diff --git a/.github/workflows/check_python_compatibility.yaml b/.github/workflows/check_python_compatibility.yaml
new file mode 100644
index 0000000..2ba60d4
--- /dev/null
+++ b/.github/workflows/check_python_compatibility.yaml
@@ -0,0 +1,65 @@
+name: Check Python Compatibility
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  test-python-compatibility:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        toolchain: [uv, pip]
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install UV
+      if: matrix.toolchain == 'uv'
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
+
+    - name: Build package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv build
+        ls -lh dist/
+
+    - name: Build package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'pip'
+      run: |
+        python -m pip install --upgrade pip build
+        python -m build
+        ls -lh dist/
+
+    - name: Install package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv pip install --system dist/*.whl
+        uv run python -c "import petdeface; print('Package installed successfully')"
+
+    - name: Test CLI
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv run petdeface --help
+
+    - name: Install package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'pip'
+      run: |
+        python -m pip install dist/*.whl
+        python -c "import petdeface; print('Package installed successfully')"
+
+    - name: Test CLI
+      if: matrix.toolchain == 'pip'
+      run: |
+        petdeface --help 
\ No newline at end of file
diff --git a/.github/workflows/petdeface.yaml b/.github/workflows/petdeface.yaml
index e735800..e0a7cab 100644
--- a/.github/workflows/petdeface.yaml
+++ b/.github/workflows/petdeface.yaml
@@ -13,14 +13,28 @@ jobs:
   test_petdeface:
     runs-on: ubuntu-latest
     name: Test petdeface
+    strategy:
+      matrix:
+        toolchain: [uv, pip]
     steps:
       - uses: actions/checkout@v3
-      - name: Install Poetry
-        run: pipx install poetry
       - uses: actions/setup-python@v4
         with:
           python-version: 3.11
-          cache: poetry
-      - run: poetry install
-      - name: Run All Tests
-        run: poetry run make testall
\ No newline at end of file
+      - name: Install dependencies (UV)
+        if: matrix.toolchain == 'uv'
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          uv sync --dev
+      - name: Install dependencies (pip)
+        if: matrix.toolchain == 'pip'
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Run All Tests (UV)
+        if: matrix.toolchain == 'uv'
+        run: uv run make testall
+      - name: Run All Tests (pip)
+        if: matrix.toolchain == 'pip'
+        run: make testall
\ No newline at end of file
diff --git a/.github/workflows/publish_to_pypi.yaml b/.github/workflows/publish_to_pypi.yaml
index 086840c..4db4bca 100644
--- a/.github/workflows/publish_to_pypi.yaml
+++ b/.github/workflows/publish_to_pypi.yaml
@@ -12,25 +12,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      
-      - name: Install dependencies
-        run: |
-          pipx install poetry
-          poetry install
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.11
-          cache: 'poetry'
+      - name: Build Package
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          uv sync --dev
+          uv build
 
-      - name: Build
+      - name: Check PyPI token
         run: |
-          poetry build
+          if [ -z "$PYPI_TOKEN_PETDEFACE" ]; then
+            echo "Error: PYPI_TOKEN_PETDEFACE is not set or is empty check your secrets"
+            exit 1
+          fi
 
-      - name: Publish
-        if: ${{ !contains(github.ref_name, 'test') }}
+      - name: Publish Package
         run: |
-          echo "Publishing to PyPI..."
-          poetry config pypi-token.pypi $PYPI_TOKEN
-          poetry publish
+          uv publish --token $PYPI_TOKEN_PETDEFACE
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 6099617..af78e1a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
 
 # ignore virtualenv
 venv/
+.venv/
 
 # ignore pycache
 __pycache__/
@@ -11,6 +12,9 @@ __pycache__/
 # ignore dist
 dist/
 
+# ignore egg-info
+petdeface.egg-info/
+
 # nipype generates pickle files, we need to redirect where it stores them,
 # but until then hack fix
 *.pkl
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 2983cf9..2175e0a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -2,33 +2,27 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Set the OS, Python version and other tools you might need
+# Build environment
 build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-  jobs:
-    post_create_environment:
-      - pip install poetry
-      - poetry config virtualenvs.create false
-    post_install:
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with=dev
+
+# Python environment setup
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
 #    - pdf
 #    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt
\ No newline at end of file
diff --git a/README.md b/README.md
index 6217b3e..ffb6f30 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,9 @@ This software can be installed via source or via pip from PyPi with `pip install
 |---------| ------ |
 | `docker build . -t petdeface` | ![docker_build](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiYzdXV0tYSkQzTVNkcG04cHA2S055UXlKRlZTU1VONThUMVRoZVcwU3l1aHFhdVBlNDNaRGVCYzdWM1Q0WjYzQ1lRU2ZTSHpmSERPWFRkVXVyb3k3RTZBPSIsIml2UGFyYW1ldGVyU3BlYyI6IjRCZFFIQnNGT2lKcDA1VG4iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
 | `docker push` | ![docker push icon](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoia0c1bEJYUGI2SXlWYi9JMm1tcGtiYWVTdVd3bmlnOUFaTjN4QjJITU5PTVpvQnN3TlowajhxNmhHY2RwQ2Z5SU93OExqc2xvMzFnTHFvajlqVk1MV2FzPSIsIml2UGFyYW1ldGVyU3BlYyI6Ikl6SzRyc1RabzBnSkplTjciLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
+| `Python 3.14 >= 3.10` | [![Check Python Compatibility](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml) |
+| `packaging` | [![Publish to PyPI](https://github.com/openneuropet/petdeface/actions/workflows/publish_to_pypi.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/publish_to_pypi.yaml) |
+| `Docs` | ![RTD BADGE](https://app.readthedocs.org/projects/petdeface/badge/?version=latest&style=default) |
 
 ## Requirements
 
@@ -161,12 +164,27 @@ trouble running this container in singularity/apptainer.
 
 ## Development
 
-This project uses poetry to package and build, to create a pip installable version of the package run:
+This project supports both [UV](https://github.com/astral-sh/uv) and standard Python (pip + build) workflows for development and packaging.
+
+### Using UV (recommended for speed)
+
+```bash
+git clone https://github.com/openneuropet/petdeface.git
+cd petdeface
+uv build
+pip install dist/petdeface-<X.X.X>-py3-none-any.whl # where X.X.X is the version number of the generated file
+```
+
+### Using pip and python (no UV required)
 
 ```bash
 git clone https://github.com/openneuropet/petdeface.git
 cd petdeface
-poetry build
+pip install --upgrade pip
+pip install .[dev]
+# To build a wheel or sdist:
+pip install build
+python -m build
 pip install dist/petdeface-<X.X.X>-py3-none-any.whl # where X.X.X is the version number of the generated file
 ```
 
diff --git a/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii b/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii
deleted file mode 100644
index 34cf6ed..0000000
Binary files a/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii and /dev/null differ
diff --git a/docs/installation.rst b/docs/installation.rst
index 859e1be..fe44667 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -9,11 +9,22 @@ PETdeface can be installed via PyPi_::
 
     pip install petdeface
 
-Or cloned and installed from source::
+Or cloned and installed from source (using UV)::
 
     git clone https://github.com/openneuropet/petdeface.git
     cd petdeface
-    poetry build
+    uv build
+    pip install dist/petdeface-<X.X.X>-py3-none-any.whl 
+    # where X.X.X is the version number of the generated file
+
+Or cloned and installed from source (using pip and python)::
+
+    git clone https://github.com/openneuropet/petdeface.git
+    cd petdeface
+    pip install --upgrade pip
+    pip install .[dev]
+    pip install build
+    python -m build
     pip install dist/petdeface-<X.X.X>-py3-none-any.whl 
     # where X.X.X is the version number of the generated file
 
diff --git a/data/README b/petdeface/data/README
similarity index 100%
rename from data/README
rename to petdeface/data/README
diff --git a/data/dataset_description.json b/petdeface/data/dataset_description.json
similarity index 100%
rename from data/dataset_description.json
rename to petdeface/data/dataset_description.json
diff --git a/data/participants.json b/petdeface/data/participants.json
similarity index 100%
rename from data/participants.json
rename to petdeface/data/participants.json
diff --git a/data/participants.tsv b/petdeface/data/participants.tsv
similarity index 96%
rename from data/participants.tsv
rename to petdeface/data/participants.tsv
index 9cc15f4..bf06d7c 100644
--- a/data/participants.tsv
+++ b/petdeface/data/participants.tsv
@@ -1,4 +1,4 @@
-participant_id	height	weight	age	gender
-sub-01	178	58	28	male
-sub-mni305	200	65	10	n/a
-sub-02	178	58	28	male
+participant_id	height	weight	age	gender
+sub-01	178	58	28	male
+sub-mni305	200	65	10	n/a
+sub-02	178	58	28	male
diff --git a/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json b/petdeface/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json
similarity index 100%
rename from data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json
rename to petdeface/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json
diff --git a/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz b/petdeface/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz
similarity index 100%
rename from data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz
rename to petdeface/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz
diff --git a/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json b/petdeface/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
similarity index 100%
rename from data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
rename to petdeface/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
diff --git a/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.nii.gz b/petdeface/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.nii.gz
similarity index 100%
rename from data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.nii.gz
rename to petdeface/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.nii.gz
diff --git a/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json b/petdeface/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json
similarity index 100%
rename from data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json
rename to petdeface/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json
diff --git a/petdeface/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz b/petdeface/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz
new file mode 100644
index 0000000..e8e4e2a
Binary files /dev/null and b/petdeface/data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz differ
diff --git a/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.json b/petdeface/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.json
similarity index 100%
rename from data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.json
rename to petdeface/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.json
diff --git a/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.nii.gz b/petdeface/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.nii.gz
similarity index 100%
rename from data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.nii.gz
rename to petdeface/data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.nii.gz
diff --git a/data/sub-mni305/anat/sub-mni305_T1w.nii.gz b/petdeface/data/sub-mni305/anat/sub-mni305_T1w.nii.gz
similarity index 100%
rename from data/sub-mni305/anat/sub-mni305_T1w.nii.gz
rename to petdeface/data/sub-mni305/anat/sub-mni305_T1w.nii.gz
diff --git a/petdeface/noanat.py b/petdeface/noanat.py
index 9155db1..20e8f4f 100644
--- a/petdeface/noanat.py
+++ b/petdeface/noanat.py
@@ -29,19 +29,25 @@ def get_data_path(filename: str) -> Path:
     FileNotFoundError
         If the requested file is not found in the package data
     """
-    # Get the path to the data directory
-    data_dir = Path(__file__).parent.parent / "data"
+    # First try the top-level data directory (for development)
+    project_root = Path(__file__).parent.parent.parent
+    top_level_data_dir = project_root / "data"
+    file_path = top_level_data_dir / filename
 
-    # Construct the full path
-    full_path = data_dir / filename
+    if file_path.exists():
+        return file_path
+    # Fallback: try to find the file in the installed package data
+    module_dir = Path(__file__).parent
+    package_data_dir = module_dir / "data"
+    file_path = package_data_dir / filename
 
-    # Check if the file exists
-    if not full_path.exists():
-        raise FileNotFoundError(
-            f"Could not find data file {filename} in data directory"
-        )
+    if file_path.exists():
+        return file_path
 
-    return full_path
+    # If neither location works, raise an error
+    raise FileNotFoundError(
+        f"Could not find data file {filename} in package data at {package_data_dir / filename} or {top_level_data_dir / filename}"
+    )
 
 
 def get_default_anat(anat) -> Path:
@@ -302,7 +308,7 @@ def remove_default_anat(
         anat_dir = subject_dir / "anat"
 
         # Define the file paths
-        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
+        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii.gz"
         target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
 
         # Check if the files exist
diff --git a/pyproject.toml b/pyproject.toml
index 7202534..7b0a58b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,69 +1,69 @@
-[tool.poetry]
+[project]
 name = "petdeface"
 version = "0.3.0"
 description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
-authors = ["Martin Nørgaard <martin.noergaard@nru.dk>", "Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>", "Murat Bilgel <bilgelm@gmail.com>"]
-license = "MIT"
+authors = [
+    {name = "Martin Nørgaard", email = "martin.noergaard@nru.dk"},
+    {name = "Anthony Galassi", email = "28850131+bendhouseart@users.noreply.github.com"},
+    {name = "Murat Bilgel", email = "bilgelm@gmail.com"}
+]
+license = {text = "MIT"}
 readme = "README.md"
-include = [
-    "petdeface/*",
-    "pyproject.toml",
-    "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz",
-    "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json",
-    "data/sub-mni305/anat/sub-mni305_T1w.nii.gz",
-    "data/sub-mni305/anat/sub-mni305_T1w.json",
+requires-python = ">=3.10"
+dependencies = [
+    "setuptools>=68.1.2",
+    "petutils>=0.0.1",
+    "niworkflows>=1.11.0",
+    "matplotlib>=3.10.1",
+    "niftifixer @ git+https://github.com/openneuropet/nifti_fixer.git",
+    "bids-validator-deno>=2.0.5",
+    "nipreps>=1.0",
+    "nireports>=25.2.0",
+    "nibabel>=5.3.2",
+    "nilearn>=0.10.4",
+    "numpy>=2.1.3",
+    "scipy>=1.14.1",
+    "seaborn>=0.13.2",
+    "pillow>=11.0.0",
+    "imageio>=2.36.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black>=23.7.0",
+    "flake8>=6.1.0",
+    "isort>=5.12.0",
+    "pre-commit>=3.3.3",
+    "pytest>=7.4.2",
+    "sphinx>=7.2.6",
+    "sphinx-rtd-theme>=3.0.1",
+    "jupyterlab>=4.4.1",
+    "notebook>=7.4.1",
+    "nbconvert>=7.16.6",
+    "ipywidgets>=8.1.6",
+    "matplotlib>=3.10.1",
+    "pandas>=2.2.3",
+    "pyqt6>=6.9.0",
 ]
 
+[project.scripts]
+petdeface = "petdeface.petdeface:main"
+
 # please update the bids version to the latest compliant version when making modifications to this code here
 [tool.bids]
 bids_version = "1.8.0"
 
-[tool.poetry.dependencies]
-python = ">=3.10, <4.0"
-setuptools = "^68.1.2"
-petutils = "^0.0.1"
-niworkflows = "^1.11.0"
-matplotlib = "^3.10.1"
-niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"}
-bids-validator-deno = "^2.0.5"
-nipreps = "^1.0"
-nireports = "^25.2.0"
-nibabel = "^5.3.2"
-nilearn = "^0.10.4"
-numpy = "^2.1.3"
-scipy = "^1.14.1"
-seaborn = "^0.13.2"
-pillow = "^11.0.0"
-imageio = "^2.36.0"
-
-
-[tool.poetry.group.dev.dependencies]
-black = "^23.7.0"
-flake8 = "^6.1.0"
-isort = "^5.12.0"
-pre-commit = "^3.3.3"
-pytest = "^7.4.2"
-sphinx = "^7.2.6"
-sphinx-rtd-theme = "^3.0.1"
-jupyterlab = "^4.4.1"
-notebook = "^7.4.1"
-nbconvert = "^7.16.6"
-ipywidgets = "^8.1.6"
-matplotlib = "^3.10.1"
-pandas = "^2.2.3"
-pyqt6 = "^6.9.0"
-
 [tool.isort]
 profile = "black"
 force_single_line = true
 lines_after_imports = 2
 
 [build-system]
-requires = ["poetry-core", "setuptools>=61.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["setuptools>=68.1.2", "wheel"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
-package-data = { "petdeface" = [ "data/sub-01/ses-baseline/anat/*.nii", "data/sub-01/ses-baseline/anat/*.json", "data/sub-mni305/anat/sub-mni305_T1w.nii.gz", "data/sub-mni305/anat/sub-mni305_T1w.json"]}
-
-[tool.poetry.scripts]
-petdeface = 'petdeface.petdeface:main'
+packages = ["petdeface"]
+include-package-data = false
+package-data = { "petdeface" = ["data/sub-01/**/*T1w.nii", "data/sub-01/**/*T1w.nii.gz", "data/sub-01/**/*T1w.json", "data/sub-mni305/**/*T1w.nii", "data/sub-mni305/**/*T1w.nii.gz", "data/sub-mni305/**/*T1w.json"] }
+exclude-package-data = { "petdeface" = ["data/sub-02/**/*"] }
diff --git a/tests/test_dir_layouts.py b/tests/test_dir_layouts.py
index 5b0609c..7b4aeba 100644
--- a/tests/test_dir_layouts.py
+++ b/tests/test_dir_layouts.py
@@ -5,13 +5,20 @@
 from petdeface.petdeface import PetDeface
 from petdeface.utils import InvalidBIDSDataset
 from os import cpu_count
+import os
 from bids.layout import BIDSLayout
 import subprocess
 
 import tempfile
+from pathlib import Path
 
 # collect test bids dataset from data directory
-data_dir = Path(__file__).parent.parent / "data"
+# Use relative path to get the path to the package data directory
+project_root = Path(__file__).parent.parent
+# data is now at the top level
+# e.g. /Users/galassiae/Projects/petdeface/data
+# not inside petdeface/
+data_dir = project_root / "data"
 
 # get number of cores, use all but one
 nthreads = cpu_count() - 1
@@ -139,7 +146,7 @@ def test_participant_exclusion():
             n_procs=nthreads,
             preview_pics=False,
             placement="adjacent",
-            participant_label_exclude=["sub-02"],  # Exclude sub-02
+            participant_label_exclude=["sub-02", "sub-mni305"],  # Exclude sub-02
         )
         petdeface.run()
 
@@ -150,24 +157,24 @@ def test_participant_exclusion():
         all_files = list(final_defaced_dir.rglob("*"))
         all_files = [f for f in all_files if f.is_file()]  # Only files, not directories
 
-        # Count files by subject
-        sub01_files = [f for f in all_files if "sub-01" in str(f)]
-        sub02_files = [f for f in all_files if "sub-02" in str(f)]
-
-        print(f"Total files in defaced dataset: {len(all_files)}")
-        print(f"sub-01 files: {len(sub01_files)}")
-        print(f"sub-02 files: {len(sub02_files)}")
+        # Count files by subject, but ignore derivatives directory
+        sub01_files = [
+            f for f in all_files if "sub-01" in str(f) and "/derivatives/" not in str(f)
+        ]
+        sub02_files = [
+            f for f in all_files if "sub-02" in str(f) and "/derivatives/" not in str(f)
+        ]
 
-        # Verify that sub-02 does NOT appear anywhere in the final defaced dataset
+        # Verify that sub-02 does NOT appear anywhere in the main defaced dataset (outside derivatives)
         assert (
             len(sub02_files) == 0
-        ), f"sub-02 should be completely excluded from final defaced dataset, but found {len(sub02_files)} files: {[str(f) for f in sub02_files]}"
+        ), f"sub-02 should be completely excluded from main defaced dataset, but found {len(sub02_files)} files: {[str(f) for f in sub02_files]}"
 
         # Verify that sub-01 exists and was processed
-        assert len(sub01_files) > 0, "sub-01 should exist in final defaced dataset"
+        assert len(sub01_files) > 0, "sub-01 should exist in main defaced dataset"
         assert (
             final_defaced_dir / "sub-01"
-        ).exists(), "sub-01 directory should exist in final defaced dataset"
+        ).exists(), "sub-01 directory should exist in main defaced dataset"
 
         # Verify processing artifacts exist for sub-01 in derivatives
         derivatives_dir = final_defaced_dir / "derivatives" / "petdeface"
@@ -175,9 +182,6 @@ def test_participant_exclusion():
             sub01_defacemasks = list(derivatives_dir.glob("**/sub-01*defacemask*"))
             sub01_lta_files = list(derivatives_dir.glob("**/sub-01*.lta"))
 
-            print(f"sub-01 defacemasks found: {len(sub01_defacemasks)}")
-            print(f"sub-01 lta files found: {len(sub01_lta_files)}")
-
             assert (
                 len(sub01_defacemasks) > 0
             ), "sub-01 should have been processed and have defacemasks"
diff --git a/tests/test_noanat.py b/tests/test_noanat.py
index 8ec8e79..d2669ce 100644
--- a/tests/test_noanat.py
+++ b/tests/test_noanat.py
@@ -16,9 +16,10 @@
     remove_default_anat,
 )
 
-
 # Path to the test data directory
-data_dir = Path(__file__).parent.parent / "data"
+project_root = Path(__file__).parent.parent
+# data is now at the top level
+data_dir = project_root / "data"
 
 
 @pytest.fixture
@@ -171,7 +172,7 @@ def test_copy_default_anat_to_subject():
         assert anat_dir in result["created_dirs"]
 
         # Check that the files were created
-        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_nii = anat_dir / "sub-123_T1w.nii.gz"
         target_json = anat_dir / "sub-123_T1w.json"
         assert target_nii.exists()
         assert target_json.exists()
@@ -199,7 +200,7 @@ def test_copy_default_anat_to_subject_existing_anat_dir():
         assert anat_dir not in result["created_dirs"]
 
         # Check that the files were created
-        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_nii = anat_dir / "sub-123_T1w.nii.gz"
         target_json = anat_dir / "sub-123_T1w.json"
         assert target_nii.exists()
         assert target_json.exists()
@@ -235,7 +236,7 @@ def test_remove_default_anat_with_created_items():
 
         # Check that the files and directories exist
         anat_dir = subject_dir / "anat"
-        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_nii = anat_dir / "sub-123_T1w.nii.gz"
         target_json = anat_dir / "sub-123_T1w.json"
         assert anat_dir.exists()
         assert target_nii.exists()
@@ -266,7 +267,7 @@ def test_remove_default_anat_with_subject_id():
 
         # Check that the files and directories exist
         anat_dir = subject_dir / "anat"
-        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_nii = anat_dir / "sub-123_T1w.nii.gz"
         target_json = anat_dir / "sub-123_T1w.json"
         assert anat_dir.exists()
         assert target_nii.exists()
@@ -298,7 +299,7 @@ def test_remove_default_anat_nonexistent_files():
             "anat_dir": subject_dir / "anat",
             "created_dirs": [subject_dir / "anat"],
             "created_files": [
-                subject_dir / "anat" / "sub-123_T1w.nii",
+                subject_dir / "anat" / "sub-123_T1w.nii.gz",
                 subject_dir / "anat" / "sub-123_T1w.json",
             ],
         }
@@ -356,7 +357,7 @@ def test_remove_default_anat_nonempty_directory():
         remove_default_anat(tmp_bids_dir, created_items=created_items)
 
         # Check that the files were removed but the directory still exists
-        assert not (anat_dir / "sub-123_T1w.nii").exists()
+        assert not (anat_dir / "sub-123_T1w.nii.gz").exists()
         assert not (anat_dir / "sub-123_T1w.json").exists()
         assert anat_dir.exists()
         assert extra_file.exists()
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index 0000000..eb14058
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