diff --git a/.circleci/config.yml b/.circleci/config.yml
new file mode 100644
index 0000000..60adb12
--- /dev/null
+++ b/.circleci/config.yml
@@ -0,0 +1,390 @@
+version: 2.1
+orbs:
+  codecov: codecov/codecov@3.2.4
+
+.dockersetup: &dockersetup
+  docker:
+    - image: cimg/python:3.12
+  working_directory: /src/fmripost_aroma
+
+runinstall: &runinstall
+    name: Install fMRIPost-AROMA
+    command: |
+      VERSION=0+build
+      if [[ -n "$CIRCLE_TAG" ]]; then
+        VERSION="$CIRCLE_TAG"
+      fi
+      git checkout $CIRCLE_BRANCH
+      echo "${VERSION}" > /src/fmripost_aroma/src/fmripost_aroma/VERSION
+      echo "include src/fmripost_aroma/VERSION" >> /src/fmripost_aroma/src/fmripost_aroma/MANIFEST.in
+      pip install .[tests] --progress-bar off
+
+      # Precaching fonts, set 'Agg' as default backend for matplotlib
+      python -c "from matplotlib import font_manager"
+      sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
+      # Write the config file
+      mkdir /root/.nipype
+      CFG=/root/.nipype/nipype.cfg
+      printf "[execution]\nstop_on_first_crash = true\n" > ${CFG}
+      echo "poll_sleep_duration = 0.01" >> ${CFG}
+      echo "hash_method = content" >> ${CFG}
+
+jobs:
+
+  build:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - run: *runinstall
+
+  download_ds005115_raw:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: ds005115_raw-01
+      - run: *runinstall
+      - run:
+          name: Download ds005115_raw test data
+          command: |
+            cd /src/fmripost_aroma/.circleci
+            python get_data.py $PWD/data ds005115_raw
+      - save_cache:
+          key: ds005115_raw-01
+          paths:
+            - /src/fmripost_aroma/.circleci/data/ds005115_raw
+
+  download_ds005115_resampling:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: ds005115_resampling-01
+      - run: *runinstall
+      - run:
+          name: Download ds005115_resampling test data
+          command: |
+            cd /src/fmripost_aroma/.circleci
+            python get_data.py $PWD/data ds005115_resampling
+      - save_cache:
+          key: ds005115_resampling-01
+          paths:
+            - /src/fmripost_aroma/.circleci/data/ds005115_resampling
+
+  download_ds005115_deriv_no_mni6:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: ds005115_deriv_no_mni6-01
+      - run: *runinstall
+      - run:
+          name: Download ds005115_deriv_no_mni6 test data
+          command: |
+            cd /src/fmripost_aroma/.circleci
+            python get_data.py $PWD/data ds005115_deriv_no_mni6
+      - save_cache:
+          key: ds005115_deriv_no_mni6-01
+          paths:
+            - /src/fmripost_aroma/.circleci/data/ds005115_deriv_no_mni6
+
+  download_ds005115_deriv_mni6:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: ds005115_deriv_mni6-01
+      - run: *runinstall
+      - run:
+          name: Download ds005115_deriv_mni6 test data
+          command: |
+            cd /src/fmripost_aroma/.circleci
+            python get_data.py $PWD/data ds005115_deriv_mni6
+      - save_cache:
+          key: ds005115_deriv_mni6-01
+          paths:
+            - /src/fmripost_aroma/.circleci/data/ds005115_deriv_mni6
+
+  ds005115_deriv_only:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: multishell_output-01
+      - run: *runinstall
+      - run:
+          name: Test the PYAFQ standalone recon workflow
+          no_output_timeout: 1h
+          command: |
+            pytest -rP -o log_cli=true -m "pyafq_recon_full" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            mkdir /src/coverage
+            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.pyafq_recon_full
+            # remove nifti files before uploading artifacts
+            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.pyafq_recon_full
+      - store_artifacts:
+          path: /src/fmripost_aroma/.circleci/out/pyafq_recon_full/
+
+  ds005115_deriv_and_raw:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: multishell_output-01
+      - run: *runinstall
+      - run:
+          name: Test the PYAFQ workflow with mrtrix tractography
+          no_output_timeout: 1h
+          command: |
+            pytest -rP -o log_cli=true -m "pyafq_recon_external_trk" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            mkdir /src/coverage
+            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.pyafq_recon_external_trk
+            # remove nifti files before uploading artifacts
+            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.pyafq_recon_external_trk
+      - store_artifacts:
+          path: /src/fmripost_aroma/.circleci/out/pyafq_recon_external_trk/
+
+  ds005115_resampling_and_raw:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: multishell_output-01
+      - run: *runinstall
+      - run:
+          name: Test scalar_mapping workflow
+          no_output_timeout: 1h
+          command: |
+            pytest -rP -o log_cli=true -m "scalar_mapper" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            mkdir /src/coverage
+            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.scalar_mapper
+            # remove nifti files before uploading artifacts
+            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.scalar_mapper
+      - store_artifacts:
+          path: /src/fmripost_aroma/.circleci/out/scalar_mapper/
+
+  pytests:
+    <<: *dockersetup
+    resource_class: medium+
+    environment:
+      CIRCLE_CPUS: 3
+    steps:
+      - checkout
+      - restore_cache:
+          key: singleshell_output-01
+      - run: *runinstall
+      - run:
+          name: Test the DIPY recon workflows
+          command: |
+            pytest -rP -o log_cli=true -m "amico_noddi" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            mkdir /src/coverage
+            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.amico_noddi
+            # remove nifti files before uploading artifacts
+            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.amico_noddi
+      - store_artifacts:
+          path: /src/fmripost_aroma/.circleci/out/amico_noddi/
+
+  merge_coverage:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - attach_workspace:
+          at: /src/coverage
+      - run: *runinstall
+      - run:
+          name: Merge coverage files
+          command: |
+            cd /src/coverage/
+            coverage combine
+            coverage xml
+      - store_artifacts:
+          path: /src/coverage
+      - codecov/upload:
+          file: /src/coverage/coverage.xml
+
+  deployable:
+    resource_class: small
+    docker:
+      - image: busybox:latest
+    steps:
+      - run: echo Deploying!
+
+  build_and_deploy:
+    environment:
+      TZ: "/usr/share/zoneinfo/America/New_York"
+    docker:
+      - image: cimg/base:2020.09
+    working_directory: /tmp/src/fmripost_aroma
+    steps:
+      - checkout
+      - setup_remote_docker:
+         version: docker24
+         docker_layer_caching: true
+      - run:
+          name: Build Docker image
+          no_output_timeout: 3h
+          command: |
+            sudo apt-get update
+            sudo apt-get install -y python3-pip
+            pip install hatch
+            # Get version, update files.
+            THISVERSION=$(hatch version)
+            if [[ ${THISVERSION:0:1} == "0" ]] ; then
+              echo "WARNING: latest git tag could not be found"
+              echo "Please, make sure you fetch all tags from upstream with"
+              echo "the command ``git fetch --tags --verbose`` and push"
+              echo "them to your fork with ``git push origin --tags``"
+            fi
+            sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
+            sed -i "s/title = {fmripost_aroma}/title = {fmripost_aroma ${CIRCLE_TAG:-$THISVERSION}}/" fmripost_aroma/src/fmripost_aroma/data/boilerplate.bib
+            # Build docker image
+            e=1 && for i in {1..5}; do
+              docker build \
+                --cache-from=nipreps/fmripost_aroma \
+                --rm=false \
+                -t nipreps/fmripost_aroma:latest \
+                --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+                --build-arg VCS_REF=`git rev-parse --short HEAD` \
+                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
+              && e=0 && break || sleep 15
+            done && [ "$e" -eq "0" ]
+      - run:
+          name: Deploy to Docker Hub
+          no_output_timeout: 40m
+          command: |
+            if [[ -n "$DOCKER_PASS" ]]; then
+              docker login -u $DOCKER_USER -p $DOCKER_PASS
+              docker tag nipreps/fmripost_aroma nipreps/fmripost_aroma:unstable
+              docker push nipreps/fmripost_aroma:unstable
+              if [[ -n "$CIRCLE_TAG" ]]; then
+                docker push nipreps/fmripost_aroma:latest
+                docker tag nipreps/fmripost_aroma nipreps/fmripost_aroma:$CIRCLE_TAG
+                docker push nipreps/fmripost_aroma:$CIRCLE_TAG
+              fi
+            fi
+
+workflows:
+  version: 2
+  build_test_deploy:
+    jobs:
+
+      - build:
+          filters:
+            tags:
+              only: /.*/
+
+      - download_ds005115_raw:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+
+      - download_ds005115_resampling:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+
+      - download_ds005115_deriv_no_mni6:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+
+      - download_ds005115_deriv_mni6:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+
+      - ds005115_resampling_and_raw:
+          requires:
+            - download_ds005115_raw
+            - download_ds005115_resampling
+          filters:
+            tags:
+              only: /.*/
+
+      - ds005115_deriv_and_raw:
+          requires:
+            - download_ds005115_raw
+            - download_ds005115_deriv_no_mni6
+          filters:
+            tags:
+              only: /.*/
+
+      - ds005115_deriv_only:
+          requires:
+            - download_ds005115_deriv_mni6
+          filters:
+            tags:
+              only: /.*/
+
+      - pytests:
+          requires:
+            - download_ds005115_raw
+            - download_ds005115_resampling
+            - download_ds005115_deriv_no_mni6
+            - download_ds005115_deriv_mni6
+          filters:
+            tags:
+              only: /.*/
+
+      - merge_coverage:
+          requires:
+            - ds005115_deriv_only
+            - ds005115_deriv_and_raw
+            - ds005115_resampling_and_raw
+            - pytests
+          filters:
+            branches:
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
+            tags:
+              only: /.*/
+
+      - deployable:
+          requires:
+            - ds005115_deriv_only
+            - ds005115_deriv_and_raw
+            - ds005115_resampling_and_raw
+            - pytests
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+
+      - build_and_deploy:
+          requires:
+            - deployable
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
diff --git a/.circleci/get_data.py b/.circleci/get_data.py
new file mode 100755
index 0000000..390309d
--- /dev/null
+++ b/.circleci/get_data.py
@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+"""Download test data."""
+import sys
+
+from fmripost_aroma.tests.utils import download_test_data
+
+if __name__ == '__main__':
+    data_dir = sys.argv[1]
+    dset = sys.argv[2]
+    download_test_data(dset, data_dir)
diff --git a/docs/installation.rst b/docs/installation.rst
index fe34306..30556fd 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -3,24 +3,18 @@
 ------------
 Installation
 ------------
-There are two ways to install *fMRIPost-AROMA*:
-
-* using container technologies (RECOMMENDED); or
-* within a `Manually Prepared Environment (Python 3.10+)`_, also known as
-  *bare-metal installation*.
+*fMRIPost-AROMA* should be installed using container technologies.
 
 The ``fmripost-aroma`` command-line adheres to the `BIDS-Apps recommendations
 for the user interface <usage.html#execution-and-the-bids-format>`__.
 Therefore, the command-line has the following structure::
 
-  $ fmripost-aroma <input_bids_path> <derivatives_path> <analysis_level> <named_options>
+  $ fmripost-aroma <input_bids_path> -d <derivatives_path> <analysis_level> <named_options>
 
 The ``fmripost-aroma`` command-line options are documented in the :ref:`usage`
 section.
 
-The command as shown works for a *bare-metal* environment set-up (second option above).
-If you choose the recommended container-based installation, then
-the command-line will be composed of a preamble to configure the
+The command-line will be composed of a preamble to configure the
 container execution followed by the ``fmripost-aroma`` command-line options
 as if you were running it on a *bare-metal* installation.
 The command-line structure above is then modified as follows::
@@ -40,39 +34,13 @@ For detailed information of containerized execution of *NiPreps*, please visit t
 `Docker <https://www.nipreps.org/apps/docker/>`__
 or `Singularity <https://www.nipreps.org/apps/singularity/>`__ subsections.
 
-
-Manually Prepared Environment (Python 3.10+)
-============================================
-
-.. warning::
-
-   This method is not recommended! Please consider using containers.
-
-Make sure all of *fMRIPost-AROMA*'s `External Dependencies`_ are installed.
-These tools must be installed and their binaries available in the
-system's ``$PATH``.
-A relatively interpretable description of how your environment can be set-up
-is found in the `Dockerfile <https://github.com/nipreps/fmripost-aroma/blob/master/Dockerfile>`_.
-As an additional installation setting, FreeSurfer requires a license file (see :ref:`fs_license`).
-
-On a functional Python 3.10 (or above) environment with ``pip`` installed,
-*fMRIPost-AROMA* can be installed using the habitual command ::
-
-    $ python -m pip install fmripost-aroma
-
-Check your installation with the ``--version`` argument ::
-
-    $ fmripost-aroma --version
-
-
 External Dependencies
 ---------------------
 *fMRIPost-AROMA* is written using Python 3.8 (or above), and is based on
 nipype_.
 
 *fMRIPost-AROMA* requires some other neuroimaging software tools that are
-not handled by the Python's packaging system (Pypi) used to deploy
-the ``fmripost-aroma`` package:
+not handled by the Python's packaging system (Pypi):
 
 - FSL_ (version 6.0.7.7)
 - ANTs_ (version 2.5.1)
diff --git a/docs/outputs.rst b/docs/outputs.rst
index 3dfbef0..ff8b16c 100644
--- a/docs/outputs.rst
+++ b/docs/outputs.rst
@@ -75,10 +75,10 @@ ICA outputs are stored in the ``func/`` subfolder::
 
   sub-<label>/
     func/
-      sub-<label>_space-<label>_desc-melodic_mixing.tsv
-      sub-<label>_space-<label>_desc-melodic_mixing.json
-      sub-<label>_space-<label>_desc-melodic_components.nii.gz
-      sub-<label>_space-<label>_desc-melodic_components.json
+      sub-<label>_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
+      sub-<label>_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.json
+      sub-<label>_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
+      sub-<label>_space-MNI152NLin6Asym_res-2_desc-melodic_components.json
 
 
 Functional derivatives
@@ -90,10 +90,9 @@ these will be indicated with ``[specifiers]``::
 
   sub-<label>/
     func/
-      sub-<label>_[specifiers]_space-<label>_desc-brain_mask.nii.gz
-      sub-<label>_[specifiers]_space-<label>_desc-aggrDenoised_bold.nii.gz
-      sub-<label>_[specifiers]_space-<label>_desc-nonaggrDenoised_bold.nii.gz
-      sub-<label>_[specifiers]_space-<label>_desc-orthaggrDenoised_bold.nii.gz
+      sub-<label>_[specifiers]_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
+      sub-<label>_[specifiers]_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
+      sub-<label>_[specifiers]_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
 
 **Regularly gridded outputs (images)**.
 Volumetric output spaces labels (``<label>`` above, and in the following) include
@@ -108,18 +107,18 @@ Confounds_ are saved as a :abbr:`TSV (tab-separated value)` file::
     func/
       sub-<label>_[specifiers]_desc-aroma_metrics.tsv
       sub-<label>_[specifiers]_desc-aroma_metrics.json
-      sub-<label>_[specifiers]_desc-confounds_timeseries.tsv
-      sub-<label>_[specifiers]_desc-confounds_timeseries.json
+      sub-<label>_[specifiers]_desc-melodic_timeseries.tsv
+      sub-<label>_[specifiers]_desc-melodic_timeseries.json
 
 Confounds
 ---------
 
 *fMRIPost-AROMA* outputs a set of confounds that can be used to denoise the data.
-These are stored in a TSV file (``desc-confounds_timeseries.tsv``) and a JSON file
-(``desc-confounds_timeseries.json``) that contains metadata about the confounds.
+These are stored in a TSV file (``desc-melodic_timeseries.tsv``) and a JSON file
+(``desc-melodic_timeseries.json``) that contains metadata about the confounds.
 
-The confounds generated by *fMRIPost-AROMA* are ICA component time series,
-which may be labeled as "accepted" or "rejected" based on the ICA-AROMA classification.
+The confounds generated by *fMRIPost-AROMA* are ICA component time series
+classified as "rejected" by ICA-AROMA.
 
 Confounds and "carpet"-plot on the visual reports
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/docs/spaces.rst b/docs/spaces.rst
index cb87146..b4f122c 100644
--- a/docs/spaces.rst
+++ b/docs/spaces.rst
@@ -2,6 +2,10 @@
 
 .. _output-spaces:
 
+.. warning::
+   Output spaces are not currently supported.
+   fMRIPost-AROMA currently only generates denoised data in MNI152NLin6Asym space.
+
 Defining standard and nonstandard spaces where data will be resampled
 =====================================================================
 The command line interface of *fMRIPost-AROMA* allows resampling the preprocessed data
diff --git a/docs/usage.rst b/docs/usage.rst
index 43b6804..e5d30d3 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -4,6 +4,12 @@
 
 Usage Notes
 ===========
+
+.. warning::
+   *fMRIPost-AROMA* requires preprocessing outputs in MNI152NLin6Asym space with
+   2 mm3 voxels (i.e., ``res-02``).
+   Make sure you run fMRIPrep with ``--output-spaces MNI152NLin6Asym:res-02``.
+
 .. warning::
    *fMRIPost-AROMA* includes a tracking system to report usage statistics and errors
    for debugging and grant reporting purposes.
diff --git a/pyproject.toml b/pyproject.toml
index 5c147e4..8bec10f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -182,3 +182,15 @@ inline-quotes = "single"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.pytest.ini_options]
+addopts = '-m "not integration"'
+markers = [
+    "integration: mark test as an integration test",
+    "ds005115_deriv_only: ds005115 with full fMRIPrep and derivatives only",
+    "ds005115_deriv_and_raw: ds005115 with full fMRIPrep and raw BIDS",
+    "ds005115_resampling_and_raw: ds005115 with resampling-level fMRIPrep and raw BIDS",
+]
+env = [
+    "RUNNING_PYTEST = 1",
+]
diff --git a/src/fmripost_aroma/cli/parser.py b/src/fmripost_aroma/cli/parser.py
index 65a32b3..b04130c 100644
--- a/src/fmripost_aroma/cli/parser.py
+++ b/src/fmripost_aroma/cli/parser.py
@@ -543,9 +543,6 @@ def parse_args(args=None, namespace=None):
     work_dir = config.execution.work_dir
     version = config.environment.version
 
-    if config.execution.fmripost_aroma_dir is None:
-        config.execution.fmripost_aroma_dir = output_dir
-
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory
@@ -585,7 +582,7 @@ def parse_args(args=None, namespace=None):
         validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
     # Setup directories
-    config.execution.log_dir = config.execution.fmripost_aroma_dir / 'logs'
+    config.execution.log_dir = config.execution.output_dir / 'logs'
     # Check and create output and working directories
     config.execution.log_dir.mkdir(exist_ok=True, parents=True)
     work_dir.mkdir(exist_ok=True, parents=True)
diff --git a/src/fmripost_aroma/cli/run.py b/src/fmripost_aroma/cli/run.py
index eabb18a..cab8652 100644
--- a/src/fmripost_aroma/cli/run.py
+++ b/src/fmripost_aroma/cli/run.py
@@ -152,7 +152,7 @@ def main():
             from fmripost_aroma.utils.telemetry import process_crashfile
 
             crashfolders = [
-                config.execution.fmripost_aroma_dir
+                config.execution.output_dir
                 / f'sub-{s}'
                 / 'log'
                 / config.execution.run_uuid
@@ -176,7 +176,7 @@ def main():
             sentry_sdk.capture_message(success_message, level='info')
 
         # Bother users with the boilerplate only iff the workflow went okay.
-        boiler_file = config.execution.fmripost_aroma_dir / 'logs' / 'CITATION.md'
+        boiler_file = config.execution.output_dir / 'logs' / 'CITATION.md'
         if boiler_file.exists():
             if config.environment.exec_env in (
                 'singularity',
@@ -198,9 +198,9 @@ def main():
             from templateflow import api
 
             dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
-            _copy_any(dseg_tsv, str(config.execution.fmripost_aroma_dir / 'desc-aseg_dseg.tsv'))
+            _copy_any(dseg_tsv, str(config.execution.output_dir / 'desc-aseg_dseg.tsv'))
             _copy_any(
-                dseg_tsv, str(config.execution.fmripost_aroma_dir / 'desc-aparcaseg_dseg.tsv')
+                dseg_tsv, str(config.execution.output_dir / 'desc-aparcaseg_dseg.tsv')
             )
         errno = 0
     finally:
@@ -216,13 +216,13 @@ def main():
         # Generate reports phase
         failed_reports = generate_reports(
             subject_list=config.execution.participant_label,
-            output_dir=config.execution.fmripost_aroma_dir,
+            output_dir=config.execution.output_dir,
             run_uuid=config.execution.run_uuid,
         )
         write_derivative_description(
-            config.execution.bids_dir, config.execution.fmripost_aroma_dir
+            config.execution.bids_dir, config.execution.output_dir
         )
-        write_bidsignore(config.execution.fmripost_aroma_dir)
+        write_bidsignore(config.execution.output_dir)
 
         if sentry_sdk is not None and failed_reports:
             sentry_sdk.capture_message(
diff --git a/src/fmripost_aroma/cli/workflow.py b/src/fmripost_aroma/cli/workflow.py
index 9e153f2..61a5a71 100644
--- a/src/fmripost_aroma/cli/workflow.py
+++ b/src/fmripost_aroma/cli/workflow.py
@@ -48,7 +48,7 @@ def build_workflow(config_file, retval):
     config.load(config_file)
     build_log = config.loggers.workflow
 
-    fmripost_aroma_dir = config.execution.fmripost_aroma_dir
+    output_dir = config.execution.output_dir
     version = config.environment.version
 
     retval['return_code'] = 1
@@ -68,7 +68,7 @@ def build_workflow(config_file, retval):
     msg = check_pipeline_version(
         'fMRIPost-AROMA',
         version,
-        fmripost_aroma_dir / 'dataset_description.json',
+        output_dir / 'dataset_description.json',
     )
     if msg is not None:
         build_log.warning(msg)
@@ -92,7 +92,7 @@ def build_workflow(config_file, retval):
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         retval['return_code'] = generate_reports(
             subject_list=config.execution.participant_label,
-            output_dir=config.execution.fmripost_aroma_dir,
+            output_dir=config.execution.output_dir,
             run_uuid=config.execution.run_uuid,
         )
         return retval
@@ -137,7 +137,7 @@ def build_boilerplate(config_file, workflow):
     from fmripost_aroma import config
 
     config.load(config_file)
-    logs_path = config.execution.fmripost_aroma_dir / 'logs'
+    logs_path = config.execution.output_dir / 'logs'
     boilerplate = workflow.visit_desc()
     citation_files = {ext: logs_path / f'CITATION.{ext}' for ext in ('bib', 'tex', 'md', 'html')}
 
diff --git a/src/fmripost_aroma/config.py b/src/fmripost_aroma/config.py
index 0aa49f1..d3764df 100644
--- a/src/fmripost_aroma/config.py
+++ b/src/fmripost_aroma/config.py
@@ -403,8 +403,6 @@ class execution(_Config):
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
     debug = []
     """Debug mode(s)."""
-    fmripost_aroma_dir = None
-    """Root of fMRIPost-AROMA BIDS Derivatives dataset. Depends on output_layout."""
     fs_license_file = _fs_license
     """An existing file containing a FreeSurfer license."""
     layout = None
@@ -451,7 +449,6 @@ class execution(_Config):
         'bids_dir',
         'derivatives',
         'bids_database_dir',
-        'fmripost_aroma_dir',
         'fs_license_file',
         'layout',
         'log_dir',
diff --git a/src/fmripost_aroma/data/tests/config.toml b/src/fmripost_aroma/data/tests/config.toml
index 6f92048..13b6060 100644
--- a/src/fmripost_aroma/data/tests/config.toml
+++ b/src/fmripost_aroma/data/tests/config.toml
@@ -18,7 +18,6 @@ log_level = 40
 low_mem = false
 md_only_boilerplate = false
 notrack = true
-fmripost_aroma_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/out"
 output_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/out"
 output_spaces = "MNI152NLin6Asym:res-2"
 reports_only = false
diff --git a/src/fmripost_aroma/interfaces/resampler.py b/src/fmripost_aroma/interfaces/resampler.py
index cf56900..80ea7bc 100644
--- a/src/fmripost_aroma/interfaces/resampler.py
+++ b/src/fmripost_aroma/interfaces/resampler.py
@@ -36,12 +36,7 @@ class _ResamplerOutputSpec(TraitedSpec):
 
 
 class Resampler(SimpleInterface):
-    """Extract timeseries and compute connectivity matrices.
-
-    Write out time series using Nilearn's NiftiLabelMasker
-    Then write out functional correlation matrix of
-    timeseries using numpy.
-    """
+    """Apply the resampler workflow."""
 
     input_spec = _ResamplerInputSpec
     output_spec = _ResamplerOutputSpec
diff --git a/src/fmripost_aroma/tests/data/test_ds005115_deriv_and_raw_outputs.txt b/src/fmripost_aroma/tests/data/test_ds005115_deriv_and_raw_outputs.txt
new file mode 100644
index 0000000..9a51152
--- /dev/null
+++ b/src/fmripost_aroma/tests/data/test_ds005115_deriv_and_raw_outputs.txt
@@ -0,0 +1,13 @@
+dataset_description.json
+sub-01
+sub-01/ses-01
+sub-01/ses-01/func
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-melodic_timeseries.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01.html
diff --git a/src/fmripost_aroma/tests/data/test_ds005115_deriv_only_outputs.txt b/src/fmripost_aroma/tests/data/test_ds005115_deriv_only_outputs.txt
new file mode 100644
index 0000000..9a51152
--- /dev/null
+++ b/src/fmripost_aroma/tests/data/test_ds005115_deriv_only_outputs.txt
@@ -0,0 +1,13 @@
+dataset_description.json
+sub-01
+sub-01/ses-01
+sub-01/ses-01/func
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-melodic_timeseries.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01.html
diff --git a/src/fmripost_aroma/tests/data/test_ds005115_resampling_and_raw_outputs.txt b/src/fmripost_aroma/tests/data/test_ds005115_resampling_and_raw_outputs.txt
new file mode 100644
index 0000000..9a51152
--- /dev/null
+++ b/src/fmripost_aroma/tests/data/test_ds005115_resampling_and_raw_outputs.txt
@@ -0,0 +1,13 @@
+dataset_description.json
+sub-01
+sub-01/ses-01
+sub-01/ses-01/func
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-melodic_timeseries.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01.html
diff --git a/src/fmripost_aroma/tests/run_local_tests.py b/src/fmripost_aroma/tests/run_local_tests.py
old mode 100644
new mode 100755
index 648ec01..7271ec3
--- a/src/fmripost_aroma/tests/run_local_tests.py
+++ b/src/fmripost_aroma/tests/run_local_tests.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 """Run tests locally by calling Docker."""
 
 import argparse
@@ -12,7 +13,9 @@ def _get_parser():
     -------
     parser.parse_args() : argparse dict
     """
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
     parser.add_argument(
         '-k',
         dest='test_regex',
diff --git a/src/fmripost_aroma/tests/test_base.py b/src/fmripost_aroma/tests/test_base.py
index 4f1b7bd..2868cbd 100644
--- a/src/fmripost_aroma/tests/test_base.py
+++ b/src/fmripost_aroma/tests/test_base.py
@@ -10,7 +10,7 @@ def test_init_ica_aroma_wf(tmp_path_factory):
     tempdir = tmp_path_factory.mktemp('test_init_ica_aroma_wf')
 
     with mock_config():
-        config.execution.fmripost_aroma_dir = tempdir / 'out'
+        config.execution.output_dir = tempdir / 'out'
         config.execution.work_dir = tempdir / 'work'
         config.workflow.denoise_method = ['nonaggr', 'orthaggr']
         config.workflow.melodic_dim = -200
@@ -29,7 +29,7 @@ def test_init_denoise_wf(tmp_path_factory):
     tempdir = tmp_path_factory.mktemp('test_init_denoise_wf')
 
     with mock_config():
-        config.execution.fmripost_aroma_dir = tempdir / 'out'
+        config.execution.output_dir = tempdir / 'out'
         config.execution.work_dir = tempdir / 'work'
 
         wf = init_denoise_wf(bold_file='sub-01_task-rest_bold.nii.gz')
diff --git a/src/fmripost_aroma/tests/test_cli.py b/src/fmripost_aroma/tests/test_cli.py
new file mode 100644
index 0000000..8b812fc
--- /dev/null
+++ b/src/fmripost_aroma/tests/test_cli.py
@@ -0,0 +1,147 @@
+"""Command-line interface tests."""
+
+import os
+import sys
+from unittest.mock import patch
+
+import pytest
+from fmripost_aroma.cli import run
+from fmripost_aroma.cli.parser import parse_args
+from fmripost_aroma.cli.workflow import build_boilerplate, build_workflow
+from fmripost_aroma.reports.core import generate_reports
+from fmripost_aroma.tests.utils import (
+    check_generated_files,
+    download_test_data,
+    get_test_data_path,
+)
+from fmripost_aroma.utils.bids import write_derivative_description
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_deriv_only()
+def test_ds005115_deriv_only(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 fMRIPrep derivatives with MNI152NLin6Asym-space data."""
+    test_name = 'test_ds005115_deriv_only'
+
+    fmriprep_dir = download_test_data('ds005115_deriv_mni6', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        fmriprep_dir,
+        out_dir,
+        'participant',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_deriv_and_raw()
+def test_ds005115_deriv_and_raw(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 raw BIDS + fMRIPrep derivatives w/o MNI152NLin6Asym data."""
+    test_name = 'test_ds005115_deriv_and_raw'
+
+    raw_dir = download_test_data('ds005115_raw', data_dir)
+    fmriprep_dir = download_test_data('ds005115_deriv_no_mni6', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        raw_dir,
+        out_dir,
+        'participant',
+        '--derivatives',
+        f'fmriprep={fmriprep_dir}',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_resampling_and_raw()
+def test_ds005115_resampling_and_raw(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 raw BIDS + resampling-level fMRIPrep derivatives."""
+    test_name = 'test_ds005115_resampling_and_raw'
+
+    raw_dir = download_test_data('ds005115_raw', data_dir)
+    fmriprep_dir = download_test_data('ds005115_resampling', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        raw_dir,
+        out_dir,
+        'participant',
+        '--derivatives',
+        f'fmriprep={fmriprep_dir}',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+def _run_and_generate(test_name, parameters, test_main=True):
+    from fmripost_aroma import config
+
+    parameters.append('--clean-workdir')
+    parameters.append('--stop-on-first-crash')
+    parameters.append('--notrack')
+    parameters.append('-v')
+
+    if test_main:
+        # This runs, but for some reason doesn't count toward coverage.
+        argv = ['fmripost_aroma'] + parameters
+        with patch.object(sys, 'argv', argv):
+            with pytest.raises(SystemExit) as e:
+                run.main()
+
+            assert e.value.code == 0
+    else:
+        # XXX: I want to drop this option and use the main function,
+        # but the main function doesn't track coverage correctly.
+        parse_args(parameters)
+        config_file = config.execution.work_dir / f'config-{config.execution.run_uuid}.toml'
+        config.loggers.cli.warning(f'Saving config file to {config_file}')
+        config.to_filename(config_file)
+
+        retval = build_workflow(config_file, retval={})
+        xcpd_wf = retval['workflow']
+        xcpd_wf.run()
+        write_derivative_description(config.execution.bids_dir, config.execution.output_dir)
+
+        build_boilerplate(str(config_file), xcpd_wf)
+        session_list = (
+            config.execution.bids_filters.get('bold', {}).get('session')
+            if config.execution.bids_filters
+            else None
+        )
+        generate_reports(
+            subject_list=config.execution.participant_label,
+            output_dir=config.execution.output_dir,
+            run_uuid=config.execution.run_uuid,
+            session_list=session_list,
+        )
+
+    output_list_file = os.path.join(get_test_data_path(), f'{test_name}_outputs.txt')
+    check_generated_files(config.execution.output_dir, output_list_file)
diff --git a/src/fmripost_aroma/tests/tests.py b/src/fmripost_aroma/tests/tests.py
index 3b1a913..01596aa 100644
--- a/src/fmripost_aroma/tests/tests.py
+++ b/src/fmripost_aroma/tests/tests.py
@@ -62,7 +62,7 @@ def mock_config():
     yield
 
     shutil.rmtree(config.execution.work_dir)
-    shutil.rmtree(config.execution.fmripost_aroma_dir)
+    shutil.rmtree(config.execution.output_dir)
 
     if not _old_fs:
         del os.environ['FREESURFER_HOME']
diff --git a/src/fmripost_aroma/tests/utils.py b/src/fmripost_aroma/tests/utils.py
index 00daf06..8ddf37d 100644
--- a/src/fmripost_aroma/tests/utils.py
+++ b/src/fmripost_aroma/tests/utils.py
@@ -1,12 +1,206 @@
 """Utility functions for tests."""
 
+import os
+import subprocess
+import tarfile
+from contextlib import contextmanager
+from glob import glob
+from gzip import GzipFile
+from io import BytesIO
 from pathlib import Path
 
+import requests
+from nipype import logging
+
+LOGGER = logging.getLogger('nipype.utils')
+
+
+def get_nodes(wf_results):
+    """Load nodes from a Nipype workflow's results."""
+    return {node.fullname: node for node in wf_results.nodes}
+
+
+def download_test_data(dset, data_dir=None):
+    """Download test data."""
+    URLS = {
+        'ds005115_raw': 'https://upenn.box.com/shared/static',
+        'ds005115_resampling': 'https://upenn.box.com/shared/static',
+        'ds005115_deriv_no_mni6': 'https://upenn.box.com/shared/static',
+        'ds005115_deriv_mni6': 'https://upenn.box.com/shared/static',
+    }
+    if dset == '*':
+        for k in URLS:
+            download_test_data(k, data_dir=data_dir)
+
+        return
+
+    if dset not in URLS:
+        raise ValueError(f'dset ({dset}) must be one of: {", ".join(URLS.keys())}')
+
+    if not data_dir:
+        data_dir = os.path.join(os.path.dirname(get_test_data_path()), 'test_data')
+
+    dset_name = dset
+    if dset == 'ds001419':
+        dset_name = 'ds001419-fmriprep'
+
+    out_dir = os.path.join(data_dir, dset_name)
+
+    if os.path.isdir(out_dir):
+        LOGGER.info(
+            f'Dataset {dset} already exists. '
+            'If you need to re-download the data, please delete the folder.'
+        )
+        return out_dir
+    else:
+        LOGGER.info(f'Downloading {dset} to {out_dir}')
+
+    os.makedirs(out_dir, exist_ok=True)
+    with requests.get(URLS[dset], stream=True) as req:
+        with tarfile.open(fileobj=GzipFile(fileobj=BytesIO(req.content))) as t:
+            t.extractall(out_dir)
+
+    return out_dir
+
+
+def check_generated_files(output_dir, output_list_file):
+    """Compare files generated by xcp_d with a list of expected files."""
+    found_files = sorted(glob(os.path.join(output_dir, '**/*'), recursive=True))
+    found_files = [os.path.relpath(f, output_dir) for f in found_files]
+
+    # Ignore figures
+    found_files = [f for f in found_files if 'figures' not in f]
+
+    # Ignore logs
+    found_files = [f for f in found_files if 'log' not in f.split(os.path.sep)]
+
+    with open(output_list_file) as fileobj:
+        expected_files = fileobj.readlines()
+        expected_files = [f.rstrip() for f in expected_files]
+
+    if sorted(found_files) != sorted(expected_files):
+        expected_not_found = sorted(set(expected_files) - set(found_files))
+        found_not_expected = sorted(set(found_files) - set(expected_files))
+
+        msg = ''
+        if expected_not_found:
+            msg += '\nExpected but not found:\n\t'
+            msg += '\n\t'.join(expected_not_found)
+
+        if found_not_expected:
+            msg += '\nFound but not expected:\n\t'
+            msg += '\n\t'.join(found_not_expected)
+        raise ValueError(msg)
+
+
+def run_command(command, env=None):
+    """Run a given shell command with certain environment variables set."""
+    merged_env = os.environ
+    if env:
+        merged_env.update(env)
+
+    process = subprocess.Popen(
+        command,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        shell=True,
+        env=merged_env,
+    )
+    while True:
+        line = process.stdout.readline()
+        line = str(line, 'utf-8')[:-1]
+        print(line)
+        if line == '' and process.poll() is not None:
+            break
+
+    if process.returncode != 0:
+        raise Exception(
+            f'Non zero return code: {process.returncode}\n' f'{command}\n\n{process.stdout.read()}'
+        )
+
+
+@contextmanager
+def chdir(path):
+    """Temporarily change directories.
+
+    Taken from https://stackoverflow.com/a/37996581/2589328.
+    """
+    oldpwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(oldpwd)
+
+
+def reorder_expected_outputs():
+    """Load each of the expected output files and sort the lines alphabetically.
+
+    This function is called manually by devs when they modify the test outputs.
+    """
+    test_data_path = get_test_data_path()
+    expected_output_files = sorted(glob(os.path.join(test_data_path, 'test_*_outputs.txt')))
+    for expected_output_file in expected_output_files:
+        LOGGER.info(f'Sorting {expected_output_file}')
+
+        with open(expected_output_file) as fileobj:
+            file_contents = fileobj.readlines()
+
+        file_contents = sorted(set(file_contents))
+
+        with open(expected_output_file, 'w') as fileobj:
+            fileobj.writelines(file_contents)
+
+
+def list_files(startpath):
+    """List files in a directory."""
+    tree = ''
+    for root, _, files in os.walk(startpath):
+        level = root.replace(startpath, '').count(os.sep)
+        indent = ' ' * 4 * (level)
+        tree += f'{indent}{os.path.basename(root)}/\n'
+        subindent = ' ' * 4 * (level + 1)
+        for f in files:
+            tree += f'{subindent}{f}\n'
+
+    return tree
+
+
+@contextmanager
+def modified_environ(*remove, **update):
+    """
+    Temporarily updates the ``os.environ`` dictionary in-place.
+
+    The ``os.environ`` dictionary is updated in-place so that the modification
+    is sure to work in all situations.
+
+    :param remove: Environment variables to remove.
+    :param update: Dictionary of environment variables and values to add/update.
+    """
+    env = os.environ
+    update = update or {}
+    remove = remove or []
+
+    # List of environment variables being updated or removed.
+    stomped = (set(update.keys()) | set(remove)) & set(env.keys())
+    # Environment variables and values to restore on exit.
+    update_after = {k: env[k] for k in stomped}
+    # Environment variables and values to remove on exit.
+    remove_after = frozenset(k for k in update if k not in env)
+
+    try:
+        env.update(update)
+        [env.pop(k, None) for k in remove]
+        yield
+    finally:
+        env.update(update_after)
+        [env.pop(k) for k in remove_after]
+
 
 def get_test_data_path():
     """Return the path to test datasets, terminated with separator.
 
-    Test-related data are kept in tests folder in "data".
+    Test-related data are kept in tests folder in 'data'.
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
     """
     return Path(__file__).resolve().parent.parent.parent.parent / 'tests' / 'data'
diff --git a/src/fmripost_aroma/utils/bids.py b/src/fmripost_aroma/utils/bids.py
index 0e2e970..7f3ab13 100644
--- a/src/fmripost_aroma/utils/bids.py
+++ b/src/fmripost_aroma/utils/bids.py
@@ -111,9 +111,9 @@ def collect_derivatives(
     derivs_cache = defaultdict(list, {})
     if derivatives_dataset is not None:
         layout = derivatives_dataset
-        if isinstance(derivatives_dataset, Path):
-            derivatives_dataset = BIDSLayout(
-                derivatives_dataset,
+        if isinstance(layout, Path):
+            layout = BIDSLayout(
+                layout,
                 config=['bids', 'derivatives'],
                 validate=False,
             )
diff --git a/src/fmripost_aroma/workflows/aroma.py b/src/fmripost_aroma/workflows/aroma.py
index cf31149..3a903c8 100644
--- a/src/fmripost_aroma/workflows/aroma.py
+++ b/src/fmripost_aroma/workflows/aroma.py
@@ -260,7 +260,7 @@ def init_ica_aroma_wf(
 
     ds_report_ica_aroma = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='figures',
             desc='aroma',
@@ -291,7 +291,7 @@ def init_ica_aroma_wf(
 
     ds_components = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             compress=True,
             datatype='func',
@@ -312,7 +312,7 @@ def init_ica_aroma_wf(
 
     ds_mixing = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             res='2',
@@ -328,7 +328,7 @@ def init_ica_aroma_wf(
 
     ds_aroma_features = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             desc='aroma',
@@ -349,7 +349,7 @@ def init_ica_aroma_wf(
 
     ds_aroma_confounds = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             desc='melodic',
@@ -373,7 +373,7 @@ def init_ica_aroma_wf(
 
     ds_report_metrics = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='figures',
             desc='metrics',
@@ -456,7 +456,7 @@ def init_denoise_wf(bold_file):
 
         ds_denoised = pe.Node(
             DerivativesDataSink(
-                base_directory=config.execution.fmripost_aroma_dir,
+                base_directory=config.execution.output_dir,
                 source_file=bold_file,
                 compress=True,
                 datatype='func',
diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py
index a2af08c..ee2f202 100644
--- a/src/fmripost_aroma/workflows/base.py
+++ b/src/fmripost_aroma/workflows/base.py
@@ -72,7 +72,7 @@ def init_fmripost_aroma_wf():
         single_subject_wf = init_single_subject_wf(subject_id)
 
         single_subject_wf.config['execution']['crashdump_dir'] = str(
-            config.execution.fmripost_aroma_dir
+            config.execution.output_dir
             / f'sub-{subject_id}'
             / 'log'
             / config.execution.run_uuid
@@ -84,7 +84,7 @@ def init_fmripost_aroma_wf():
 
         # Dump a copy of the config file into the log directory
         log_dir = (
-            config.execution.fmripost_aroma_dir
+            config.execution.output_dir
             / f'sub-{subject_id}'
             / 'log'
             / config.execution.run_uuid
@@ -207,6 +207,15 @@ def init_single_subject_wf(subject_id: str):
         # Patch standard-space BOLD files into 'bold' key
         subject_data['bold'] = listify(subject_data['bold_mni152nlin6asym'])
 
+    if not subject_data['bold_mni152nlin6asym']:
+        task_id = config.execution.task_id
+        raise RuntimeError(
+            f"No MNI152NLin6Asym:res-2 BOLD images found for participant {subject_id} and "
+            f"task {task_id if task_id else '<all>'}. "
+            "All workflows require MNI152NLin6Asym:res-2 BOLD images. "
+            f"Please check your BIDS filters: {config.execution.bids_filters}."
+        )
+
     # Make sure we always go through these two checks
     if not subject_data['bold']:
         task_id = config.execution.task_id
@@ -246,7 +255,7 @@ def init_single_subject_wf(subject_id: str):
     ds_report_summary = pe.Node(
         DerivativesDataSink(
             source_file=subject_data['bold'][0],
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             desc='summary',
             datatype='figures',
         ),
@@ -258,7 +267,7 @@ def init_single_subject_wf(subject_id: str):
     ds_report_about = pe.Node(
         DerivativesDataSink(
             source_file=subject_data['bold'][0],
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             desc='about',
             datatype='figures',
         ),
@@ -288,9 +297,6 @@ def init_single_run_wf(bold_file):
     """Set up a single-run workflow for fMRIPost-AROMA."""
     from nipype.interfaces import utility as niu
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-    from niworkflows.interfaces.utility import KeySelect
-    from niworkflows.utils.spaces import Reference
-    from smriprep.workflows.outputs import init_template_iterator_wf
 
     from fmripost_aroma.utils.bids import collect_derivatives, extract_entities
     from fmripost_aroma.workflows.aroma import init_denoise_wf, init_ica_aroma_wf
@@ -345,6 +351,27 @@ def init_single_run_wf(bold_file):
             ),
         )
 
+    config.loggers.workflow.info(
+        (
+            f'Collected run data for {os.path.basename(bold_file)}:\n'
+            f'{yaml.dump(functional_cache, default_flow_style=False, indent=4)}'
+        ),
+    )
+
+    if config.workflow.dummy_scans is not None:
+        skip_vols = config.workflow.dummy_scans
+    else:
+        if not functional_cache['confounds']:
+            raise ValueError(
+                'No confounds detected. '
+                'Automatical dummy scan detection cannot be performed. '
+                'Please set the `--dummy-scans` flag explicitly.'
+            )
+        skip_vols = get_nss(functional_cache['confounds'])
+
+    ica_aroma_wf.inputs.inputnode.confounds = functional_cache['confounds']
+    ica_aroma_wf.inputs.inputnode.skip_vols = skip_vols
+
     mni6_buffer = pe.Node(
         niu.IdentityInterface(
             fields=['bold_mni152nlin6asym', 'bold_mask_mni152nlin6asym'],
@@ -353,10 +380,15 @@ def init_single_run_wf(bold_file):
     )
     if 'bold_mni152nlin6asym' not in functional_cache:
         # Resample to MNI152NLin6Asym:res-2, for ICA-AROMA classification
+        run_stc = (
+            bool(bold_metadata.get('SliceTiming')) and 'slicetiming' not in config.workflow.ignore
+        )
+
         resample_raw_wf = init_resample_volumetric_wf(
             bold_file=bold_file,
-            precomputed=functional_cache,
-            space=Reference.from_string('MNI152NLin6Asym:res-2')[0],
+            metadata=bold_metadata,
+            functional_cache=functional_cache,
+            run_stc=run_stc,
             name=_get_wf_name(bold_file, 'resample_raw'),
         )
         workflow.connect([
@@ -378,27 +410,6 @@ def init_single_run_wf(bold_file):
         ]),
     ])  # fmt:skip
 
-    config.loggers.workflow.info(
-        (
-            f'Collected run data for {os.path.basename(bold_file)}:\n'
-            f'{yaml.dump(functional_cache, default_flow_style=False, indent=4)}'
-        ),
-    )
-
-    if config.workflow.dummy_scans is not None:
-        skip_vols = config.workflow.dummy_scans
-    else:
-        if not functional_cache['confounds']:
-            raise ValueError(
-                'No confounds detected. '
-                'Automatical dummy scan detection cannot be performed. '
-                'Please set the `--dummy-scans` flag explicitly.'
-            )
-        skip_vols = get_nss(functional_cache['confounds'])
-
-    ica_aroma_wf.inputs.inputnode.confounds = functional_cache['confounds']
-    ica_aroma_wf.inputs.inputnode.skip_vols = skip_vols
-
     if config.workflow.denoise_method:
         # Now denoise the output-space BOLD data using ICA-AROMA
         denoise_wf = init_denoise_wf(bold_file=bold_file)
@@ -417,84 +428,6 @@ def init_single_run_wf(bold_file):
             ]),
         ])  # fmt:skip
 
-    # Skip this for now
-    if config.workflow.denoise_method and spaces.get_spaces() and False:
-        templates = spaces.get_spaces()
-        template_iterator_wf = init_template_iterator_wf(
-            spaces=spaces,
-            sloppy=config.execution.sloppy,
-        )
-        template_iterator_wf.inputs.inputnode.anat2std_xfm = functional_cache[
-            'anat2outputspaces_xfm'
-        ]
-        template_iterator_wf.inputs.inputnode.template = templates
-
-        # Now denoise the output-space BOLD data using ICA-AROMA
-        denoise_std_wf = init_denoise_wf(bold_file=bold_file)
-        denoise_std_wf.inputs.inputnode.skip_vols = skip_vols
-
-        workflow.connect([
-            (ica_aroma_wf, denoise_std_wf, [
-                ('outputnode.mixing', 'inputnode.mixing'),
-                ('outputnode.aroma_features', 'inputnode.classifications'),
-            ]),
-            (template_iterator_wf, denoise_std_wf, [
-                ('outputnode.space', 'inputnode.space'),
-                ('outputnode.cohort', 'inputnode.cohort'),
-                ('outputnode.res', 'inputnode.res'),
-            ]),
-        ])  # fmt:skip
-
-        if functional_cache['bold_outputspaces']:
-            # No transforms necessary
-            std_buffer = pe.Node(
-                KeySelect(
-                    fields=['bold', 'bold_mask'],
-                    keys=[str(space) for space in spaces.references],
-                ),
-                name='std_buffer',
-            )
-            std_buffer.inputs.bold = functional_cache['bold_outputspaces']
-            std_buffer.inputs.bold_mask = functional_cache['bold_mask_outputspaces']
-            workflow.connect([
-                (template_iterator_wf, std_buffer, [('outputnode.space', 'key')]),
-                (std_buffer, denoise_std_wf, [
-                    ('bold', 'inputnode.bold_file'),
-                    ('bold_mask', 'inputnode.bold_mask'),
-                ]),
-            ])  # fmt:skip
-        else:
-            # Warp native BOLD to requested output spaces
-            xfms = [
-                functional_cache['hmc'],
-                functional_cache['boldref2fmap'],
-                functional_cache['bold2anat'],
-            ]
-            all_xfms = pe.Node(niu.Merge(2), name='all_xfms')
-            all_xfms.inputs.in1 = xfms
-            workflow.connect([
-                (template_iterator_wf, all_xfms, [('outputnode.anat2std_xfm', 'in2')]),
-            ])  # fmt:skip
-
-            resample_std_wf = init_resample_volumetric_wf(
-                bold_file=bold_file,
-                functional_cache=functional_cache,
-                run_stc=False,
-                name=_get_wf_name(bold_file, 'resample_std'),
-            )
-            workflow.connect([
-                (template_iterator_wf, resample_std_wf, [
-                    ('outputnode.space', 'inputnode.space'),
-                    ('outputnode.res', 'inputnode.res'),
-                    ('outputnode.cohort', 'inputnode.cohort'),
-                ]),
-                (all_xfms, resample_std_wf, [('out', 'inputnode.transforms')]),
-                (resample_std_wf, denoise_std_wf, [
-                    ('outputnode.bold_std', 'inputnode.bold'),
-                    ('outputnode.bold_mask_std', 'inputnode.bold_mask'),
-                ]),
-            ])  # fmt:skip
-
     return workflow
 
 
diff --git a/src/fmripost_aroma/workflows/resampling.py b/src/fmripost_aroma/workflows/resampling.py
index 902a194..0c47cd9 100644
--- a/src/fmripost_aroma/workflows/resampling.py
+++ b/src/fmripost_aroma/workflows/resampling.py
@@ -6,6 +6,7 @@
 
 def init_resample_volumetric_wf(
     bold_file,
+    metadata,
     functional_cache,
     run_stc,
     name='resample_volumetric_wf',
@@ -35,10 +36,6 @@ def init_resample_volumetric_wf(
             fields=[
                 'bold_file',
                 'mask_file',
-                'space',
-                'res',
-                'cohort',
-                'transforms',
             ],
         ),
         name='inputnode',
@@ -56,7 +53,11 @@ def init_resample_volumetric_wf(
         name='stc_buffer',
     )
     if run_stc:
-        stc_wf = init_bold_stc_wf(name='resample_stc_wf')
+        stc_wf = init_bold_stc_wf(
+            mem_gb={'filesize': 1},
+            metadata=metadata,
+            name='resample_stc_wf',
+        )
         workflow.connect([
             (inputnode, stc_wf, [
                 ('bold_file', 'inputnode.bold_file'),