regular.sh
new file mode 100755
index 0000000..a2d9a63
--- /dev/null
+++ b/fmriprep/scripts/fmriprep_anat_sub_regular.sh
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+# Author: nikhil153
+# Last update: 16 Feb 2022
+
+if [ "$#" -ne 2 ]; then
+  echo "Please provide path to the working_dir and subject ID (i.e. subdir inside BIDS_root)"
+  exit 1
+fi
+
+WD_DIR=$1
+SUB_ID=$2
+
+BIDS_DIR="/scratch/nikhil/ukbb_processing/fmriprep/test_BIDS_DIR"
+CON_IMG="/home/nikhil/scratch/my_containers/fmriprep_v20.2.0.simg"
+#CON_IMG="/home/nikhil/scratch/my_containers/fmriprep_20.2.7.sif"
+DERIVS_DIR=${WD_DIR}/output
+
+LOG_FILE=${WD_DIR}_fmriprep_anat.log
+echo "Starting fmriprep proc with container: ${CON_IMG}"
+echo ""
+echo "Using working dir: ${WD_DIR} and subject ID: ${SUB_ID}"
+
+# Create subject specific dirs
+FMRIPREP_HOME=${DERIVS_DIR}/fmriprep_home_${SUB_ID}
+echo "Processing: ${SUB_ID} with home dir: ${FMRIPREP_HOME}"
+mkdir -p ${FMRIPREP_HOME}
+
+LOCAL_FREESURFER_DIR="${DERIVS_DIR}/freesurfer-6.0.1"
+mkdir -p ${LOCAL_FREESURFER_DIR}
+
+# Prepare some writeable bind-mount points.
+FMRIPREP_HOST_CACHE=$FMRIPREP_HOME/.cache/fmriprep
+mkdir -p ${FMRIPREP_HOST_CACHE}
+
+# CHECK IF YOU HAVE TEMPLATEFLOW
+TEMPLATEFLOW_HOST_HOME="/home/nikhil/scratch/templateflow"
+
+# Make sure FS_LICENSE is defined in the container.
+mkdir -p $FMRIPREP_HOME/.freesurfer
+export SINGULARITYENV_FS_LICENSE=$FMRIPREP_HOME/.freesurfer/license.txt
+cp ${WD_DIR}/license.txt ${SINGULARITYENV_FS_LICENSE}
+
+# Designate a templateflow bind-mount point
+export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
+
+# Singularity CMD 
+SINGULARITY_CMD="singularity run \
+-B ${BIDS_DIR}:/data_dir \
+-B ${FMRIPREP_HOME}:/home/fmriprep --home /home/fmriprep --cleanenv \
+-B ${DERIVS_DIR}:/output \
+-B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} \
+-B ${WD_DIR}:/work \
+-B ${LOCAL_FREESURFER_DIR}:/fsdir \
+ ${CON_IMG}"
+
+# Remove IsRunning files from FreeSurfer
+# find ${LOCAL_FREESURFER_DIR}/sub-$SUB_ID/ -name "*IsRunning*" -type f -delete
+
+# Compose the command line
+cmd="${SINGULARITY_CMD} /data_dir /output participant --participant-label $SUB_ID \
+-w /work --output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 \
+--fs-subjects-dir /fsdir \
+--skip_bids_validation \
+--fs-license-file /home/fmriprep/.freesurfer/license.txt \
+--return-all-components --anat-only -v \
+--write-graph  --notrack --resource-monitor"
+#--bids-filter-file ${BIDS_FILTER} --anat-only --cifti-out 91k"
+
+# Setup done, run the command
+#echo Running task ${SLURM_ARRAY_TASK_ID}
+unset PYTHONPATH
+echo Commandline: $cmd
+eval $cmd
+exitcode=$?
+
+# Output results to a table
+echo "$SUB_ID    ${SLURM_ARRAY_TASK_ID}    $exitcode"
+echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode
+rm -rf ${FMRIPREP_HOME}
+exit $exitcode
+
+echo "Submission finished!"
diff --git a/fmriprep/scripts/fmriprep_anat_sub_regular_20.2.7.sh b/fmriprep/scripts/fmriprep_anat_sub_regular_20.2.7.sh
new file mode 100755
index 0000000..f7d8b2e
--- /dev/null
+++ b/fmriprep/scripts/fmriprep_anat_sub_regular_20.2.7.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+# Author: nikhil153
+# Last update: 16 Feb 2022
+
+if [ "$#" -ne 3 ]; then
+  echo "Please provide paths to the bids_dir, working_dir and subject ID (i.e. subdir inside BIDS_DIR)"
+  exit 1
+fi
+
+BIDS_DIR=$1
+WD_DIR=$2
+SUB_ID=$3
+
+#BIDS_DIR="/scratch/nikhil/ukbb_processing/fmriprep/BIDS_DIR"
+
+CON_IMG="/home/nikhil/scratch/my_containers/fmriprep_20.2.7.sif"
+DERIVS_DIR=${WD_DIR}/output
+
+LOG_FILE=${WD_DIR}_fmriprep_anat.log
+echo "Starting fmriprep proc with container: ${CON_IMG}"
+echo ""
+echo "Using working dir: ${WD_DIR} and subject ID: ${SUB_ID}"
+
+# Create subject specific dirs
+FMRIPREP_HOME=${DERIVS_DIR}/fmriprep_home_${SUB_ID}
+echo "Processing: ${SUB_ID} with home dir: ${FMRIPREP_HOME}"
+mkdir -p ${FMRIPREP_HOME}
+
+LOCAL_FREESURFER_DIR="${DERIVS_DIR}/freesurfer-6.0.1"
+mkdir -p ${LOCAL_FREESURFER_DIR}
+
+# Prepare some writeable bind-mount points.
+FMRIPREP_HOST_CACHE=$FMRIPREP_HOME/.cache/fmriprep
+mkdir -p ${FMRIPREP_HOST_CACHE}
+
+# CHECK IF YOU HAVE TEMPLATEFLOW
+TEMPLATEFLOW_HOST_HOME="/home/nikhil/scratch/templateflow"
+
+# Make sure FS_LICENSE is defined in the container.
+mkdir -p $FMRIPREP_HOME/.freesurfer
+export SINGULARITYENV_FS_LICENSE=$FMRIPREP_HOME/.freesurfer/license.txt
+cp ${WD_DIR}/license.txt ${SINGULARITYENV_FS_LICENSE}
+
+# Designate a templateflow bind-mount point
+export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
+
+# Singularity CMD 
+SINGULARITY_CMD="singularity run \
+-B ${BIDS_DIR}:/data_dir \
+-B ${FMRIPREP_HOME}:/home/fmriprep --home /home/fmriprep --cleanenv \
+-B ${DERIVS_DIR}:/output \
+-B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} \
+-B ${WD_DIR}:/work \
+-B ${LOCAL_FREESURFER_DIR}:/fsdir \
+ ${CON_IMG}"
+
+# Remove IsRunning files from FreeSurfer
+find ${LOCAL_FREESURFER_DIR}/sub-$SUB_ID/ -name "*IsRunning*" -type f -delete
+
+# Compose the command line
+cmd="${SINGULARITY_CMD} /data_dir /output participant --participant-label $SUB_ID \
+-w /work --output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 \
+--fs-subjects-dir /fsdir \
+--skip_bids_validation \
+--bids-database-dir /work/20220307-205306_5bde9faa-a6da-4842-894a-dd7260903416/bids_db/
+--fs-license-file /home/fmriprep/.freesurfer/license.txt \
+--return-all-components --anat-only -v \
+--write-graph  --notrack"
+#--bids-filter-file ${BIDS_FILTER} --anat-only --cifti-out 91k"
+#--bids-database-dir /work/20220221-200330_10ebc3d4-edd1-4752-8c9f-6f6dc1302c83/ \
+
+# Setup done, run the command
+#echo Running task ${SLURM_ARRAY_TASK_ID}
+unset PYTHONPATH
+echo Commandline: $cmd
+eval $cmd
+exitcode=$?
+
+# Output results to a table
+echo "$SUB_ID    ${SLURM_ARRAY_TASK_ID}    $exitcode"
+echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode
+rm -rf ${FMRIPREP_HOME}
+exit $exitcode
+
+echo "Submission finished!"
diff --git a/fmriprep/scripts/fmriprep_anat_sub_squashfs.sh b/fmriprep/scripts/fmriprep_anat_sub_squashfs.sh
new file mode 100755
index 0000000..de2ddc6
--- /dev/null
+++ b/fmriprep/scripts/fmriprep_anat_sub_squashfs.sh
@@ -0,0 +1,97 @@
+#!/bin/bash
+
+# Author: nikhil153
+# Last update: 16 Feb 2022
+
+if [ "$#" -ne 2 ]; then
+  echo "Please provide path to the working_dir and subject ID (i.e. subdir inside BIDS_root)"
+  exit 1
+fi
+
+WD_DIR=$1
+SUB_ID=$2
+
+BIDS_DIR="/neurohub/ukbb/imaging/"
+CON_IMG="/home/nikhil/scratch/my_containers/fmriprep_20.2.7.sif"
+DERIVS_DIR=${WD_DIR}/output
+
+LOG_FILE=${WD_DIR}_fmriprep_anat.log
+echo "Starting fmriprep proc with container: ${CON_IMG}"
+echo ""
+echo "Using working dir: ${WD_DIR} and subject ID: ${SUB_ID}"
+
+# Create subject specific dirs
+FMRIPREP_HOME=${DERIVS_DIR}/fmriprep_home_${SUB_ID}
+echo "Processing: ${SUB_ID} with home dir: ${FMRIPREP_HOME}"
+mkdir -p ${FMRIPREP_HOME}
+
+LOCAL_FREESURFER_DIR="${DERIVS_DIR}/freesurfer-6.0.1"
+mkdir -p ${LOCAL_FREESURFER_DIR}
+
+# Prepare some writeable bind-mount points.
+FMRIPREP_HOST_CACHE=$FMRIPREP_HOME/.cache/fmriprep
+mkdir -p ${FMRIPREP_HOST_CACHE}
+
+# CHECK IF YOU HAVE TEMPLATEFLOW
+TEMPLATEFLOW_HOST_HOME="/home/nikhil/scratch/templateflow"
+
+# Make sure FS_LICENSE is defined in the container.
+mkdir -p $FMRIPREP_HOME/.freesurfer
+export SINGULARITYENV_FS_LICENSE=$FMRIPREP_HOME/.freesurfer/license.txt
+cp ${WD_DIR}/license.txt ${SINGULARITYENV_FS_LICENSE}
+
+# Designate a templateflow bind-mount point
+export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
+
+# SquashFS list
+UKBB_SQUASHFS="
+ neurohub_ukbb_t1_ses2_0_bids.squashfs
+ neurohub_ukbb_participants.squashfs
+ neurohub_ukbb_t1_ses2_0_jsonpatch.squashfs
+ "
+
+UKBB_SQUASHFS_DIR=/project/6008063/neurohub/ukbb/imaging
+UKBB_OVERLAYS=$(echo "" $UKBB_SQUASHFS | sed -e "s# # --overlay $UKBB_SQUASHFS_DIR/#g")
+echo "overlays:"
+echo $UKBB_OVERLAYS
+
+data_dir=$BIDS_DIR
+
+echo "data dir: $data_dir"
+
+# Singularity CMD 
+SINGULARITY_CMD="singularity run \
+${UKBB_OVERLAYS} \
+-B ${FMRIPREP_HOME}:/home/fmriprep --home /home/fmriprep --cleanenv \
+-B ${DERIVS_DIR}:/output \
+-B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} \
+-B ${WD_DIR}:/work \
+-B ${LOCAL_FREESURFER_DIR}:/fsdir \
+ ${CON_IMG}"
+
+# Remove IsRunning files from FreeSurfer
+# find ${LOCAL_FREESURFER_DIR}/sub-$SUB_ID/ -name "*IsRunning*" -type f -delete
+
+# Compose the command line
+cmd="${SINGULARITY_CMD} ${data_dir} /output participant --participant-label $SUB_ID \
+-w /work --output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 \
+--fs-subjects-dir /fsdir \
+--fs-license-file /home/fmriprep/.freesurfer/license.txt \
+--return-all-components --anat-only -v \
+--write-graph  --notrack --resource-monitor"
+#--bids-filter-file ${BIDS_FILTER} --anat-only --cifti-out 91k"
+
+# Setup done, run the command
+#echo Running task ${SLURM_ARRAY_TASK_ID}
+echo Commandline: $cmd
+unset PYTHONPATH
+eval $cmd
+exitcode=$?
+
+# Output results to a table
+echo "$SUB_ID    ${SLURM_ARRAY_TASK_ID}    $exitcode"
+echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode
+rm -rf ${FMRIPREP_HOME}
+exit $exitcode
+
+echo "Submission finished!"
diff --git a/fmriprep/scripts/slurm/fmriprep_anat_slurm_long_run1.sh b/fmriprep/scripts/slurm/fmriprep_anat_slurm_long_run1.sh
new file mode 100755
index 0000000..512af66
--- /dev/null
+++ b/fmriprep/scripts/slurm/fmriprep_anat_slurm_long_run1.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#SBATCH -J ukbb_test_run
+#SBATCH --time=23:00:00
+#SBATCH --account=rrg-jbpoline
+#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=8G
+# Outputs ----------------------------------
+#SBATCH -o ./slurm_logs/ukbb_long_run1/%x-%A-%a_%j.out
+#SBATCH -e ./slurm_logs/ukbb_long_run1/%x-%A-%a_%j.err
+#SBATCH --mail-user=nikhil.bhagwat@mcgill.ca
+#SBATCH --mail-type=ALL
+# ------------------------------------------
+
+#SBATCH --array=1-300
+
+BIDS_DIR="/scratch/nikhil/ukbb_processing/fmriprep/BIDS_DIR_ses-2/"
+SUBJECT_LIST="../../metadata/ukbb_subject_ids_long_run_1.txt"
+WD_DIR="/scratch/nikhil/ukbb_processing/fmriprep/UKB_WD_ses-2/run1/"
+
+echo "Starting task $SLURM_ARRAY_TASK_ID"
+SUB_ID=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $SUBJECT_LIST)
+echo "Subject ID: ${SUB_ID}"
+
+module load singularity/3.8
+../fmriprep_anat_sub_regular_20.2.7.sh ${BIDS_DIR} ${WD_DIR} ${SUB_ID}
diff --git a/fmriprep/scripts/slurm/run1/fmriprep_anat_slurm_long_run1.sh b/fmriprep/scripts/slurm/run1/fmriprep_anat_slurm_long_run1.sh
new file mode 100755
index 0000000..796e09a
--- /dev/null
+++ b/fmriprep/scripts/slurm/run1/fmriprep_anat_slurm_long_run1.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#SBATCH -J ukbb_test_run
+#SBATCH --time=23:00:00
+#SBATCH --account=rrg-jbpoline
+#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=8G
+# Outputs ----------------------------------
+#SBATCH -o ./logs/%x-%A-%a_%j.out
+#SBATCH -e ./logs/%x-%A-%a_%j.err
+#SBATCH --mail-user=nikhil.bhagwat@mcgill.ca
+#SBATCH --mail-type=ALL
+# ------------------------------------------
+
+#SBATCH --array=1-300
+
+BIDS_DIR="/scratch/nikhil/ukbb_processing/fmriprep/BIDS_DIR_ses-2/"
+SUBJECT_LIST="../../metadata/ukbb_subject_ids_long_run_1.txt"
+WD_DIR="/scratch/nikhil/ukbb_processing/fmriprep/UKB_WD_ses-2/run1/"
+
+echo "Starting task $SLURM_ARRAY_TASK_ID"
+SUB_ID=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $SUBJECT_LIST)
+echo "Subject ID: ${SUB_ID}"
+
+module load singularity/3.8
+../fmriprep_anat_sub_regular_20.2.7.sh ${BIDS_DIR} ${WD_DIR} ${SUB_ID}
diff --git a/fmriprep/scripts/slurm/run2/fmriprep_anat_slurm_long_run2.sh b/fmriprep/scripts/slurm/run2/fmriprep_anat_slurm_long_run2.sh
new file mode 100755
index 0000000..9e35da2
--- /dev/null
+++ b/fmriprep/scripts/slurm/run2/fmriprep_anat_slurm_long_run2.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#SBATCH -J ukbb_test_run
+#SBATCH --time=23:00:00
+#SBATCH --account=rrg-jbpoline
+#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=8G
+# Outputs ----------------------------------
+#SBATCH -o ./logs/%x-%A-%a_%j.out
+#SBATCH -e ./logs/%x-%A-%a_%j.err
+#SBATCH --mail-user=nikhil.bhagwat@mcgill.ca
+#SBATCH --mail-type=ALL
+# ------------------------------------------
+
+#SBATCH --array=1-300
+
+BIDS_DIR="/scratch/nikhil/ukbb_processing/fmriprep/BIDS_DIR_ses-2/"
+SUBJECT_LIST="../../metadata/ukbb_subject_ids_long_run_2.txt"
+WD_DIR="/scratch/nikhil/ukbb_processing/fmriprep/UKB_WD_ses-2/run2/"
+
+echo "Starting task $SLURM_ARRAY_TASK_ID"
+SUB_ID=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $SUBJECT_LIST)
+echo "Subject ID: ${SUB_ID}"
+
+module load singularity/3.8
+../fmriprep_anat_sub_regular_20.2.7.sh ${BIDS_DIR} ${WD_DIR} ${SUB_ID}
diff --git a/fmriprep/scripts/unsquash_data.sh b/fmriprep/scripts/unsquash_data.sh
new file mode 100755
index 0000000..9790073
--- /dev/null
+++ b/fmriprep/scripts/unsquash_data.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# Author: nikhil153
+# Last update: 18 Feb 2022
+# Script to extract subset of data from squashFS into regular FS
+
+if [ "$#" -ne 3 ]; then
+  echo "Please provide squashFS, output_dir and list of subjects from /fmriprep/metadata dir"
+  exit 1
+fi
+
+SQUASHFS=$1 #neurohub_ukbb_t1_ses2_0_bids.squashfs
+OUTPUT_DIR=$2
+SUBJECT_LIST=$3
+
+CON_IMG=/project/rpp-aevans-ab/neurohub/ukbb/example_singularity.sif
+UKBB_SQUASHFS_DIR=/project/6008063/neurohub/ukbb/imaging
+
+#SquashFS list
+if [ ${SQUASHFS} == "anat" ]; then
+  echo "Using only anat data with all sessions"
+  UKBB_SQUASHFS="
+   neurohub_ukbb_t1_ses2_0_bids.squashfs
+   neurohub_ukbb_t1_ses3_0_bids.squashfs
+   neurohub_ukbb_participants.squashfs
+   neurohub_ukbb_t1_ses2_0_jsonpatch.squashfs
+   "
+
+else
+  echo "Using anat and func scans with all sessions"
+  # TODO
+
+fi
+
+UKBB_OVERLAYS=$(echo "" $UKBB_SQUASHFS | sed -e "s# # --overlay $UKBB_SQUASHFS_DIR/#g")
+echo "overlays:"
+echo $UKBB_OVERLAYS
+
+#CMD="for i in `cat $SUBJECT_LIST`; do echo $i; cp /neurohub/ukbb/imaging/${i} /output/; done"
+
+singularity run $UKBB_OVERLAYS -B $OUTPUT_DIR:/output \
+ -B /home/nikhil/scratch/ukbb_processing/ukbm/fmriprep:/fmriprep \
+ $CON_IMG /fmriprep/scripts/copy_ukb_data.sh /fmriprep/metadata/$SUBJECT_LIST