diff --git a/README.md b/README.md
index 6ec8498..6217b3e 100644
--- a/README.md
+++ b/README.md
@@ -36,9 +36,9 @@ This software can be installed via source or via pip from PyPi with `pip install
 
 ```bash
 usage: petdeface.py [-h] [--anat_only] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--docker] [--singularity] [--n_procs N_PROCS]
-                    [--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing] [--preview_pics]
+                    [--skip_bids_validator] [--version] [--placement PLACEMENT] [--remove_existing]
                     [--participant_label_exclude participant_label_exclude [participant_label_exclude ...]] [--session_label SESSION [SESSION ...]]
-                    [--session_label_exclude session_label_exclude [session_label_exclude ...]]
+                    [--session_label_exclude session_label_exclude [session_label_exclude ...]] [--open_browser]
                     bids_dir [output_dir] [analysis_level]
 
 PetDeface
@@ -63,15 +63,18 @@ options:
                         Where to place the defaced images. Options are 'adjacent': next to the bids_dir (default) in a folder appended with _defaced'inplace':
                         defaces the dataset in place, e.g. replaces faced PET and T1w images w/ defaced at bids_dir'derivatives': does all of the defacing within
                         the derivatives folder in bids_dir.
-  --remove_existing, -r
-                        Remove existing output files in output_dir.
-  --preview_pics        Create preview pictures of defacing, defaults to false for docker
+  --remove_existing, -r Remove existing output files in output_dir.
+  --preview_pics        Create preview pictures of defacing, defaults to false for docker (only works if FreeView is installed on machine)
   --participant_label_exclude participant_label_exclude [participant_label_exclude ...]
                         Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02
   --session_label SESSION [SESSION ...]
                         Select only a specific session(s) to include in the defacing workflow
   --session_label_exclude session_label_exclude [session_label_exclude ...]
                         Select a specific session(s) to exclude from the defacing workflow
+  --use_template_anat   Use template anatomical image when no T1w is available for PET scans. 
+                        Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' 
+                        (averaged PET image).
+  --open_browser        Open browser to show QA reports after completion
 ```
 
 Working example usage:
@@ -80,6 +83,26 @@ Working example usage:
 petdeface /inputfolder /outputfolder --n_procs 16 --skip_bids_validator --placement adjacent
 ```
 
+### Template Anatomical Images
+
+When PET scans lack corresponding T1w anatomical images, PETdeface can use template anatomical images for registration and defacing. Three options are available:
+
+- **`--use_template_anat t1`**: Uses a T1w template included with the PETdeface library
+- **`--use_template_anat mni`**: Uses the MNI standard brain template  
+- **`--use_template_anat pet`**: Creates a template by averaging the PET data across time
+
+**Important**: When using template anatomical images, it's crucial to validate the defacing quality. Inspect the output using the generated HTML report (with `--open_browser`) or a NIfTI viewer to ensure the defacing is valid for your data.
+
+**Recommended workflow for subjects missing T1w images**:
+1. First, exclude subjects missing T1w using `--participant_label_exclude`
+2. Run defacing on subjects with T1w images
+3. Then run defacing separately on subjects missing T1w using `--participant_label` and test different templates (`t1`, `mni`, `pet`) to determine which works best for your data
+
+Example usage with template anatomical:
+```bash
+petdeface /inputfolder /outputfolder --use_template_anat t1 --n_procs 16
+```
+
 ### Docker Usage
 
 Requirements:
diff --git a/data/participants.tsv b/data/participants.tsv
index 42e9d14..9cc15f4 100644
--- a/data/participants.tsv
+++ b/data/participants.tsv
@@ -1,3 +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
diff --git a/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii b/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii
deleted file mode 100644
index 34cf6ed..0000000
Binary files a/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii and /dev/null differ
diff --git a/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz b/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz
new file mode 100644
index 0000000..e8e4e2a
Binary files /dev/null and b/data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz differ
diff --git a/data/sub-mni305/anat/sub-mni305_T1w.nii.gz b/data/sub-mni305/anat/sub-mni305_T1w.nii.gz
new file mode 100644
index 0000000..6cbd30f
Binary files /dev/null and b/data/sub-mni305/anat/sub-mni305_T1w.nii.gz differ
diff --git a/docs/usage.rst b/docs/usage.rst
index be09293..3d1fede 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -123,6 +123,10 @@ options:
                         Select only a specific session(s) to include in the defacing workflow
   --session_label_exclude session_label_exclude [session_label_exclude ...]
                         Select a specific session(s) to exclude from the defacing workflow
+  --use_template_anat   Use template anatomical image when no T1w is available for PET scans. 
+                        Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' 
+                        (averaged PET image).
+  --open_browser        Following defacing this flag will open the browser to view the defacing results
 
 Docker Based
 ------------
@@ -174,4 +178,31 @@ PETdeface will do it's best to locate a valid FreeSurfer license file on the hos
 to the container by checking `FREESURFER_HOME`  and `FREESURFER_LICENSE` environment variables. If you 
 receive an error message relating to the FreeSurfer license file, try setting and exporting the 
 `FREESURFER_LICENSE` environment variable to the location of the FreeSurfer license file on the host 
-machine.
\ No newline at end of file
+machine.
+
+Template Anatomical Images
+-------------------------
+
+When PET scans lack corresponding T1w anatomical images, PETdeface can use template anatomical images for 
+registration and defacing. Three options are available:
+
+- **`--use_template_anat t1`**: Uses a T1w template included with the PETdeface library
+- **`--use_template_anat mni`**: Uses the MNI standard brain template  
+- **`--use_template_anat pet`**: Creates a template by averaging a subjects PET image and using that averaged image in place of a T1 image 
+
+**Important**: When using template anatomical images, it's crucial to validate the defacing quality. 
+Inspect the output using the generated HTML report (with `--open_browser`) or a NIfTI viewer to ensure 
+the defacing is valid for your data.
+
+**Recommended workflow for subjects missing T1w images**:
+
+1. First, exclude subjects missing T1w using `--participant_label_exclude`
+2. Run defacing on subjects with T1w images  
+3. Then run defacing separately on subjects missing T1w using `--participant_label` and test 
+   different templates (`t1`, `mni`, `pet`) to determine which works best for your data
+
+Example usage with template anatomical:
+
+.. code-block:: bash
+
+    petdeface /inputfolder /outputfolder --use_template_anat t1 --n_procs 16
\ No newline at end of file
diff --git a/petdeface/__init__.py b/petdeface/__init__.py
index e69de29..b10b789 100644
--- a/petdeface/__init__.py
+++ b/petdeface/__init__.py
@@ -0,0 +1,73 @@
+"""
+PET Deface - A nipype PET and MR defacing pipeline for BIDS datasets.
+
+This package provides tools for defacing PET and MR images using FreeSurfer's MiDeFace.
+"""
+
+import sys
+from pathlib import Path
+
+# Add the package directory to sys.path when running as script
+if __name__ == "__main__" or (
+    len(sys.argv) > 0 and sys.argv[0].endswith("petdeface.py")
+):
+    # Running as script - add current directory to path
+    package_dir = Path(__file__).parent
+    if str(package_dir) not in sys.path:
+        sys.path.insert(0, str(package_dir))
+
+# Import main components
+try:
+    from .petdeface import PetDeface, deface, cli, main
+    from .mideface import ApplyMideface, Mideface
+    from .pet import WeightedAverage
+    from .qa import run_qa
+    from .utils import run_validator
+    from .noanat import copy_default_anat_to_subject, remove_default_anat
+except ImportError:
+    # Fallback for when running as script
+    try:
+        from petdeface import PetDeface, deface, cli, main
+        from mideface import ApplyMideface, Mideface
+        from pet import WeightedAverage
+        from qa import run_qa
+        from utils import run_validator
+        from noanat import copy_default_anat_to_subject, remove_default_anat
+    except ImportError:
+        # Last resort - import from current directory
+        import os
+
+        sys.path.insert(0, os.path.dirname(__file__))
+        from petdeface import PetDeface, deface, cli, main
+        from mideface import ApplyMideface, Mideface
+        from pet import WeightedAverage
+        from qa import run_qa
+        from utils import run_validator
+        from noanat import copy_default_anat_to_subject, remove_default_anat
+
+# Version info
+try:
+    from importlib.metadata import version
+
+    __version__ = version("petdeface")
+except ImportError:
+    __version__ = "unknown"
+
+__bids_version__ = "1.8.0"
+
+# Main exports
+__all__ = [
+    "PetDeface",
+    "deface",
+    "cli",
+    "main",
+    "ApplyMideface",
+    "Mideface",
+    "WeightedAverage",
+    "run_qa",
+    "run_validator",
+    "copy_default_anat_to_subject",
+    "remove_default_anat",
+    "__version__",
+    "__bids_version__",
+]
diff --git a/petdeface/noanat.py b/petdeface/noanat.py
new file mode 100644
index 0000000..9155db1
--- /dev/null
+++ b/petdeface/noanat.py
@@ -0,0 +1,337 @@
+"""Functionality for handling cases where anatomical images are not available."""
+
+import nibabel
+import numpy
+import shutil
+import os
+import re
+import tempfile
+from pathlib import Path
+from typing import Union, Dict, Optional
+
+
+def get_data_path(filename: str) -> Path:
+    """Get the path to a data file included in the package.
+
+    Parameters
+    ----------
+    filename : str
+        Name of the file to get the path for. This should be relative to the data directory.
+        For example: "sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz"
+
+    Returns
+    -------
+    Path
+        Path to the requested data file
+
+    Raises
+    ------
+    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"
+
+    # Construct the full path
+    full_path = 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"
+        )
+
+    return full_path
+
+
+def get_default_anat(anat) -> Path:
+    """Get the path to the default anatomical image.
+
+    Returns
+    -------
+    Path
+        Path to the default T1w image that should be used when no anatomical
+        image is available for a PET scan.
+    """
+    if anat == "t1":
+        return get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz")
+    elif anat == "mni":
+        return get_data_path("sub-mni305/anat/sub-mni305_T1w.nii.gz")
+    elif anat == "pet":
+        return tempfile.TemporaryDirectory()
+    else:
+        raise Exception(
+            f"Choice of file for template anat must be one of: t1, mni, or pet. given: {anat}"
+        )
+
+
+def get_default_anat_data(anat) -> nibabel.Nifti1Image:
+    """Get the default anatomical image as a nibabel image object.
+
+    Returns
+    -------
+    nibabel.Nifti1Image
+        The default T1w image loaded as a nibabel image object
+    """
+    return nibabel.load(get_default_anat(anat))
+
+
+def extract_subject_id(input_str: str) -> str:
+    """Extract subject ID from various input formats.
+
+    This function can handle:
+    - Full paths (e.g., "/path/to/sub-123/anat/file.nii")
+    - Subject IDs with prefix (e.g., "sub-123")
+    - Raw subject IDs (e.g., "123")
+
+    Parameters
+    ----------
+    input_str : str
+        Input string containing a subject ID in any format
+
+    Returns
+    -------
+    str
+        Extracted subject ID without the 'sub-' prefix
+
+    Raises
+    ------
+    ValueError
+        If no valid subject ID can be extracted
+    """
+    # Pattern to match 'sub-XXXX' in various contexts
+    # The pattern captures everything after 'sub-' until it hits a non-alphanumeric character or the end of the string
+    pattern = r"sub-([a-zA-Z0-9]+)(?:_|$)"
+
+    # Try to find a match
+    match = re.search(pattern, input_str)
+
+    if match:
+        # Return the captured group (the subject ID without 'sub-' prefix)
+        return match.group(1)
+    else:
+        # If no 'sub-' prefix is found, check if the input is a valid subject ID
+        if re.match(r"^[a-zA-Z0-9]+$", input_str):
+            return input_str
+        else:
+            # Try a more flexible approach for paths
+            path_match = re.search(r"sub-([a-zA-Z0-9]+)", input_str)
+            if path_match:
+                return path_match.group(1)
+            else:
+                raise ValueError(
+                    f"Could not extract a valid subject ID from '{input_str}'"
+                )
+
+
+def copy_default_anat_to_subject(
+    bids_dir: Union[str, Path],
+    subject_id: str,
+    pet_image=Union[str, Path],
+    default_anat="t1",
+) -> dict:
+    """Copy the default anatomical image to a PET subject's folder in a BIDS dataset.
+
+    This function extracts the subject ID from the provided string using regex,
+    then copies the default anatomical image and its JSON metadata to the subject's folder in the BIDS dataset.
+
+    Parameters
+    ----------
+    bids_dir : Union[str, Path]
+        Path to the BIDS dataset
+    subject_id : str
+        Subject ID in any format:
+        - Full path (e.g., "/path/to/sub-123/anat/file.nii")
+        - Subject ID with prefix (e.g., "sub-123")
+        - Raw subject ID (e.g., "123")
+    pet_image: Union[str, Path]
+        Path to the pet image that is lacking an anatomical
+    default_anat : str
+        The anat file to use as a 'default' can be a the t1w, mni, or averaged PET image
+        defaults to the t1w included in this library.
+
+    Returns
+    -------
+    dict
+        A dictionary containing information about the created files and directories:
+        {
+            'subject_dir': Path to the subject directory,
+            'anat_dir': Path to the anatomical directory,
+            'created_dirs': List of paths to newly created directories,
+            'created_files': List of paths to newly created files
+        }
+
+    Raises
+    ------
+    FileNotFoundError
+        If the BIDS directory or subject directory does not exist
+    ValueError
+        If the subject ID is invalid or cannot be extracted
+    """
+    # Convert bids_dir to Path if it's a string
+    bids_dir = Path(bids_dir)
+
+    # Check if the BIDS directory exists
+    if not bids_dir.exists():
+        raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
+
+    # Extract subject ID using regex
+    try:
+        extracted_id = extract_subject_id(subject_id)
+    except ValueError as e:
+        raise ValueError(f"Invalid subject ID: {e}")
+
+    # Create the subject directory structure
+    subject_dir = bids_dir / f"sub-{extracted_id}"
+
+    # Check if the subject directory exists
+    if not subject_dir.exists():
+        raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
+
+    anat_dir = subject_dir / "anat"
+
+    # Create the anatomical directory if it doesn't exist
+    created_dirs = []
+    if not anat_dir.exists():
+        anat_dir.mkdir(parents=True, exist_ok=True)
+        created_dirs.append(anat_dir)
+
+    # Define the target file paths
+    target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii.gz"
+    target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
+
+    # Get the source file paths
+    source_nii = get_default_anat(anat=default_anat)
+    if type(source_nii) is tempfile.TemporaryDirectory:
+        # load the pet image for that subject
+        input_image = nibabel.load(pet_image)
+        # average the pet file
+        average = numpy.mean(input_image.dataobj, axis=3)
+        # save the average to the source nifti path, in this case a temp file
+        with source_nii as tmpdirname:
+            save_path = os.path.join(
+                tmpdirname, f"sub-{extracted_id}_desc-totallyat1w.nii.gz"
+            )
+            nibabel.save(nibabel.Nifti1Image(average, input_image.affine), save_path)
+            shutil.copy2(save_path, target_nii)
+    else:
+        shutil.copy2(source_nii, target_nii)
+
+    source_json = get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json")
+    created_files = []
+    created_files.append(target_nii)
+
+    shutil.copy2(source_json, target_json)
+    created_files.append(target_json)
+
+    print(f"Copied {default_anat} anatomical image to {target_nii}")
+    print(f"Copied {default_anat} anatomical metadata to {target_json}")
+
+    # Return information about created files and directories
+    return {
+        "subject_dir": subject_dir,
+        "anat_dir": anat_dir,
+        "created_dirs": created_dirs,
+        "created_files": created_files,
+    }
+
+
+def remove_default_anat(
+    bids_dir: Union[str, Path],
+    subject_id: Optional[str] = None,
+    created_items: Optional[Dict] = None,
+) -> None:
+    """Remove the default anatomical image and directory created for a subject.
+
+    This function can be used in two ways:
+    1. With the bids_dir and subject_id to identify what to remove
+    2. With the bids_dir and the dictionary returned by copy_default_anat_to_subject
+
+    Parameters
+    ----------
+    bids_dir : Union[str, Path]
+        Path to the BIDS dataset
+    subject_id : Optional[str]
+        Subject ID in any format (if created_items is not provided)
+    created_items : Optional[Dict]
+        Dictionary returned by copy_default_anat_to_subject (if subject_id is not provided)
+
+    Returns
+    -------
+    None
+
+    Raises
+    ------
+    ValueError
+        If neither subject_id nor created_items is provided, or if both are provided
+    FileNotFoundError
+        If the BIDS directory or subject directory does not exist
+    """
+    # Convert bids_dir to Path if it's a string
+    bids_dir = Path(bids_dir)
+
+    # Check if the BIDS directory exists
+    if not bids_dir.exists():
+        raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
+
+    # Determine which approach to use
+    if subject_id is not None and created_items is not None:
+        raise ValueError("Cannot provide both subject_id and created_items")
+    elif subject_id is None and created_items is None:
+        raise ValueError("Must provide either subject_id or created_items")
+
+    if created_items is not None:
+        # Use the dictionary returned by copy_default_anat_to_subject
+        anat_dir = created_items["anat_dir"]
+        created_files = created_items["created_files"]
+        created_dirs = created_items["created_dirs"]
+    else:
+        # Extract subject ID using regex
+        try:
+            extracted_id = extract_subject_id(subject_id)
+        except ValueError as e:
+            raise ValueError(f"Invalid subject ID: {e}")
+
+        # Create the subject directory structure
+        subject_dir = bids_dir / f"sub-{extracted_id}"
+
+        # Check if the subject directory exists
+        if not subject_dir.exists():
+            raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
+
+        anat_dir = subject_dir / "anat"
+
+        # Define the file paths
+        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
+        target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
+
+        # Check if the files exist
+        created_files = []
+        if target_nii.exists():
+            created_files.append(target_nii)
+        if target_json.exists():
+            created_files.append(target_json)
+
+        # Check if the directory exists and is empty
+        created_dirs = []
+        if anat_dir.exists():
+            # Only add to created_dirs if it's empty or only contains our files
+            remaining_files = set(anat_dir.iterdir()) - set(created_files)
+            if not remaining_files:
+                created_dirs.append(anat_dir)
+    if os.getenv("PETDEFACE_DEBUG", "").lower() != "true":
+        # Remove the files
+        for file_path in created_files:
+            if file_path.exists():
+                file_path.unlink()
+                print(f"Removed file: {file_path}")
+
+        # Remove the directories (only if they're empty)
+        for dir_path in created_dirs:
+            if dir_path.exists() and not any(dir_path.iterdir()):
+                dir_path.rmdir()
+                print(f"Removed directory: {dir_path}")
+
+        print("Cleanup completed successfully")
+    else:
+        print("PETDEFACE_DEBUG=true, leaving template T1w's in place")
diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py
index ab5aa07..3aef18d 100755
--- a/petdeface/petdeface.py
+++ b/petdeface/petdeface.py
@@ -6,14 +6,11 @@
 import sys
 import shutil
 from bids import BIDSLayout, BIDSLayoutIndexer
-import importlib
 import glob
 from platform import system
-
-# import shutil
+from pathlib import Path
 import subprocess
 from typing import Union
-
 from nipype.interfaces.freesurfer import MRICoreg
 from nipype.interfaces.io import DataSink
 from nipype.interfaces.base.traits_extension import File as traits_extensionFile
@@ -22,23 +19,36 @@
 from niworkflows.utils.bids import collect_data
 from niworkflows.utils.bids import collect_participants
 from niworkflows.utils.misc import check_valid_fs_license
-
 from petutils.petutils import collect_anat_and_pet
 from importlib.metadata import version
 
-
-try:
-    from mideface import ApplyMideface
-    from mideface import Mideface
+# Determine if we're running as a script (including through debugger)
+is_script = (
+    __name__ == "__main__"
+    or len(sys.argv) > 0
+    and sys.argv[0].endswith("petdeface.py")
+    or "debugpy" in sys.modules
+)
+
+if is_script:
+    # Running as script - add current directory to path for local imports
+    current_dir = Path(__file__).parent
+    if str(current_dir) not in sys.path:
+        sys.path.insert(0, str(current_dir))
+
+    # Import using absolute imports (script mode)
+    from mideface import ApplyMideface, Mideface
     from pet import WeightedAverage
-    from utils import run_validator
     from qa import run_qa
-except ModuleNotFoundError:
-    from .mideface import ApplyMideface
-    from .mideface import Mideface
+    from utils import run_validator
+    from noanat import copy_default_anat_to_subject, remove_default_anat
+else:
+    # Running as module - use relative imports
+    from .mideface import ApplyMideface, Mideface
     from .pet import WeightedAverage
-    from .utils import run_validator
     from .qa import run_qa
+    from .utils import run_validator
+    from .noanat import copy_default_anat_to_subject, remove_default_anat
 
 
 # collect version from pyproject.toml
@@ -52,6 +62,8 @@
 # can be found in the pyproject.toml file under the [tool.bids] section
 __bids_version__ = "1.8.0"
 
+temp_anat_subjects = []
+
 
 if __version__ == "unable to locate version number":
     # we try to load the version using import lib
@@ -274,6 +286,7 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
                 anat_only=args.anat_only,
                 session_label=args.session_label,
                 session_label_exclude=args.session_label_exclude,
+                use_template_anat=args.use_template_anat,
             )
         except FileNotFoundError as error:
             single_subject_wf = None
@@ -313,6 +326,7 @@ def init_single_subject_wf(
     anat_only=False,
     session_label=[],
     session_label_exclude=[],
+    use_template_anat=None,
 ) -> Workflow:
     """
     Organize the preprocessing pipeline for a single subject.
@@ -323,7 +337,7 @@ def init_single_subject_wf(
     :type bids_data: pathlib.Path, BIDSLayout]
     :param output_dir: _description_, defaults to None
     :type output_dir: pathlib.Path, optional
-    :param preview_pics: _description_, defaults to False
+    :param preview_pics: _description_, defaults to False (soon to be deprecated)
     :type preview_pics: bool, optional
     :param anat_only: _description_, defaults to False
     :type anat_only: bool, optional
@@ -331,6 +345,8 @@ def init_single_subject_wf(
     :type session: list, optional
     :param session_label_exclude: _description_, will exclude any session(s) supplied to this argument, defaults to []
     :type session_label_exclude: list, optional
+    :param use_template_anat: _description_, will attempt to deface PET images lacking a T1w with existing template T1w packaged in petdeface, default to False,
+    :type use_template_anat: str, optional
     :raises FileNotFoundError: _description_
     :return: _description_
     :rtype: Workflow
@@ -360,10 +376,26 @@ def init_single_subject_wf(
 
     # check if any t1w images exist for the pet images
     for pet_image, t1w_image in subject_data.items():
-        if t1w_image == "":
+        if t1w_image == "" and not use_template_anat:
             raise FileNotFoundError(
                 f"Could not find t1w image for pet image {pet_image}"
             )
+        elif t1w_image == "" and use_template_anat:
+            created_items = copy_default_anat_to_subject(
+                bids_dir=bids_data.root,
+                subject_id=str(pet_image),
+                pet_image=pet_image,
+                default_anat=use_template_anat,
+            )
+            global temp_anat_subjects
+            temp_anat_subjects.append(created_items)
+            subject_data[pet_image] = str(
+                created_items.get("created_files", ["", ""])[0]
+            )
+
+    # if we're adding in new t1w's and folder's we'll need to refresh the BIDS.layout object to reflect
+    # those new changes
+    bids_data = BIDSLayout(bids_data.root)
 
     bids_dir = bids_data.root
 
@@ -404,39 +436,82 @@ def init_single_subject_wf(
         if determine_in_docker():
             preview_pics = False
 
-        deface_t1w = Node(
-            Mideface(
-                in_file=pathlib.Path(t1w_file),
-                pics=preview_pics,
-                odir=".",
-                code=f"{anat_string}",
-            ),
-            name=f"deface_t1w_{anat_string}",
+        # Check if this is a template anatomical image created from PET averaging
+        is_template_from_pet = use_template_anat == "pet" and "desc-totallyat1w" in str(
+            t1w_file
         )
-        t1w_wf.connect(
-            [
-                (
-                    deface_t1w,
-                    datasink,
-                    [
-                        ("out_file", f"{anat_string.replace('_', '.')}.anat"),
-                        (
-                            "out_facemask",
-                            f"{anat_string.replace('_', '.')}.anat.@defacemask",
-                        ),
-                        (
-                            "out_before_pic",
-                            f"{anat_string.replace('_', '.')}.anat.@before",
-                        ),
-                        (
-                            "out_after_pic",
-                            f"{anat_string.replace('_', '.')}.anat.@after",
-                        ),
-                    ],
+
+        if is_template_from_pet:
+            # For PET-averaged templates, we need to create a facemask without defacing the template
+            # We'll use Mideface to generate the facemask but not apply it to the template
+
+            # Create a node that generates facemask but doesn't deface the template
+            template_facemask = Node(
+                Mideface(
+                    in_file=pathlib.Path(t1w_file),
+                    pics=False,  # No preview pics for templates
+                    odir=".",
+                    code=f"{anat_string}_template",
                 ),
-            ]
-        )
-        t1w_workflows[t1w_file] = {"workflow": t1w_wf, "anat_string": anat_string}
+                name=f"deface_t1w_{anat_string}",
+            )
+
+            # Only connect the facemask output, not the defaced template
+            # This way we get the facemask for PET defacing but don't deface the template itself
+            t1w_wf.connect(
+                [
+                    (
+                        template_facemask,
+                        datasink,
+                        [
+                            (
+                                "out_facemask",
+                                f"{anat_string.replace('_', '.')}.anat.@defacemask",
+                            ),
+                        ],
+                    ),
+                ]
+            )
+        else:
+            # Normal defacing for real anatomical images
+            deface_t1w = Node(
+                Mideface(
+                    in_file=pathlib.Path(t1w_file),
+                    pics=preview_pics,
+                    odir=".",
+                    code=f"{anat_string}",
+                ),
+                name=f"deface_t1w_{anat_string}",
+            )
+            t1w_wf.connect(
+                [
+                    (
+                        deface_t1w,
+                        datasink,
+                        [
+                            ("out_file", f"{anat_string.replace('_', '.')}.anat"),
+                            (
+                                "out_facemask",
+                                f"{anat_string.replace('_', '.')}.anat.@defacemask",
+                            ),
+                            (
+                                "out_before_pic",
+                                f"{anat_string.replace('_', '.')}.anat.@before",
+                            ),
+                            (
+                                "out_after_pic",
+                                f"{anat_string.replace('_', '.')}.anat.@after",
+                            ),
+                        ],
+                    ),
+                ]
+            )
+
+        t1w_workflows[t1w_file] = {
+            "workflow": t1w_wf,
+            "anat_string": anat_string,
+            "is_template_from_pet": is_template_from_pet,
+        }
 
     workflow = Workflow(name=name)
     if anat_only:
@@ -455,9 +530,10 @@ def init_single_subject_wf(
             if ses_id.replace("ses-", "") in sessions_to_exclude:
                 continue
 
-            # collect tracer
+            # collect tracer for filename only
+            tracer_info = ""
             if re.search("trc-[^_|\/]*", str(pet_file)):
-                pet_string += "_" + re.search("trc-[^_|\/]*", str(pet_file)).group(0)
+                tracer_info = "_" + re.search("trc-[^_|\/]*", str(pet_file)).group(0)
 
             # collect recontstruction
             if re.search("rec-[^_|\/]*", str(pet_file)):
@@ -468,7 +544,8 @@ def init_single_subject_wf(
                 run_id = "_" + re.search("run-[^_|\/]*", str(pet_file)).group(0)
             except AttributeError:
                 run_id = ""
-            pet_wf_name = f"pet_{pet_string}{run_id}_wf"
+            # Create workflow name with tracer for uniqueness
+            pet_wf_name = f"pet_{pet_string}{tracer_info}{run_id}_wf"
             pet_wf = Workflow(name=pet_wf_name)
 
             weighted_average = Node(
@@ -478,7 +555,12 @@ def init_single_subject_wf(
             # rename registration file to something more descriptive than registration.lta
             # we do this here to account for mulitple runs during the same session
             mricoreg = MRICoreg(reference_file=t1w_file)
-            mricoreg.inputs.out_lta_file = f"{pet_string}{run_id}_desc-pet2anat_pet.lta"
+            if use_template_anat:
+                mricoreg.inputs.dof = 12
+
+            mricoreg.inputs.out_lta_file = (
+                f"{pet_string}{tracer_info}{run_id}_desc-pet2anat_pet.lta"
+            )
 
             coreg_pet_to_t1w = Node(mricoreg, "coreg_pet_to_t1w")
 
@@ -662,12 +744,20 @@ def wrap_up_defacing(
                 mapping_dict[defaced] = raw
 
     if placement == "adjacent":
-        if output_dir is None or output_dir == path_to_dataset:
+        if (
+            output_dir is None
+            or output_dir == path_to_dataset
+            or pathlib.Path(output_dir)
+            == pathlib.Path(os.path.join(path_to_dataset, "derivatives", "petdeface"))
+        ):
             final_destination = f"{path_to_dataset}_defaced"
         else:
             final_destination = output_dir
 
         # copy original dataset to new location, respecting exclusions
+        # Use a set to track copied files to avoid duplicates
+        copied_files = set()
+
         for entry in raw_only.files:
             # Check if this file belongs to an excluded subject
             should_exclude = False
@@ -688,12 +778,21 @@ def wrap_up_defacing(
             if should_exclude:
                 continue
 
+            # Create the destination path
             copy_path = entry.replace(str(path_to_dataset), str(final_destination))
+
+            # Check if we've already copied a file with the same basename
+            # This prevents duplicates like trc-sf51/pet/file.nii.gz and pet/file.nii.gz
+            basename = os.path.basename(entry)
+            if basename in copied_files:
+                continue
+
             pathlib.Path(copy_path).parent.mkdir(
                 parents=True, exist_ok=True, mode=0o775
             )
             if entry != copy_path:
                 shutil.copy(entry, copy_path)
+                copied_files.add(basename)
 
         # update paths in mapping dict
         move_defaced_images(mapping_dict, final_destination)
@@ -823,10 +922,11 @@ def __init__(
         skip_bids_validator=False,
         remove_existing=True,
         placement="adjacent",
-        preview_pics=True,
+        preview_pics=False,
         participant_label_exclude=[],
         session_label=[],
         session_label_exclude=[],
+        use_template_anat=False,
     ):
         self.bids_dir = bids_dir
         self.remove_existing = remove_existing
@@ -840,8 +940,9 @@ def __init__(
         self.participant_label_exclude = participant_label_exclude
         self.session_label = session_label
         self.session_label_exclude = session_label_exclude
+        self.use_template_anat = use_template_anat
 
-        # Build comprehensive exclusion indexer considering both include and exclude parameters
+        # Build the exclusion indexer
         self.exclude_indexer = self._build_exclusion_indexer()
 
         # check if freesurfer license is valid
@@ -933,8 +1034,16 @@ def run(self):
                 "participant_label_exclude": self.participant_label_exclude,
                 "session_label": self.session_label,
                 "session_label_exclude": self.session_label_exclude,
+                "use_template_anat": self.use_template_anat,
             }
         )
+
+        # we want to remove any "t1ws" that we previously substituted in before we copy all
+        # of them into the final directory
+        global temp_anat_subjects
+        for temp_anat_subject in temp_anat_subjects:
+            remove_default_anat(bids_dir=self.bids_dir, created_items=temp_anat_subject)
+
         wrap_up_defacing(
             self.bids_dir,
             self.output_dir,
@@ -1060,10 +1169,17 @@ def cli():
         default=[],
     )
     parser.add_argument(
-        "--open-browser",
+        "--use_template_anat",
+        help="Use template anatomical image when no T1w is available for PET scans. Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' (averaged PET image).",
+        type=str,
+        required=False,
+        default=False,
+    )
+    parser.add_argument(
+        "--open_browser",
+        help="Open browser to show QA reports after completion",
         action="store_true",
         default=False,
-        help="Open browser automatically after QA report generation",
     )
 
     arguments = parser.parse_args()
@@ -1262,6 +1378,7 @@ def main():  # noqa: max-complexity: 12
             participant_label_exclude=args.participant_label_exclude,
             session_label=args.session_label,
             session_label_exclude=args.session_label_exclude,
+            use_template_anat=args.use_template_anat,
         )
         petdeface.run()
 
@@ -1272,23 +1389,12 @@ def main():  # noqa: max-complexity: 12
 
         try:
             # Determine the defaced directory based on placement
-            if args.placement == "adjacent":
-                defaced_dir = args.bids_dir.parent / f"{args.bids_dir.name}_defaced"
-            elif args.placement == "inplace":
-                defaced_dir = args.bids_dir
-            elif args.placement == "derivatives":
-                defaced_dir = args.bids_dir / "derivatives" / "petdeface"
-            else:
-                defaced_dir = (
-                    args.output_dir
-                    if args.output_dir
-                    else args.bids_dir / "derivatives" / "petdeface"
-                )
 
             # Run QA
             qa_result = run_qa(
                 faced_dir=str(args.bids_dir),
-                defaced_dir=str(defaced_dir),
+                defaced_dir=str(args.output_dir),
+                output_dir=str(args.bids_dir / "derivatives" / "petdeface"),
                 subject=(
                     " ".join(args.participant_label) if args.participant_label else None
                 ),
diff --git a/petdeface/qa.py b/petdeface/qa.py
index 4c21f5f..108349e 100644
--- a/petdeface/qa.py
+++ b/petdeface/qa.py
@@ -2,6 +2,7 @@
 import os
 import tempfile
 import shutil
+import sys
 from glob import glob
 import nilearn
 from nilearn import plotting
@@ -17,15 +18,36 @@
 import seaborn as sns
 from PIL import Image, ImageDraw
 from nipype import Workflow, Node
-from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT
 from tempfile import TemporaryDirectory
 from pathlib import Path
 
+# Handle imports for both script and module execution (including debugger)
+is_script = (
+    __name__ == "__main__"
+    or len(sys.argv) > 0
+    and sys.argv[0].endswith("qa.py")
+    or "debugpy" in sys.modules
+)
+
+if is_script:
+    # Running as script - add current directory to path for local imports
+    current_dir = Path(__file__).parent
+    if str(current_dir) not in sys.path:
+        sys.path.insert(0, str(current_dir))
+
+# Import nireports - this should work in both script and module mode
+from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT
+
 
 def preprocess_single_subject(s, output_dir):
     """Preprocess a single subject's images (for parallel processing)."""
     temp_dir = os.path.join(output_dir, "temp_3d_images")
 
+    # Debug: Print what files we're processing
+    print(f"Preprocessing subject {s['id']}:")
+    print(f"  Original: {s['orig_path']}")
+    print(f"  Defaced: {s['defaced_path']}")
+
     # Extract BIDS suffix from original path to preserve meaningful naming
     orig_basename = os.path.basename(s["orig_path"])
     defaced_basename = os.path.basename(s["defaced_path"])
@@ -484,7 +506,13 @@ def create_comparison_html(
         ("original", orig_img, orig_basename, "hot"),  # Colored for original
         ("defaced", defaced_img, defaced_basename, "gray"),  # Grey for defaced
     ]:
-        # save image to temp folder for later loading
+        # Debug: Print what we're processing
+        print(f"Processing {label} image: {basename}")
+        print(f"  Image shape: {img.shape}")
+        print(f"  Image data type: {img.get_data_dtype()}")
+        print(
+            f"  Image min/max: {img.get_fdata().min():.3f}/{img.get_fdata().max():.3f}"
+        )
 
         # Create single sagittal slice using matplotlib directly
         img_data = img.get_fdata()
@@ -819,6 +847,13 @@ def get_unique_key(file_path):
     defaced_map = {get_unique_key(f): f for f in defaced_files}
     common_keys = sorted(set(orig_map.keys()) & set(defaced_map.keys()))
 
+    # Debug: Print what files are being found
+    print(f"Found {len(orig_files)} files in original directory")
+    print(f"Found {len(defaced_files)} files in defaced directory")
+    print(f"Found {len(common_keys)} common files")
+    for key in common_keys:
+        print(f"  {key}: {orig_map[key]} -> {defaced_map[key]}")
+
     subjects = []
     for key in common_keys:
         orig_path = orig_map[key]
@@ -833,19 +868,40 @@ def get_unique_key(file_path):
         else:
             subject_id = sub_id
 
+        # Check if this is a T1w file (prioritize T1w over PET)
+        is_t1w = "T1w" in orig_path or "T1w" in defaced_path
+
         subjects.append(
             {
                 "id": subject_id,
                 "orig_path": orig_path,
                 "defaced_path": defaced_path,
+                "is_t1w": is_t1w,
             }
         )
 
-    if not subjects:
+    # Sort subjects to prioritize T1w files over PET files
+    subjects.sort(key=lambda x: (not x["is_t1w"], x["id"]))
+
+    # For each subject, only keep the T1w file if available, otherwise keep the first file
+    filtered_subjects = []
+    seen_subjects = set()
+
+    for subject in subjects:
+        subject_id = subject["id"]
+        if subject_id not in seen_subjects:
+            filtered_subjects.append(subject)
+            seen_subjects.add(subject_id)
+        elif subject["is_t1w"]:
+            # Replace the existing entry with the T1w version
+            filtered_subjects = [s for s in filtered_subjects if s["id"] != subject_id]
+            filtered_subjects.append(subject)
+
+    if not filtered_subjects:
         print("No matching NIfTI files found in both datasets.")
         exit(1)
 
-    return subjects
+    return filtered_subjects
 
 
 def create_side_by_side_index_html(subjects, output_dir, size="compact"):
@@ -1349,7 +1405,7 @@ def run_qa(
     </html>
     """
 
-    index_file = os.path.join(output_dir, "index.html")
+    index_file = os.path.join(output_dir, "petdeface_report.html")
     with open(index_file, "w") as f:
         f.write(index_html)
 
@@ -1387,7 +1443,7 @@ def run_qa(
 
     print(f"Created side-by-side view: {side_by_side_file}")
     print(f"Created animated view: {animated_file}")
-    print(f"Created main index: {index_file}")
+    print(f"Created main report: {index_file}")
     print(f"Saved command to: {command_file}")
 
     # Open browser if requested
@@ -1396,13 +1452,13 @@ def run_qa(
         print(f"Opened browser to: {index_file}")
 
     print(f"\nAll files generated in: {output_dir}")
-    print(f"Open index.html in your browser to view comparisons")
+    print(f"Open petdeface_report.html in your browser to view comparisons")
 
     return {
         "output_dir": output_dir,
         "side_by_side_file": side_by_side_file,
         "animated_file": animated_file,
-        "index_file": index_file,
+        "report_file": index_file,
         "command_file": command_file,
         "subjects_processed": len(successful),
         "total_subjects": len(preprocessed_subjects),
diff --git a/petdeface/utils.py b/petdeface/utils.py
index f176e83..fb10f13 100644
--- a/petdeface/utils.py
+++ b/petdeface/utils.py
@@ -1,7 +1,49 @@
+"""Utility functions for the petdeface package."""
+from importlib import resources
+from pathlib import Path
 import subprocess
 from pathlib import Path
 import json
-import sys
+
+
+def get_data_path(filename: str) -> Path:
+    """Get the path to a data file included in the package.
+
+    Parameters
+    ----------
+    filename : str
+        Name of the file to get the path for. This should be relative to the data directory.
+        For example: "sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz"
+
+    Returns
+    -------
+    Path
+        Path to the requested data file
+
+    Raises
+    ------
+    FileNotFoundError
+        If the requested file is not found in the package data
+    """
+    try:
+        with resources.path("petdeface.data", filename) as path:
+            return path
+    except Exception as e:
+        raise FileNotFoundError(
+            f"Could not find data file {filename} in package data"
+        ) from e
+
+
+def get_default_anat() -> Path:
+    """Get the path to the default anatomical image.
+
+    Returns
+    -------
+    Path
+        Path to the default T1w image that should be used when no anatomical
+        image is available for a PET scan.
+    """
+    return get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz")
 
 
 class InvalidBIDSDataset(Exception):
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index b397c86..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,3306 +0,0 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
-
-[[package]]
-name = "acres"
-version = "0.5.0"
-description = "Access resources on your terms"
-optional = false
-python-versions = ">=3.9"
-files = [
-    {file = "acres-0.5.0-py3-none-any.whl", hash = "sha256:fcc32b974b510897de0f041609b4234f9ff03e2e960aea088f63973fb106c772"},
-    {file = "acres-0.5.0.tar.gz", hash = "sha256:128b6447bf5df3b6210264feccbfa018b4ac5bd337358319aec6563f99db8f3a"},
-]
-
-[[package]]
-name = "alabaster"
-version = "0.7.16"
-description = "A light, configurable Sphinx theme"
-optional = false
-python-versions = ">=3.9"
-files = [
-    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
-    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
-]
-
-[[package]]
-name = "astor"
-version = "0.8.1"
-description = "Read/rewrite/write Python ASTs"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-files = [
-    {file = "astor-0.8.1-py2.py3-none-any.whl", hash = "sha256:070a54e890cefb5b3739d19f30f5a5ec840ffc9c50ffa7d23cc9fc1a38ebbfc5"},
-    {file = "astor-0.8.1.tar.gz", hash = "sha256:6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e"},
-]
-
-[[package]]
-name = "attrs"
-version = "24.2.0"
-description = "Classes Without Boilerplate"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
-    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
-]
-
-[package.extras]
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-
-[metadata]
-lock-version = "2.0"
-python-versions = ">=3.10, <4.0"
-content-hash = "980a7566badf67e01072461de1f2e76d23db2238b660a4aa4d44181073092a8e"
diff --git a/pyproject.toml b/pyproject.toml
index c37aa7a..54f030f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,6 +8,10 @@ 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",
 ]
 
 # please update the bids version to the latest compliant version when making modifications to this code here
@@ -19,13 +23,13 @@ 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"
-matplotlib = "^3.9.2"
 numpy = "^2.1.3"
 scipy = "^1.14.1"
 seaborn = "^0.13.2"
@@ -41,6 +45,13 @@ 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"
@@ -48,8 +59,11 @@ force_single_line = true
 lines_after_imports = 2
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core", "setuptools>=61.0"]
 build-backend = "poetry.core.masonry.api"
 
+[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'
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..58be81c
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,15 @@
+from setuptools import setup, find_packages
+
+setup(
+    name="petdeface",
+    version="0.2.2",
+    packages=find_packages(),
+    include_package_data=True,
+    package_data={
+        "petdeface": ["data/*", "data/*/*", "data/*/*/*"],
+    },
+    install_requires=[
+        "nibabel",
+        "numpy",
+    ],
+)
diff --git a/tests/test_noanat.py b/tests/test_noanat.py
new file mode 100644
index 0000000..8ec8e79
--- /dev/null
+++ b/tests/test_noanat.py
@@ -0,0 +1,362 @@
+import pytest
+from pathlib import Path
+import shutil
+import tempfile
+import os
+import re
+import numpy as np
+import nibabel as nib
+from unittest.mock import patch, MagicMock
+from petdeface.noanat import (
+    get_data_path,
+    get_default_anat,
+    get_default_anat_data,
+    extract_subject_id,
+    copy_default_anat_to_subject,
+    remove_default_anat,
+)
+
+
+# Path to the test data directory
+data_dir = Path(__file__).parent.parent / "data"
+
+
+@pytest.fixture
+def real_nifti_file():
+    """Get the path to the real NIfTI file in the data directory."""
+    nii_path = (
+        data_dir / "sub-01" / "ses-baseline" / "anat" / "sub-01_ses-baseline_T1w.nii.gz"
+    )
+    assert nii_path.exists(), f"Expected NIfTI file not found at {nii_path}"
+    return nii_path
+
+
+@pytest.fixture
+def real_json_file():
+    """Get the path to the real JSON file in the data directory."""
+    json_path = (
+        data_dir / "sub-01" / "ses-baseline" / "anat" / "sub-01_ses-baseline_T1w.json"
+    )
+    assert json_path.exists(), f"Expected JSON file not found at {json_path}"
+    return json_path
+
+
+@pytest.fixture
+def temp_data_dir(real_nifti_file, real_json_file):
+    """Create a temporary directory with test data files."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create the directory structure
+        data_dir = Path(tmpdir) / "data"
+        anat_dir = data_dir / "sub-01" / "ses-baseline" / "anat"
+        anat_dir.mkdir(parents=True)
+
+        # Copy the real NIfTI file
+        nii_path = anat_dir / "sub-01_ses-baseline_T1w.nii.gz"
+        shutil.copy2(real_nifti_file, nii_path)
+
+        # Copy the real JSON file
+        json_path = anat_dir / "sub-01_ses-baseline_T1w.json"
+        shutil.copy2(real_json_file, json_path)
+
+        yield data_dir
+
+
+@pytest.fixture
+def mock_get_data_path(temp_data_dir):
+    """Patch get_data_path to use the temporary data directory."""
+
+    def mock_get_path(filename):
+        path = temp_data_dir / filename
+        if not path.exists():
+            raise FileNotFoundError(f"File not found: {filename}")
+        return path
+
+    with patch("petdeface.noanat.get_data_path") as mock:
+        mock.side_effect = mock_get_path
+        yield mock
+
+
+@pytest.fixture
+def mock_get_default_anat(real_nifti_file):
+    """Mock the get_default_anat function."""
+    with patch("petdeface.noanat.get_default_anat") as mock:
+        mock.return_value = real_nifti_file
+        yield mock
+
+
+@pytest.fixture
+def mock_get_default_anat_data(real_nifti_file):
+    """Mock the get_default_anat_data function."""
+    with patch("petdeface.noanat.get_default_anat_data") as mock:
+        mock.return_value = nib.load(real_nifti_file)
+        yield mock
+
+
+def test_get_data_path():
+    """Test that get_data_path can find files in the data directory."""
+    # Test with a file that exists in the data directory
+    path = get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz")
+    assert path.exists()
+    assert ".nii" in path.suffixes
+    assert ".gz" in path.suffixes
+
+    # Test with a file that doesn't exist
+    with pytest.raises(FileNotFoundError):
+        get_data_path("nonexistent_file.nii")
+
+
+def test_get_default_anat():
+    """Test that get_default_anat returns the correct path."""
+    path = get_default_anat(anat="t1")
+    assert path.exists()
+    assert ".nii" in path.suffixes
+    path = get_default_anat(anat="mni")
+    assert path.exists()
+    assert "mni305" in str(path)
+
+
+def test_get_default_anat_data():
+    """Test that get_default_anat_data returns a nibabel image."""
+    img = get_default_anat_data(anat="t1")
+    assert img is not None
+    assert len(img.shape) == 3
+
+
+def test_extract_subject_id():
+    """Test that extract_subject_id correctly extracts subject IDs from various formats."""
+    # Test with full path
+    assert extract_subject_id("/path/to/sub-123/anat/file.nii") == "123"
+
+    # Test with subject ID with prefix
+    assert extract_subject_id("sub-123") == "123"
+
+    # Test with raw subject ID
+    assert extract_subject_id("123") == "123"
+
+    # Test with subject ID followed by underscore
+    assert extract_subject_id("sub-123_something") == "123"
+
+    # Test with invalid input
+    with pytest.raises(ValueError):
+        extract_subject_id("invalid-subject")
+
+
+def test_copy_default_anat_to_subject():
+    """Test that copy_default_anat_to_subject correctly copies files to a subject directory."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+
+        # Copy the default anatomical image to the subject directory
+        result = copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+        # Check that the result dictionary contains the expected keys
+        assert "subject_dir" in result
+        assert "anat_dir" in result
+        assert "created_dirs" in result
+        assert "created_files" in result
+
+        # Check that the subject directory is correct
+        assert result["subject_dir"] == subject_dir
+
+        # Check that the anatomical directory was created
+        anat_dir = subject_dir / "anat"
+        assert result["anat_dir"] == anat_dir
+        assert anat_dir.exists()
+        assert anat_dir in result["created_dirs"]
+
+        # Check that the files were created
+        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_json = anat_dir / "sub-123_T1w.json"
+        assert target_nii.exists()
+        assert target_json.exists()
+        assert target_nii in result["created_files"]
+        assert target_json in result["created_files"]
+
+
+def test_copy_default_anat_to_subject_existing_anat_dir():
+    """Test that copy_default_anat_to_subject works when the anatomical directory already exists."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory and anatomical directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+        anat_dir = subject_dir / "anat"
+        anat_dir.mkdir()
+
+        # Copy the default anatomical image to the subject directory
+        result = copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+        # Check that the anatomical directory was not created (it already existed)
+        assert anat_dir not in result["created_dirs"]
+
+        # Check that the files were created
+        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_json = anat_dir / "sub-123_T1w.json"
+        assert target_nii.exists()
+        assert target_json.exists()
+        assert target_nii in result["created_files"]
+        assert target_json in result["created_files"]
+
+
+def test_copy_default_anat_to_subject_nonexistent_subject():
+    """Test that copy_default_anat_to_subject raises an error when the subject directory doesn't exist."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Try to copy the default anatomical image to a nonexistent subject directory
+        with pytest.raises(FileNotFoundError):
+            copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+
+def test_remove_default_anat_with_created_items():
+    """Test that remove_default_anat correctly removes files and directories when using created_items."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+
+        # Copy the default anatomical image to the subject directory
+        created_items = copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+        # Check that the files and directories exist
+        anat_dir = subject_dir / "anat"
+        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_json = anat_dir / "sub-123_T1w.json"
+        assert anat_dir.exists()
+        assert target_nii.exists()
+        assert target_json.exists()
+
+        # Remove the default anatomical image and directory
+        remove_default_anat(tmp_bids_dir, created_items=created_items)
+
+        # Check that the files and directories were removed
+        assert not target_nii.exists()
+        assert not target_json.exists()
+        assert not anat_dir.exists()
+
+
+def test_remove_default_anat_with_subject_id():
+    """Test that remove_default_anat correctly removes files and directories when using subject_id."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+
+        # Copy the default anatomical image to the subject directory
+        copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+        # Check that the files and directories exist
+        anat_dir = subject_dir / "anat"
+        target_nii = anat_dir / "sub-123_T1w.nii"
+        target_json = anat_dir / "sub-123_T1w.json"
+        assert anat_dir.exists()
+        assert target_nii.exists()
+        assert target_json.exists()
+
+        # Remove the default anatomical image and directory
+        remove_default_anat(tmp_bids_dir, subject_id="sub-123")
+
+        # Check that the files and directories were removed
+        assert not target_nii.exists()
+        assert not target_json.exists()
+        assert not anat_dir.exists()
+
+
+def test_remove_default_anat_nonexistent_files():
+    """Test that remove_default_anat handles nonexistent files gracefully."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+
+        # Create a dictionary with nonexistent files and directories
+        created_items = {
+            "subject_dir": subject_dir,
+            "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.json",
+            ],
+        }
+
+        # Remove the default anatomical image and directory
+        remove_default_anat(tmp_bids_dir, created_items=created_items)
+
+        # Check that the function didn't raise an error
+
+
+def test_remove_default_anat_invalid_input():
+    """Test that remove_default_anat raises an error with invalid input."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Try to remove the default anatomical image with both subject_id and created_items
+        with pytest.raises(ValueError):
+            remove_default_anat(tmp_bids_dir, subject_id="sub-123", created_items={})
+
+        # Try to remove the default anatomical image with neither subject_id nor created_items
+        with pytest.raises(ValueError):
+            remove_default_anat(tmp_bids_dir)
+
+        # Try to remove the default anatomical image with a nonexistent BIDS directory
+        with pytest.raises(FileNotFoundError):
+            remove_default_anat(Path(tmpdir) / "nonexistent", subject_id="sub-123")
+
+        # Try to remove the default anatomical image with a nonexistent subject directory
+        with pytest.raises(FileNotFoundError):
+            remove_default_anat(tmp_bids_dir, subject_id="sub-123")
+
+
+def test_remove_default_anat_nonempty_directory():
+    """Test that remove_default_anat doesn't remove a nonempty directory."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create a temporary BIDS dataset
+        tmp_bids_dir = Path(tmpdir) / "bids_dataset"
+        tmp_bids_dir.mkdir()
+
+        # Create a subject directory
+        subject_dir = tmp_bids_dir / "sub-123"
+        subject_dir.mkdir()
+
+        # Copy the default anatomical image to the subject directory
+        created_items = copy_default_anat_to_subject(tmp_bids_dir, "sub-123")
+
+        # Add an extra file to the anatomical directory
+        anat_dir = subject_dir / "anat"
+        extra_file = anat_dir / "extra_file.txt"
+        extra_file.write_text("This is an extra file")
+
+        # Remove the default anatomical image and 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.json").exists()
+        assert anat_dir.exists()
+        assert extra_file.exists()