diff --git a/.dockerignore b/.dockerignore
index 21a12aa02..c5e8d9867 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -11,7 +11,7 @@ coverage_html
 templates
 **/tests
 **/bids-examples
-lib/*/.git
+lib/**/.git
 
 
 # General
diff --git a/.github/workflows/tests_octave.yml b/.github/workflows/tests_octave.yml
index 93a5ede66..051b0eb76 100644
--- a/.github/workflows/tests_octave.yml
+++ b/.github/workflows/tests_octave.yml
@@ -71,7 +71,7 @@ jobs:
     - name: Install python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Clone bidspm
       uses: actions/checkout@v3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3bca001d9..9060be88e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -56,7 +56,7 @@ repos:
     args: [--config=pyproject.toml]
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.11.0
   hooks:
   - id: pyupgrade
     args: [--py38-plus]
@@ -73,7 +73,7 @@ repos:
   - id: flynt
 
 - repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.10.0
+  rev: v3.11.0
   hooks:
   - id: reorder-python-imports
     args: [--py38-plus, --add-import, from __future__ import annotations]
diff --git a/Makefile b/Makefile
index 0184660dc..cd04ea4b9 100644
--- a/Makefile
+++ b/Makefile
@@ -34,7 +34,7 @@ ARG    = -nodisplay -nosplash -nodesktop
 
 install:
 	npm install -g bids-validator
-	pip3 install .
+	pip3 install .[dev]
 
 help: ## Show what this Makefile can do
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
@@ -122,7 +122,6 @@ clean_docker:
 
 build_image: Dockerfile ## Build stable docker image from the main branch
 	docker build . -f Dockerfile -t cpplab/bidspm:unstable
-	VERSION=$(cat version.txt | cut -c2-)
 
 Dockerfile_matlab:
 	docker run --rm kaczmarj/neurodocker:0.9.1 generate docker \
@@ -138,4 +137,7 @@ Dockerfile_matlab:
 build_image_matlab: Dockerfile_matlab
 	docker build . -f Dockerfile_matlab -t cpplab/bidspm_matlab:unstable
 
+docker_data:
+	make -C demos/openneuro data_ds000001
+
 ################################################################################
diff --git a/demos/MoAE/test_moae.m b/demos/MoAE/test_moae.m
index e8427c5d7..e287fbeb6 100644
--- a/demos/MoAE/test_moae.m
+++ b/demos/MoAE/test_moae.m
@@ -84,13 +84,22 @@
 
   cd(WD);
 
-  % with Octave running more n-1 loop in CI is fine
+  % Octave
+  % running more n-1 loop in CI is fine
   % but not running crashes with a segmentation fault
   % /home/runner/work/_temp/fb8e9d58-fa9f-4f93-8c96-387973f3632e.sh: line 2:
   % 7487 Segmentation fault      (core dumped) octave $OCTFLAGS --eval "run system_tests_facerep;"
   %
   % not sure why
-  if bids.internal.is_octave()
+  %
+
+  % Windows
+  % Error using overwriteDir
+  %    C:\Users\runneradmin\AppData\Local\Temp\8f7c44ca98d0\outputs\derivatives\bidspm-stats\
+  %           sub-01\task-auditory_space-individual_FWHM-6 could not be removed.
+  % Error in setBatchSubjectLevelGLMSpec (line 73)
+  %    overwriteDir(ffxDir, opt);
+  if bids.internal.is_octave() || ispc()
     break
   end
 
diff --git a/pyproject.toml b/pyproject.toml
index 8e2dc7bb7..99a677f7e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,6 +69,7 @@ dev = [
     "coverage",
     "pytest",
     "ruamel.yaml",
+    'pandas'
 ]
 
 [project.scripts]
diff --git a/tests/Makefile b/tests/Makefile
index 3a3b7c656..f52fa6034 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -10,7 +10,7 @@ clean_local:
 	rm -rf data/derivatives/bidspm-*/jobs
 
 create_dummy_dataset: clean_local
-	sh createDummyDataSet.sh
+	python create_dummy_dataset.py
 
 bids_examples:
 	rm -rf bids-examples/
diff --git a/tests/createDummyDataSet.sh b/tests/createDummyDataSet.sh
deleted file mode 100755
index 022b3ac7a..000000000
--- a/tests/createDummyDataSet.sh
+++ /dev/null
@@ -1,373 +0,0 @@
-#!/bin/bash
-
-# small bash script to create a dummy BIDS data set
-
-# defines where the BIDS data set will be created
-start_dir=$(pwd) # relative to starting directory
-raw_dir=${start_dir}/data/bidspm-raw
-preproc_dir=${start_dir}/data/derivatives/bidspm-preproc
-stats_dir=${start_dir}/data/derivatives/bidspm-stats
-roi_dir=${start_dir}/data/derivatives/bidspm-roi
-
-subject_list='ctrl01 blind01 01'
-session_list='01 02'
-roi_list='V1 A1'
-hemispheres='L R'
-
-create_raw_func_vismotion() {
-
-	target_dir=$1
-	subject=$2
-	ses=$3
-
-	suffix='_bold'
-	task_name='vismotion'
-
-	this_dir=${target_dir}/sub-${subject}/ses-${ses}/func
-
-	basename=sub-${subject}_ses-${ses}_task-${task_name}
-
-	mkdir -p "${this_dir}"
-
-	for run in $(seq 1 2); do
-		filename=${this_dir}/${basename}_run-${run}_part-mag${suffix}.nii
-		touch "${filename}"
-		filename=${this_dir}/${basename}_run-${run}_part-phase${suffix}.nii
-		touch "${filename}"
-	done
-
-	filename="${this_dir}/${basename}_run-1_events.tsv"
-	echo "onset\tduration\ttrial_type" >"${filename}"
-	echo "2\t2\tVisMot" >>"${filename}"
-	echo "4\t2\tVisStat" >>"${filename}"
-
-	filename="${this_dir}/${basename}_run-2_events.tsv"
-	echo "onset\tduration\ttrial_type" >"${filename}"
-	echo "3\t2\tVisStat" >>"${filename}"
-	echo "6\t2\tVisMot" >>"${filename}"
-
-	touch "${this_dir}/${basename}_acq-1p60mm_run-1${suffix}.nii"
-
-	filename="${this_dir}/${basename}_acq-1p60mm_run-1_events.tsv"
-	echo "onset\tduration\ttrial_type" >"${filename}"
-	echo "4\t2\tVisMot" >>"${filename}"
-	echo "8\t2\tVisStat" >>"${filename}"
-
-	touch "${this_dir}/${basename}_acq-1p60mm_dir-PA_run-1${suffix}.nii"
-
-	filename="${this_dir}/${basename}_acq-1p60mm_run-2_events.tsv"
-	echo "onset\tduration\ttrial_type" >"${filename}"
-	echo "4\t2\tVisMot" >>"${filename}"
-	echo "8\t2\tVisStat" >>"${filename}"
-
-	touch "${this_dir}/${basename}_acq-1p60mm_dir-PA_run-2${suffix}.nii"
-}
-
-create_raw_func_vislocalizer() {
-
-	target_dir=$1
-	subject=$2
-	ses=$3
-
-	suffix='_bold'
-	task_name='vislocalizer'
-
-	this_dir=${target_dir}/sub-${subject}/ses-${ses}/func
-
-	mkdir -p ${this_dir}
-
-	filename=${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag${suffix}.nii
-	touch "${filename}"
-	filename=${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-phase${suffix}.nii
-	touch "${filename}"
-
-	filename=${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_events.tsv
-	echo "onset\tduration\ttrial_type" >"${filename}"
-	echo "2\t15\tVisMot" >>"${filename}"
-	echo "25\t15\tVisStat" >>"${filename}"
-
-}
-
-create_raw_func_rest() {
-
-	target_dir=$1
-	subject=$2
-	ses=$3
-
-	suffix='_bold'
-	task_name='rest'
-
-	this_dir=${target_dir}/sub-${subject}/ses-${ses}/func
-
-	mkdir -p "${this_dir}"
-
-	touch "${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}${suffix}.nii"
-
-}
-
-create_raw_fmap() {
-
-	target_dir=$1
-	subject=$2
-	ses=$3
-
-	this_dir=${target_dir}/sub-${subject}/ses-${ses}/fmap
-
-	mkdir -p "${this_dir}"
-
-	fmap_suffix_list='_phasediff _magnitude1 _magnitude2'
-	for suffix in ${fmap_suffix_list}; do
-		touch "${this_dir}/sub-${subject}_ses-${ses}_run-1${suffix}.nii"
-		touch "${this_dir}/sub-${subject}_ses-${ses}_run-2${suffix}.nii"
-	done
-
-	EchoTime1=0.006
-	EchoTime2=0.00746
-	template='{"EchoTime1":%f, "EchoTime2":%f, "IntendedFor":"%s"}'
-
-	suffix='_bold'
-
-	task_name='vislocalizer'
-	IntendedFor=$(echo ses-${ses}/func/sub-${subject}_ses-${ses}_task-${task_name}_part-mag${suffix}.nii)
-	json_string=$(printf "$template" "$EchoTime1" "$EchoTime2" "$IntendedFor")
-	echo "$json_string" >${this_dir}/sub-${subject}_ses-${ses}_run-1_phasediff.json
-
-	task_name='vismotion'
-	IntendedFor=$(echo ses-${ses}/func/sub-${subject}_ses-${ses}_task-${task_name}_run-1_part-mag${suffix}.nii)
-	json_string=$(printf "$template" "$EchoTime1" "$EchoTime2" "$IntendedFor")
-	echo "$json_string" >"${this_dir}/sub-${subject}_ses-${ses}_run-2_phasediff.json"
-
-}
-
-create_raw_anat() {
-
-	target_dir=$1
-	subject=$2
-
-	ses='01'
-	suffix='_T1w'
-
-	this_dir=${target_dir}/sub-${subject}/ses-01/anat
-	mkdir -p ${this_dir}
-
-	touch "${this_dir}/sub-${subject}_ses-${ses}${suffix}.nii"
-
-	# MP2RAGE
-	touch "${this_dir}/sub-${subject}_ses-${ses}_UNIT1.nii"
-	touch "${this_dir}/sub-${subject}_ses-${ses}_inv-1_MP2RAGE.nii"
-	touch "${this_dir}/sub-${subject}_ses-${ses}_inv-2_MP2RAGE.nii"
-
-	template='{"MagneticFieldStrength":%f, "RepetitionTimePreparation":%f, "InversionTime":%f, "FlipAngle":%f, "FatSat":"%s", "EchoSpacing":%f, "PartialFourierInSlice":%f}'
-
-	FlipAngle=4
-	MagneticFieldStrength=7
-	RepetitionTimePreparation=4.3
-	InversionTime=1
-	Fatsat="yes"
-	EchoSpacing=0.0072
-	PartialFourierInSlice=0.75
-
-	json_string=$(printf "$template" "$MagneticFieldStrength" "$RepetitionTimePreparation" "$InversionTime" "$FlipAngle" "$Fatsat" "$EchoSpacing" "$PartialFourierInSlice")
-	echo "$json_string" >${this_dir}/sub-${subject}_ses-${ses}_inv-1_MP2RAGE.json
-
-	InversionTime=3.2
-
-	json_string=$(printf "$template" "$MagneticFieldStrength" "$RepetitionTimePreparation" "$InversionTime" "$FlipAngle" "$Fatsat" "$EchoSpacing" "$PartialFourierInSlice")
-	echo "$json_string" >${this_dir}/sub-${subject}_ses-${ses}_inv-2_MP2RAGE.json
-
-}
-
-# RAW DATASET
-for subject in ${subject_list}; do
-	for ses in ${session_list}; do
-		create_raw_func_vismotion ${raw_dir} ${subject} ${ses}
-		create_raw_func_vislocalizer ${raw_dir} ${subject} ${ses}
-		create_raw_fmap ${raw_dir} ${subject} ${ses}
-	done
-
-	create_raw_func_rest ${raw_dir} ${subject} '02'
-	create_raw_anat ${raw_dir} ${subject}
-done
-
-# ROIs
-mkdir -p ${roi_dir}/group
-for roi in ${roi_list}; do
-	touch "${roi_dir}/group/${roi}_mask.nii"
-done
-
-for subject in ${subject_list}; do
-	this_dir=${roi_dir}/sub-${subject}/roi
-	mkdir -p "${this_dir}"
-	for roi in ${roi_list}; do
-		for hemi in ${hemispheres}; do
-			touch "${this_dir}/sub-${subject}_hemi-${hemi}_space-individual_label-${roi}_mask.nii"
-		done
-	done
-done
-
-# DERIVATIVES DATASET
-for subject in ${subject_list}; do
-
-	for ses in ${session_list}; do
-
-		# FUNC
-		create_raw_func_vismotion ${preproc_dir} ${subject} ${ses}
-		create_raw_func_vislocalizer ${preproc_dir} ${subject} ${ses}
-		create_raw_fmap ${preproc_dir} ${subject} ${ses}
-
-		this_dir=${preproc_dir}/sub-${subject}/ses-${ses}/func
-
-		## task: vismotion
-		suffix='_bold'
-		task_name='vismotion'
-
-		### derivatives
-		desc_label_list='preproc mean smth6'
-		for acq in $(seq 1 2); do
-
-			acq_entity=""
-			if [ ${acq} = 2 ]; then
-				acq_entity="_acq-1p60mm"
-			fi
-
-			basename=sub-${subject}_ses-${ses}_task-${task_name}${acq_entity}
-
-			for run in $(seq 1 2); do
-
-				filename=${this_dir}/rp_${basename}_run-${run}_part-mag${suffix}.txt
-				cp data/tsv_files/rp.txt "${filename}"
-				cp data/tsv_files/rp.tsv ${this_dir}/${basename}_run-${run}_part-mag_desc-confounds_regressors.tsv
-
-				for desc in ${desc_label_list}; do
-					touch ${this_dir}/${basename}_run-${run}_part-mag_space-individual_desc-${desc}${suffix}.nii
-					touch ${this_dir}/${basename}_run-${run}_part-mag_space-IXI549Space_desc-${desc}${suffix}.nii
-				done
-				touch ${this_dir}/${basename}_run-${run}_part-mag_space-individual_desc-stc${suffix}.nii
-
-				touch ${this_dir}/${basename}_run-${run}_part-mag_space-IXI549Space_label-brain_mask.nii
-
-			done
-
-			if [ ${ses} = '01' ]; then
-				touch ${this_dir}/${basename}_part-mag_space-individual_desc-mean${suffix}.nii
-				touch ${this_dir}/${basename}_part-mag_space-IXI549Space_desc-mean${suffix}.nii
-
-				touch ${this_dir}/mean_${basename}_part-mag${suffix}.nii
-			fi
-
-		done
-
-		## task: vislocalizer
-		suffix='_bold'
-		task_name='vislocalizer'
-
-		### derivatives
-		filename=${this_dir}/rp_sub-${subject}_ses-${ses}_task-${task_name}${suffix}.txt
-		cp data/tsv_files/rp.txt "${filename}"
-		cp data/tsv_files/rp.tsv ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_desc-confounds_regressors.tsv
-
-		desc_label_list='preproc smth6'
-		for desc in ${desc_label_list}; do
-			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_space-individual_desc-${desc}${suffix}.nii
-			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_space-IXI549Space_desc-${desc}${suffix}.nii
-			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_space-IXI549Space_label-brain_mask.nii
-		done
-		touch ${this_dir}/mean_sub-${subject}_ses-${ses}_task-${task_name}_part-mag${suffix}.nii
-
-		if [ ${ses} = '01' ]; then
-			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_space-individual_desc-mean${suffix}.nii
-			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_part-mag_space-IXI549Space_desc-mean${suffix}.nii
-		fi
-
-	done
-
-	## task: rest
-	ses='02'
-	suffix='_bold'
-	task_name='rest'
-
-	### raw & derivatives
-	create_raw_func_rest ${preproc_dir} ${subject} '02'
-	touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-individual_desc-preproc${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-individual_label-brain_mask.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-IXI549Space_desc-preproc${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-IXI549Space_label-brain_mask.nii
-
-	# ANAT
-	create_raw_anat ${preproc_dir} ${subject}
-
-	ses='01'
-	suffix='_T1w'
-
-	## derivatives
-	this_dir=${preproc_dir}/sub-${subject}/ses-01/anat
-
-	anat_prefix_list='m c1 c2 c3'
-	for prefix in ${anat_prefix_list}; do
-		touch ${this_dir}/${prefix}sub-${subject}_ses-${ses}${suffix}.nii
-	done
-
-	space='individual'
-
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_desc-biascor${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_desc-skullstripped${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_desc-preproc${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_label-brain_mask.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_label-CSF_probseg.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_label-GM_probseg.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_label-WM_probseg.nii
-
-	space='IXI549Space'
-
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_res-bold_label-CSF_probseg.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_res-bold_label-GM_probseg.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_res-bold_label-WM_probseg.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_res-hi_desc-preproc${suffix}.nii
-	touch ${this_dir}/sub-${subject}_ses-${ses}_space-${space}_desc-brain_mask.nii
-
-	# deformation fields
-	touch ${this_dir}/sub-${subject}_ses-${ses}_from-IXI549Space_to-T1w_mode-image_xfm.nii
-
-	# STATS
-	task_list='vismotion vislocalizer'
-	for task in ${task_list}; do
-
-		this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6
-		mkdir -p ${this_dir}
-
-		cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
-
-		touch ${this_dir}/mask.nii
-
-		for i in $(seq 1 9); do
-			touch ${this_dir}/beta_000${i}.nii
-		done
-
-		for i in $(seq 1 4); do
-			touch ${this_dir}/spmT_000${i}.nii
-			touch ${this_dir}/con_000${i}.nii
-			touch ${this_dir}/s6con_000${i}.nii
-		done
-	done
-
-	# different model for model comparison
-	task_list='vismotion vislocalizer'
-	for task in ${task_list}; do
-		this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6_node-globalSignal
-		mkdir -p ${this_dir}
-
-		cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
-
-		touch ${this_dir}/mask.nii
-
-		for i in $(seq 1 10); do
-			touch ${this_dir}/beta_000${i}.nii
-		done
-
-		for i in $(seq 1 2); do
-			touch ${this_dir}/spmT_000${i}.nii
-			touch ${this_dir}/con_000${i}.nii
-		done
-	done
-
-done
diff --git a/tests/create_dummy_dataset.py b/tests/create_dummy_dataset.py
new file mode 100644
index 000000000..6691deb03
--- /dev/null
+++ b/tests/create_dummy_dataset.py
@@ -0,0 +1,382 @@
+from __future__ import annotations
+
+import json
+import shutil
+from pathlib import Path
+
+import pandas as pd
+
+ROOT_DIR = Path(__file__).parent.parent
+START_DIR = Path(__file__).parent
+SUBJECTS = ["ctrl01", "blind01", "01"]
+SESSIONS = ["01", "02"]
+ROIS = ["V1", "A1"]
+HEMISPHERES = ["L", "R"]
+
+
+def touch(path: Path):
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with open(path, "a"):
+        pass
+
+
+def main(start_dir, subject_list, session_list, roi_list, hemispheres):
+    # Create BIDS directory structure
+    raw_dir = start_dir / "data" / "bidspm-raw"
+    derivative_dir = start_dir / "data" / "derivatives"
+    preproc_dir = derivative_dir / "bidspm-preproc"
+    stats_dir = derivative_dir / "bidspm-stats"
+    roi_dir = derivative_dir / "bidspm-roi"
+
+    create_raw_dataset(raw_dir, subject_list, session_list)
+    create_preproc_dataset(preproc_dir, subject_list, session_list)
+    create_roi_directories(roi_dir, roi_list, subject_list, hemispheres)
+
+    create_stats_dataset(stats_dir, subject_list)
+
+
+def create_raw_dataset(target_dir, subject_list, session_list):
+    # Create the raw BIDS dataset
+    for sub in subject_list:
+        for ses in session_list:
+            create_raw_func_vismotion(target_dir, sub, ses)
+            create_raw_func_vislocalizer(target_dir, sub, ses)
+            create_raw_fmap(target_dir, sub, ses)
+
+        create_raw_func_rest(target_dir, sub, "02")
+        create_raw_anat(target_dir, sub)
+
+
+def create_raw_func_vismotion(target_dir, sub, ses):
+    suffix = "bold"
+    task = "vismotion"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+    this_dir.mkdir(parents=True, exist_ok=True)
+
+    basename = f"sub-{sub}_ses-{ses}_task-{task}"
+
+    create_events_tsv(
+        filename=this_dir / f"{basename}_run-1_events.tsv",
+        onset=[2, 4],
+        duration=[2, 2],
+        trial_type=["VisMot", "VisStat"],
+    )
+
+    for run in range(1, 3):
+        filename = this_dir / f"{basename}_run-{run}_part-mag_{suffix}.nii"
+        touch(filename)
+        filename = this_dir / f"{basename}_run-{run}_part-phase_{suffix}.nii"
+        touch(filename)
+
+    create_events_tsv(
+        filename=this_dir / f"{basename}_run-2_events.tsv",
+        onset=[3, 6],
+        duration=[2, 2],
+        trial_type=["VisStat", "VisMot"],
+    )
+
+    touch(this_dir / f"{basename}_acq-1p60mm_run-1_{suffix}.nii")
+
+    for run in [1, 2]:
+        create_events_tsv(
+            filename=this_dir / f"{basename}_acq-1p60mm_run-{run}_events.tsv",
+            onset=[4, 8],
+            duration=[2, 2],
+            trial_type=["VisMot", "VisStat"],
+        )
+        touch(this_dir / f"{basename}_acq-1p60mm_dir-PA_run-{run}_{suffix}.nii")
+
+
+def create_raw_func_vislocalizer(target_dir, sub, ses):
+    suffix = "bold"
+    task = "vislocalizer"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+
+    basename = f"sub-{sub}_ses-{ses}_task-{task}"
+    touch(this_dir / f"{basename}_part-mag_{suffix}.nii")
+    touch(this_dir / f"{basename}_part-phase_{suffix}.nii")
+
+    create_events_tsv(
+        filename=this_dir / f"{basename}_events.tsv",
+        onset=[2, 25],
+        duration=[15, 15],
+        trial_type=["VisMot", "VisStat"],
+    )
+
+
+def create_events_tsv(filename, onset, duration, trial_type):
+    events = {
+        "onset": onset,
+        "duration": duration,
+        "trial_type": trial_type,
+    }
+    df = pd.DataFrame(events)
+    df.to_csv(filename, sep="\t", index=False)
+
+
+def create_raw_func_rest(target_dir, sub, ses):
+    suffix = "bold"
+    task = "rest"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+
+    touch(this_dir / f"sub-{sub}_ses-{ses}_task-{task}_{suffix}.nii")
+
+
+def create_raw_fmap(target_dir, sub, ses):
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "fmap"
+
+    fmap_suffix_list = ["phasediff", "magnitude1", "magnitude2"]
+    for suffix in fmap_suffix_list:
+        touch(this_dir / f"sub-{sub}_ses-{ses}_run-1_{suffix}.nii")
+        touch(this_dir / f"sub-{sub}_ses-{ses}_run-2_{suffix}.nii")
+
+    suffix = "bold"
+    task = "vislocalizer"
+
+    content = {
+        "EchoTime1": 0.006,
+        "EchoTime2": 0.00746,
+        "IntendedFor": f"ses-{ses}/func/sub-{sub}_ses-{ses}_task-{task}_part-mag_{suffix}.nii",
+    }
+
+    with open(this_dir / f"sub-{sub}_ses-{ses}_run-1_phasediff.json", "w") as f:
+        json.dump(content, f, indent=4)
+
+    task = "vismotion"
+    content[
+        "IntendedFor"
+    ] = f"ses-{ses}/func/sub-{sub}_ses-{ses}_task-{task}_run-1_part-mag_{suffix}.nii"
+    with open(this_dir / f"sub-{sub}_ses-{ses}_run-2_phasediff.json", "w") as f:
+        json.dump(content, f, indent=4)
+
+
+def create_raw_anat(target_dir, sub):
+    ses = "01"
+    suffix = "T1w"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "anat"
+
+    touch(this_dir / f"sub-{sub}_ses-{ses}_{suffix}.nii")
+
+    # MP2RAGE
+    touch(this_dir / f"sub-{sub}_ses-{ses}_UNIT1.nii")
+    touch(this_dir / f"sub-{sub}_ses-{ses}_inv-1_MP2RAGE.nii")
+    touch(this_dir / f"sub-{sub}_ses-{ses}_inv-2_MP2RAGE.nii")
+
+    content = {
+        "MagneticFieldStrength": 7,
+        "RepetitionTimePreparation": 4.3,
+        "InversionTime": 1,
+        "FlipAngle": 4,
+        "FatSat": "yes",
+        "EchoSpacing": 0.0072,
+        "PartialFourierInSlice": 0.75,
+    }
+
+    with open(this_dir / f"sub-{sub}_ses-{ses}_inv-1_MP2RAGE.json", "w") as f:
+        json.dump(content, f, indent=4)
+
+    content["InversionTime"] = 3.2
+    with open(this_dir / f"sub-{sub}_ses-{ses}_inv-2_MP2RAGE.json", "w") as f:
+        json.dump(content, f, indent=4)
+
+
+def create_preproc_dataset(target_dir, subject_list, session_list):
+    # Create the derivatives BIDS dataset
+    create_raw_dataset(target_dir, subject_list, session_list)
+
+    for sub in subject_list:
+        for ses in session_list:
+            create_preproc_func_vismotion(target_dir, sub, ses)
+            create_preproc_func_vislocalizer(target_dir, sub, ses)
+        create_preproc_func_rest(target_dir, sub, "02")
+        create_preproc_anat(target_dir, sub)
+
+
+def create_preproc_func_vismotion(target_dir, sub, ses):
+    suffix = "bold"
+    task = "vismotion"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+    this_dir.mkdir(parents=True, exist_ok=True)
+
+    for acq_entity in ["", "_acq-1p60mm"]:
+        basename = f"sub-{sub}_ses-{ses}_task-{task}{acq_entity}_part-mag"
+
+        if ses == "01":
+            touch(this_dir / f"{basename}_space-individual_desc-mean_{suffix}.nii")
+            touch(this_dir / f"{basename}_space-IXI549Space_desc-mean_{suffix}.nii")
+            touch(this_dir / f"mean_{basename}_{suffix}.nii")
+
+        for run in range(1, 3):
+            basename = f"sub-{sub}_ses-{ses}_task-{task}{acq_entity}_run-{run}_part-mag"
+
+            filename = this_dir / f"rp_{basename}_{suffix}.txt"
+            shutil.copy(ROOT_DIR / "tests" / "data" / "tsv_files" / "rp.txt", filename)
+
+            shutil.copy(
+                ROOT_DIR / "tests" / "data" / "tsv_files" / "rp.tsv",
+                this_dir / f"{basename}_desc-confounds_regressors.tsv",
+            )
+
+            desc_label_list = ["preproc", "mean", "smth6"]
+            for desc in desc_label_list:
+                touch(this_dir / f"{basename}_space-individual_desc-{desc}_{suffix}.nii")
+                touch(this_dir / f"{basename}_space-IXI549Space_desc-{desc}_{suffix}.nii")
+
+            touch(this_dir / f"{basename}_space-individual_desc-stc_{suffix}.nii")
+            touch(this_dir / f"{basename}_space-IXI549Space_desc-brain_mask.nii")
+
+
+def create_preproc_func_vislocalizer(target_dir, sub, ses):
+    suffix = "bold"
+    task = "vislocalizer"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+    this_dir.mkdir(parents=True, exist_ok=True)
+
+    basename = f"sub-{sub}_ses-{ses}_task-{task}"
+
+    filename = this_dir / f"rp_{basename}_{suffix}.txt"
+    shutil.copy(ROOT_DIR / "tests" / "data" / "tsv_files" / "rp.txt", filename)
+    shutil.copy(
+        ROOT_DIR / "tests" / "data" / "tsv_files" / "rp.tsv",
+        this_dir / f"{basename}_part-mag_desc-confounds_regressors.tsv",
+    )
+
+    basename += "_part-mag"
+
+    desc_label_list = ["preproc", "smth6"]
+    for desc in desc_label_list:
+        touch(this_dir / f"{basename}_space-individual_desc-{desc}_{suffix}.nii")
+        touch(this_dir / f"{basename}_space-IXI549Space_desc-{desc}_{suffix}.nii")
+        touch(this_dir / f"{basename}_space-IXI549Space_desc-brain_mask.nii")
+
+    if ses == "01":
+        touch(this_dir / f"{basename}_space-individual_desc-mean_{suffix}.nii")
+        touch(this_dir / f"{basename}_space-IXI549Space_desc-mean_{suffix}.nii")
+
+    touch(this_dir / f"mean_{basename}_{suffix}.nii")
+
+
+def create_preproc_func_rest(target_dir, sub, ses):
+    task = "rest"
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "func"
+
+    basename = f"sub-{sub}_ses-{ses}_task-{task}"
+
+    for space in ["individual", "IXI549Space"]:
+        touch(this_dir / f"{basename}_space-{space}_desc-preproc_bold.nii")
+        touch(this_dir / f"{basename}_space-{space}_desc-brain_mask.nii")
+
+    shutil.copy(
+        ROOT_DIR / "tests" / "data" / "tsv_files" / "rp.tsv",
+        this_dir / f"{basename}_part-mag_desc-confounds_regressors.tsv",
+    )
+
+
+def create_preproc_anat(target_dir, sub):
+    ses = "01"
+    suffix = "T1w"
+
+    this_dir = target_dir / f"sub-{sub}" / f"ses-{ses}" / "anat"
+    this_dir.mkdir(parents=True, exist_ok=True)
+
+    basename = f"sub-{sub}_ses-{ses}"
+
+    touch(this_dir / f"{basename}_{suffix}.nii")
+
+    anat_prefix_list = ["m", "c1", "c2", "c3"]
+    for prefix in anat_prefix_list:
+        touch(this_dir / f"{prefix}{basename}_{suffix}.nii")
+
+    for space in ["individual", "IXI549Space"]:
+        touch(this_dir / f"{basename}_space-{space}_desc-brain_mask.nii")
+        for label in ["CSF", "GM", "WM"]:
+            res_entity = ""
+            if space == "IXI549Space":
+                res_entity = "_res-bold"
+            touch(
+                this_dir
+                / f"{basename}_space-{space}{res_entity}_label-{label}_probseg.nii"
+            )
+
+    touch(this_dir / f"{basename}_space-individual_desc-biascor_{suffix}.nii")
+    touch(this_dir / f"{basename}_space-individual_desc-skullstripped_{suffix}.nii")
+    touch(this_dir / f"{basename}_space-individual_desc-preproc_{suffix}.nii")
+
+    touch(this_dir / f"{basename}_space-IXI549Space_res-hi_desc-preproc_{suffix}.nii")
+    touch(this_dir / f"{basename}_from-IXI549Space_to-T1w_mode-image_xfm.nii")
+
+
+def create_stats_dataset(stats_dir, subject_list):
+    task_list = ["vismotion", "vislocalizer"]
+
+    for sub in subject_list:
+        for task in task_list:
+            this_dir = stats_dir / f"sub-{sub}" / f"task-{task}_space-IXI549Space_FWHM-6"
+            this_dir.mkdir(parents=True, exist_ok=True)
+
+            shutil.copy(
+                ROOT_DIR / "tests" / "data" / "mat_files" / "SPM.mat",
+                this_dir / "SPM.mat",
+            )
+
+            touch(this_dir / "mask.nii")
+
+            for i in range(1, 10):
+                touch(this_dir / f"beta_000{i}.nii")
+
+            for i in range(1, 5):
+                touch(this_dir / f"spmT_000{i}.nii")
+                touch(this_dir / f"con_000{i}.nii")
+                touch(this_dir / f"s6con_000{i}.nii")
+
+        # Different model for model comparison
+        for task in task_list:
+            this_dir = (
+                stats_dir
+                / f"sub-{sub}"
+                / f"task-{task}_space-IXI549Space_FWHM-6_node-globalSignal"
+            )
+            this_dir.mkdir(parents=True, exist_ok=True)
+
+            shutil.copy(
+                ROOT_DIR / "tests" / "data" / "mat_files" / "SPM.mat",
+                this_dir / "SPM.mat",
+            )
+
+            touch(this_dir / "mask.nii")
+
+            for i in range(1, 11):
+                touch(this_dir / f"beta_000{i}.nii")
+
+            for i in range(1, 3):
+                touch(this_dir / f"spmT_000{i}.nii")
+                touch(this_dir / f"con_000{i}.nii")
+
+
+def create_roi_directories(roi_dir, roi_list, subject_list, hemispheres):
+    # Create ROI directories
+    roi_group_dir = roi_dir / "group"
+    roi_group_dir.mkdir(parents=True, exist_ok=True)
+
+    for roi in roi_list:
+        touch(roi_group_dir / f"{roi}_mask.nii")
+
+    for sub in subject_list:
+        this_dir = roi_dir / f"sub-{sub}" / "roi"
+        this_dir.mkdir(parents=True, exist_ok=True)
+        for roi in roi_list:
+            for hemi in hemispheres:
+                touch(
+                    this_dir
+                    / f"sub-{sub}_hemi-{hemi}_space-individual_label-{roi}_mask.nii"
+                )
+
+
+if __name__ == "__main__":
+    main(
+        start_dir=START_DIR,
+        subject_list=SUBJECTS,
+        session_list=SESSIONS,
+        roi_list=ROIS,
+        hemispheres=HEMISPHERES,
+    )
diff --git a/tests/tests_QA/test_computeDesignEfficiency.m b/tests/tests_QA/test_computeDesignEfficiency.m
index 7407c5c75..09ff0117e 100644
--- a/tests/tests_QA/test_computeDesignEfficiency.m
+++ b/tests/tests_QA/test_computeDesignEfficiency.m
@@ -13,7 +13,9 @@ function test_computeDesignEfficiency_vislocalizer()
 
   close all;
 
-  opt = setOptions('vismotion', '01');
+  subject = '01';
+
+  opt = setOptions('vismotion', subject);
 
   BIDS = bids.layout(opt.dir.input, ...
                      'use_schema', false, ...
@@ -28,9 +30,11 @@ function test_computeDesignEfficiency_vislocalizer()
   opt.TR = metadata{1}.RepetitionTime;
 
   eventsFile = bids.query(BIDS, 'data', ...
-                          'sub', opt.subjects, ...
+                          'sub', subject, ...
+                          'ses', '01', ...
                           'task', opt.taskName, ...
                           'acq', '', ...
+                          'run', 1, ...
                           'suffix', 'events');
 
   e = computeDesignEfficiency(eventsFile{1}, opt);
@@ -73,7 +77,7 @@ function test_computeDesignEfficiency_vislocalizer()
   for iBlock = 1:nbBlocks
     for cdt = 1:numel(conditions)
       for iTrial = 1:stimPerBlock
-        trial_type{end + 1} = conditions{cdt};
+        trial_type{end + 1} = conditions{cdt}; %#ok<*AGROW>
         onset(end + 1) = time;
         duration(end + 1) = stimDuration;
         time = time + stimDuration + ISI;
diff --git a/tests/tests_batches/test_setBatchMeanAnatAndMask.m b/tests/tests_batches/test_setBatchMeanAnatAndMask.m
index 2766e4aea..3e0cf8d49 100644
--- a/tests/tests_batches/test_setBatchMeanAnatAndMask.m
+++ b/tests/tests_batches/test_setBatchMeanAnatAndMask.m
@@ -52,10 +52,10 @@ function test_setBatchMeanAnatAndMask_basic()
 
   expectedBatch{2}.spm.util.imcalc = imcalc;
 
-  assertEqual(matlabbatch{1}.spm.util.imcalc.input, expectedBatch{1}.spm.util.imcalc.input);
-  assertEqual(matlabbatch{1}.spm.util.imcalc.output, expectedBatch{1}.spm.util.imcalc.output);
   assertEqual(matlabbatch{2}.spm.util.imcalc.input, expectedBatch{2}.spm.util.imcalc.input);
   assertEqual(matlabbatch{2}.spm.util.imcalc.output, expectedBatch{2}.spm.util.imcalc.output);
+  assertEqual(matlabbatch{1}.spm.util.imcalc.input, expectedBatch{1}.spm.util.imcalc.input);
+  assertEqual(matlabbatch{1}.spm.util.imcalc.output, expectedBatch{1}.spm.util.imcalc.output);
 
   assertEqual(numel(matlabbatch), 6);
 
diff --git a/tests/tests_stats/unit_tests/test_getInclusiveMask.m b/tests/tests_stats/unit_tests/test_getInclusiveMask.m
index f8328ceb2..cfab02dc6 100644
--- a/tests/tests_stats/unit_tests/test_getInclusiveMask.m
+++ b/tests/tests_stats/unit_tests/test_getInclusiveMask.m
@@ -13,14 +13,15 @@ function test_getInclusiveMask_too_many()
   subLabel = '01';
   nodeName = 'run_level';
 
-  opt = setOptions('vismotion', '01');
+  opt = setOptions('vismotion', '01', 'useTempDir', true);
 
   opt.verbosity = 2;
 
   opt.model.bm = BidsModel('file', opt.model.file);
 
-  opt.model.bm.Nodes{1}.Model.Options.Mask.label{1} = 'brain';
-  opt.model.bm.Nodes{1}.Model.Options.Mask.desc{1} = '';
+  % dummy spec to return several images
+  opt.model.bm.Nodes{1}.Model.Options.Mask.suffix{1} = 'bold';
+  opt.model.bm.Nodes{1}.Model.Options.Mask.desc{1} = 'preproc';
 
   opt.space = opt.model.bm.Input.space;
 
diff --git a/tests/tests_unit/IO/test_saveSpmScript.m b/tests/tests_unit/IO/test_saveSpmScript.m
index c58674e18..931132bd0 100644
--- a/tests/tests_unit/IO/test_saveSpmScript.m
+++ b/tests/tests_unit/IO/test_saveSpmScript.m
@@ -28,7 +28,7 @@ function test_saveSpmScript_basic()
   expectedContent = fscanf(fid1, '%s');
   fclose(fid1);
   if ispc
-    expectedContent = strrep('/', '\');
+    expectedContent = strrep(expectedContent, '/', '\');
   end
 
   fid2 = fopen(outputFilename, 'r');
diff --git a/tests/utils/createDummyData.m b/tests/utils/createDummyData.m
index 89e10150c..0091d50a9 100644
--- a/tests/utils/createDummyData.m
+++ b/tests/utils/createDummyData.m
@@ -5,7 +5,7 @@ function createDummyData()
 
   startDir = pwd;
 
-  script = fullfile(getTestDir(), 'createDummyDataSet.sh');
+  script = fullfile(getTestDir(), 'create_dummy_dataset.py');
 
   cd(fileparts(script));
 
@@ -15,7 +15,7 @@ function createDummyData()
   [status, result] = system('rm -fr data/derivatives/bidspm-stats/group');
   [status, result] = system('rm -fr data/derivatives/bidspm-*/jobs');
 
-  system('sh createDummyDataSet.sh');
+  system('python create_dummy_dataset.py');
 
   cd(startDir);
 
diff --git a/tests/utils/setOptions.m b/tests/utils/setOptions.m
index 61c8b93de..ca6c02fbe 100644
--- a/tests/utils/setOptions.m
+++ b/tests/utils/setOptions.m
@@ -1,6 +1,9 @@
 function opt = setOptions(varargin)
   %
-  % opt = setOptions(task, subLabel, 'useRaw', false, 'pipelineType', 'preproc');
+  % opt = setOptions(task, subLabel, ...
+  %                  'useRaw', false, ...
+  %                  'useTempDir', false, ...
+  %                  'pipelineType', 'preproc');
   %
 
   % (C) Copyright 2021 bidspm developers