diff --git a/config/ruff.toml b/config/ruff.toml
index 92f0d06..935bf10 100644
--- a/config/ruff.toml
+++ b/config/ruff.toml
@@ -6,6 +6,7 @@ include = [
   "src/readii/feature_extraction.py",
   "src/readii/cli/**/*.py",
   "src/readii/negative_controls_refactor/**.py",
+  "src/readii/io/writers/**.py",
 ]
 
 # extend-exclude is used to exclude directories from the flake8 checks
@@ -16,7 +17,9 @@ extend-exclude = [
   "src/readii/image_processing.py",
   "src/readii/metadata.py",
   "src/readii/negative_controls.py",
-  "src/readii/pipeline.py",]
+  "src/readii/pipeline.py",
+  "notebooks/*",
+]
 
 # Same as Black.
 line-length = 100
diff --git a/notebooks/nifti_writer_example.ipynb b/notebooks/nifti_writer_example.ipynb
new file mode 100644
index 0000000..685c59a
--- /dev/null
+++ b/notebooks/nifti_writer_example.ipynb
@@ -0,0 +1,218 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example subclass for writing NIFTI files"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Import the NIFTIWriter class created in READII along with other necessary imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from readii.io.writers.nifti_writer import NIFTIWriter\n",
+    "from readii.io.writers.base_writer import BaseWriter\n",
+    "from pathlib import Path\n",
+    "import subprocess\n",
+    "import SimpleITK as sitk\n",
+    "import pandas as pd\n",
+    "import uuid\n",
+    "import random\n",
+    "import sys\n",
+    "from readii.utils import logger"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Define a writer subclass for writing .csv files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# copy this writer from the other notebook:\n",
+    "class CSVWriter(BaseWriter): # noqa\n",
+    "\n",
+    "  # The save method is the only method that needs to be implemented for the subclasses of BaseWriter\n",
+    "  def save(self, data: list, **kwargs) -> Path:  # noqa\n",
+    "    output_path = self.resolve_path(**kwargs)\n",
+    "    with output_path.open('w') as f: # noqa\n",
+    "      pd.DataFrame(data).to_csv(f, index=False)\n",
+    "    return output_path\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Show how the NIFTI Writer can be used on SimpleITK images"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "TRASH/writer_examples/nifti_writer_examples/\n",
+      "├── PatientID-AliceSmith/\n",
+      "│   ├── AliceSmith_metadata.csv\n",
+      "│   └── Study-Study003/\n",
+      "│       ├── CT/\n",
+      "│       │   └── CT_SeriesUID-13278.nii.gz\n",
+      "│       └── RTSTRUCT/\n",
+      "│           └── RTSTRUCT_SeriesUID-39256.nii.gz\n",
+      "├── PatientID-JaneDoe/\n",
+      "│   ├── JaneDoe_metadata.csv\n",
+      "│   └── Study-Study002/\n",
+      "│       ├── CT/\n",
+      "│       │   └── CT_SeriesUID-24592.nii.gz\n",
+      "│       └── RTSTRUCT/\n",
+      "│           └── RTSTRUCT_SeriesUID-42098.nii.gz\n",
+      "└── PatientID-JohnAdams/\n",
+      "    ├── JohnAdams_metadata.csv\n",
+      "    └── Study-Study001/\n",
+      "        ├── CT/\n",
+      "        │   └── CT_SeriesUID-93810.nii.gz\n",
+      "        └── RTSTRUCT/\n",
+      "            └── RTSTRUCT_SeriesUID-46048.nii.gz\n",
+      "\n",
+      "13 directories, 9 files\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "ROOT_DIRECTORY = Path(\"TRASH\", \"writer_examples\", \"nifti_writer_examples\")\n",
+    "IMAGE_FILENAME_FORMAT = \"PatientID-{PatientID}/Study-{Study}/{Modality}/{Modality}_SeriesUID-{SeriesUID}\"\n",
+    "METADATA_FILENAME_FORMAT = \"PatientID-{PatientID}/{PatientID}\"\n",
+    "\n",
+    "data_sets = []\n",
+    "random.seed(42)  # Set random seed for reproducibility\n",
+    "\n",
+    "random_5d = lambda: random.randint(10000, 99999)\n",
+    "\n",
+    "# Set up some dummy images to save as NIFTI files\n",
+    "for MODALITY in [\"CT\", \"RTSTRUCT\"]:\n",
+    "  data_sets.extend([\n",
+    "    {\n",
+    "      \"image\": sitk.Image(10, 10, 10, sitk.sitkInt16),\n",
+    "      \"metadata\": pd.DataFrame({\"PatientID\": [\"JohnAdams\"], \"Study\": [\"Study001\"]}),\n",
+    "      \"PatientID\": \"JohnAdams\",\n",
+    "      \"Study\": \"Study001\",\n",
+    "      \"Modality\": MODALITY,\n",
+    "      \"SeriesUID\": random_5d(),\n",
+    "    },\n",
+    "    {\n",
+    "      \"image\": sitk.Image(20, 20, 20, sitk.sitkInt16),\n",
+    "      \"metadata\": pd.DataFrame({\"PatientID\": [\"JaneDoe\"], \"Study\": [\"Study002\"]}),\n",
+    "      \"PatientID\": \"JaneDoe\",\n",
+    "      \"Study\": \"Study002\",\n",
+    "      \"Modality\": MODALITY,\n",
+    "      \"SeriesUID\": random_5d(),\n",
+    "    },\n",
+    "    {\n",
+    "      \"image\": sitk.Image(30, 30, 30, sitk.sitkInt16),\n",
+    "      \"metadata\": pd.DataFrame({\"PatientID\": [\"AliceSmith\"], \"Study\": [\"Study003\"]}),\n",
+    "      \"PatientID\": \"AliceSmith\",\n",
+    "      \"Study\": \"Study003\",\n",
+    "      \"Modality\": MODALITY,\n",
+    "      \"SeriesUID\": random_5d(),\n",
+    "    }\n",
+    "  ])\n",
+    "\n",
+    "# Create a writer with the specified root directory and filename format\n",
+    "with (\n",
+    "  NIFTIWriter(\n",
+    "    root_directory=ROOT_DIRECTORY, \n",
+    "    filename_format=f\"{IMAGE_FILENAME_FORMAT}.nii.gz\",\n",
+    "    overwrite=True\n",
+    "  ) as nifti_writer,\n",
+    "  CSVWriter(\n",
+    "    root_directory=ROOT_DIRECTORY, \n",
+    "    filename_format=f\"{METADATA_FILENAME_FORMAT}_metadata.csv\",\n",
+    "  ) as metadata_writer\n",
+    "):\n",
+    "  # Iterate over the data sets and save them\n",
+    "  for data_set in data_sets:\n",
+    "\n",
+    "    # The actual data being saved is image or data, but the rest of the kwargs are \n",
+    "    # only for resolving the filename\n",
+    "    try:\n",
+    "      nifti_writer.save(\n",
+    "        image=data_set[\"image\"],\n",
+    "        PatientID=data_set[\"PatientID\"],\n",
+    "        Study=data_set[\"Study\"],\n",
+    "        Modality=data_set[\"Modality\"],\n",
+    "        SeriesUID=data_set[\"SeriesUID\"]\n",
+    "      )\n",
+    "      metadata_writer.save(\n",
+    "        data=data_set[\"metadata\"],\n",
+    "        PatientID=data_set[\"PatientID\"],\n",
+    "        Study=data_set[\"Study\"],\n",
+    "        Modality=data_set[\"Modality\"],\n",
+    "        SeriesUID=data_set[\"SeriesUID\"]\n",
+    "      )\n",
+    "    except FileExistsError as e:\n",
+    "      logger.exception(f\"Error saving data set: {e}\")\n",
+    "      sys.exit(1)\n",
+    "\n",
+    "output = subprocess.check_output([\"tree\", \"-nF\", ROOT_DIRECTORY])\n",
+    "print(output.decode(\"utf-8\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "dev",
+   "language": "python",
+   "name": "dev"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/nifti_writer_example.pdf b/notebooks/nifti_writer_example.pdf
new file mode 100644
index 0000000..876a60a
Binary files /dev/null and b/notebooks/nifti_writer_example.pdf differ
diff --git a/notebooks/writer_examples.ipynb b/notebooks/writer_examples.ipynb
new file mode 100644
index 0000000..4617515
--- /dev/null
+++ b/notebooks/writer_examples.ipynb
@@ -0,0 +1,274 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Writing Files with the a BaseWriter Subclass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from readii.io.writers.base_writer import BaseWriter\n",
+    "from readii.utils import logger\n",
+    "import SimpleITK as sitk\n",
+    "from pathlib import Path\n",
+    "import json\n",
+    "from typing import Any"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Create a subclass of BaseWriter for writing text files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Example subclass for writing text files\n",
+    "# Define a concrete subclass of BaseWriter that will handle the saving of a specific file type\n",
+    "# this is a simple example with no validation or error handling\n",
+    "class TextWriter(BaseWriter):\n",
+    "  def save(self, content: str, **kwargs: Any) -> Path:\n",
+    "    output_path = self.resolve_path(**kwargs)\n",
+    "    with open(output_path, 'w') as f:\n",
+    "      f.write(content)\n",
+    "    return output_path"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Creating and using different writers for different filename patterns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "example_file_formats = [\n",
+    "  # a placeholder can be of the format {key} or %key\n",
+    "  # {key} is useful for python code, whereas %key is useful for use in CLI or bash scripts where using {} would be problematic\n",
+    "  \"notes_%SubjectID.txt\",\n",
+    "  \"notes_{SubjectID}.txt\",\n",
+    "\n",
+    "  # You define the placeholder that you will later pass in as a keyword argument in the save method\n",
+    "  # By default, the writer automatically generates data for the current \"date\", \"time\", and \"date_time\" \n",
+    "  # so those can be used as placeholders\n",
+    "  # Every other placeholder needs to be passed in as a keyword argument in the save method\n",
+    "  \"important-file-name_{SubjectID}_{date}.txt\",\n",
+    "  \"subjects/{SubjectID}/{time}_result.txt\",\n",
+    "  \"subjects/{SubjectID}_Birthday-{SubjectBirthDate}/data_{date_time}.txt\",\n",
+    "]\n",
+    "\n",
+    "# Create text writers with different filename patterns\n",
+    "text_writers = [\n",
+    "  TextWriter(\n",
+    "    root_directory=\"TRASH/writer_examples/text_data\",\n",
+    "    filename_format=fmt\n",
+    "  ) for fmt in example_file_formats\n",
+    "]\n",
+    "\n",
+    "# Define some example data to pass to the writers\n",
+    "# this could be extracted from some data source and used to generate the file names\n",
+    "SubjectID=\"SUBJ001\"\n",
+    "SubjectBirthDate=\"2022-01-01\"\n",
+    "\n",
+    "# Test text writers\n",
+    "for writer in text_writers:\n",
+    "  path = writer.save(\n",
+    "    content = \"Sample text content\", # this is the data that will be written to the file\n",
+    "\n",
+    "    # They key-value pairs can be passed in as keyword arguments, and matched to placeholders in the filename format\n",
+    "    SubjectID=SubjectID, \n",
+    "    SubjectBirthDate=SubjectBirthDate,\n",
+    "\n",
+    "    # If you pass in a key that is not in the filename format, it will be ignored\n",
+    "    # this can also be seen as `SubjectBirthDate` is only used in one of the above filename formats\n",
+    "    RandomKey=\"This will be ignored\",\n",
+    "    RandomKey2=\"This will also be ignored\"\n",
+    "  )\n",
+    "  print(f\"{writer.__class__.__name__} with format [magenta]'{writer.pattern_resolver.formatted_pattern}':\")\n",
+    "  print(f\"File written to: [green]{path}\\n\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# More detailed example"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import pandas as pd\n",
+    "\n",
+    "# Any subclass has to be initialized with a root directory and a filename format\n",
+    "# which might not be obvious at first\n",
+    "\n",
+    "class CSVWriter(BaseWriter): # noqa\n",
+    "\n",
+    "  # The save method is the only method that needs to be implemented for the subclasses of BaseWriter\n",
+    "  def save(self, data: list, **kwargs: Any) -> Path:  # noqa\n",
+    "    output_path = self.resolve_path(**kwargs)\n",
+    "    with output_path.open('w') as f: # noqa\n",
+    "      pd.DataFrame(data).to_csv(f, index=False)\n",
+    "    return output_path\n",
+    "\n",
+    "# Make some fake data\n",
+    "subject_data_examples = [\n",
+    "  {\n",
+    "    \"PatientID\": f\"PAT{i:03d}\",\n",
+    "    \"Modality\": f\"{MODALITY}\",\n",
+    "    \"Study\": f\"Study{j:03d}\",\n",
+    "    \"DataType\": f\"{DATA_TYPE}\",\n",
+    "  }\n",
+    "  for i in range(1, 4)\n",
+    "  for j in range(1, 3)\n",
+    "  for MODALITY in [\"CT\", \"RTSTRUCT\"]\n",
+    "  for DATA_TYPE in [\"raw\", \"processed\", \"segmented\", \"labeled\"]\n",
+    "]\n",
+    "ROOT_DIRECTORY = Path(\"TRASH/writer_examples/csv_examples/patient_data\")\n",
+    "with CSVWriter(\n",
+    "  root_directory=ROOT_DIRECTORY,\n",
+    "  filename_format=\"PatientID-{PatientID}/Study-{Study}/{Modality}/{DataType}-data.csv\"\n",
+    ") as csv_writer:\n",
+    "  # Test CSV writers\n",
+    "  for patient in subject_data_examples:\n",
+    "    path = csv_writer.save(\n",
+    "      data = pd.DataFrame(patient, index=[0]), # just assume that this dataframe is some real data\n",
+    "      PatientID=patient[\"PatientID\"],\n",
+    "      Study=patient[\"Study\"],\n",
+    "      Modality=patient[\"Modality\"],\n",
+    "      DataType=patient[\"DataType\"]\n",
+    "    )\n",
+    "\n",
+    "# run the tree command and capture the output\n",
+    "output = subprocess.check_output([\"tree\", \"-nF\",  ROOT_DIRECTORY])\n",
+    "# print(output.decode(\"utf-8\"))\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Output would look like:\n",
+    "\n",
+    "```console\n",
+    "TRASH/writer_examples/csv_examples/patient_data/\n",
+    "├── PatientID-PAT001/\n",
+    "│   ├── Study-Study001/\n",
+    "│   │   ├── CT/\n",
+    "│   │   │   ├── labeled-data.csv\n",
+    "│   │   │   ├── processed-data.csv\n",
+    "│   │   │   ├── raw-data.csv\n",
+    "│   │   │   └── segmented-data.csv\n",
+    "│   │   └── RTSTRUCT/\n",
+    "│   │       ├── labeled-data.csv\n",
+    "│   │       ├── processed-data.csv\n",
+    "│   │       ├── raw-data.csv\n",
+    "│   │       └── segmented-data.csv\n",
+    "│   └── Study-Study002/\n",
+    "│       ├── CT/\n",
+    "│       │   ├── labeled-data.csv\n",
+    "│       │   ├── processed-data.csv\n",
+    "│       │   ├── raw-data.csv\n",
+    "│       │   └── segmented-data.csv\n",
+    "│       └── RTSTRUCT/\n",
+    "│           ├── labeled-data.csv\n",
+    "│           ├── processed-data.csv\n",
+    "│           ├── raw-data.csv\n",
+    "│           └── segmented-data.csv\n",
+    "├── PatientID-PAT002/\n",
+    "│   ├── Study-Study001/\n",
+    "│   │   ├── CT/\n",
+    "│   │   │   ├── labeled-data.csv\n",
+    "│   │   │   ├── processed-data.csv\n",
+    "│   │   │   ├── raw-data.csv\n",
+    "│   │   │   └── segmented-data.csv\n",
+    "│   │   └── RTSTRUCT/\n",
+    "│   │       ├── labeled-data.csv\n",
+    "│   │       ├── processed-data.csv\n",
+    "│   │       ├── raw-data.csv\n",
+    "│   │       └── segmented-data.csv\n",
+    "│   └── Study-Study002/\n",
+    "│       ├── CT/\n",
+    "│       │   ├── labeled-data.csv\n",
+    "│       │   ├── processed-data.csv\n",
+    "│       │   ├── raw-data.csv\n",
+    "│       │   └── segmented-data.csv\n",
+    "│       └── RTSTRUCT/\n",
+    "│           ├── labeled-data.csv\n",
+    "│           ├── processed-data.csv\n",
+    "│           ├── raw-data.csv\n",
+    "│           └── segmented-data.csv\n",
+    "└── PatientID-PAT003/\n",
+    "    ├── Study-Study001/\n",
+    "    │   ├── CT/\n",
+    "    │   │   ├── labeled-data.csv\n",
+    "    │   │   ├── processed-data.csv\n",
+    "    │   │   ├── raw-data.csv\n",
+    "    │   │   └── segmented-data.csv\n",
+    "    │   └── RTSTRUCT/\n",
+    "    │       ├── labeled-data.csv\n",
+    "    │       ├── processed-data.csv\n",
+    "    │       ├── raw-data.csv\n",
+    "    │       └── segmented-data.csv\n",
+    "    └── Study-Study002/\n",
+    "        ├── CT/\n",
+    "        │   ├── labeled-data.csv\n",
+    "        │   ├── processed-data.csv\n",
+    "        │   ├── raw-data.csv\n",
+    "        │   └── segmented-data.csv\n",
+    "        └── RTSTRUCT/\n",
+    "            ├── labeled-data.csv\n",
+    "            ├── processed-data.csv\n",
+    "            ├── raw-data.csv\n",
+    "            └── segmented-data.csv\n",
+    "\n",
+    "22 directories, 48 files\n",
+    "\n",
+    "\n",
+    "```\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (Pixi)",
+   "language": "python",
+   "name": "pixi-kernel-python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/writer_examples.pdf b/notebooks/writer_examples.pdf
new file mode 100644
index 0000000..b0ec9fc
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diff --git a/pixi.lock b/pixi.lock
index 6dcae5a..8ebebdf 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -54,7 +54,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/d3/c8/529101d7176fe7dfe1d99604e48d69c5dfdcadb4f06561f465c8ef12b4df/multidict-6.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/b9/54/dd730b32ea14ea797530a4479b2ed46a6fb250f682a9cfb997e968bf0261/networkx-3.4.2-py3-none-any.whl
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@@ -1664,7 +1664,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/b9/54/dd730b32ea14ea797530a4479b2ed46a6fb250f682a9cfb997e968bf0261/networkx-3.4.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0f/50/de23fde84e45f5c4fda2488c759b69990fd4512387a8632860f3ac9cd225/numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/8b/95/1f279f406cd97b62a4058188736383bf612d633874be0cca2f97b06de728/orcestra_downloader-0.10.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/60/e6/219bca783de4d7c3b479e21d0a86b1de577154855242ca55d574eea504af/orcestra_downloader-0.11.0-py3-none-any.whl
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       - pypi: https://files.pythonhosted.org/packages/7f/42/6e0f2c2d5c60f499aa29be14f860dd4539de322cd8fb84ee01553493fb4d/pillow-11.0.0-cp312-cp312-manylinux_2_28_x86_64.whl
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@@ -1747,7 +1747,7 @@ environments:
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-      - pypi: https://files.pythonhosted.org/packages/8b/95/1f279f406cd97b62a4058188736383bf612d633874be0cca2f97b06de728/orcestra_downloader-0.10.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/60/e6/219bca783de4d7c3b479e21d0a86b1de577154855242ca55d574eea504af/orcestra_downloader-0.11.0-py3-none-any.whl
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       - pypi: https://files.pythonhosted.org/packages/4f/d5/1caabedd8863526a6cfa44ee7a833bd97f945dc1d56824d6d76e11731939/pillow-11.0.0-cp312-cp312-macosx_11_0_arm64.whl
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@@ -5299,10 +5299,10 @@ packages:
   - pkg:pypi/optype?source=hash-mapping
   size: 123504
   timestamp: 1733329825349
-- pypi: https://files.pythonhosted.org/packages/8b/95/1f279f406cd97b62a4058188736383bf612d633874be0cca2f97b06de728/orcestra_downloader-0.10.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/60/e6/219bca783de4d7c3b479e21d0a86b1de577154855242ca55d574eea504af/orcestra_downloader-0.11.0-py3-none-any.whl
   name: orcestra-downloader
-  version: 0.10.0
-  sha256: 3d6dbc8426d34496bb39ba416498cfaef151f5d8df108551c01f6c61fbc65db4
+  version: 0.11.0
+  sha256: 463a1573b8c4fdf466841ac47b4a2d7dd1158e5f3055223d87c57bfa66b0046e
   requires_dist:
   - aiohttp>=3.11.4
   - click>=8.1.7
@@ -7117,8 +7117,8 @@ packages:
   timestamp: 1728642457661
 - pypi: .
   name: readii
-  version: 1.20.0
-  sha256: 081b822f21841d6330d585a4788daa01ee864f58fb2d70395cfed063961a5a3c
+  version: 1.21.0
+  sha256: 712416b55c52a31c85e7ae84be7842a9ec9df227d3b1de0018aa5d1ff0a15ad4
   requires_dist:
   - simpleitk>=2.3.1
   - matplotlib>=3.9.2,<4
diff --git a/src/readii/io/__init__.py b/src/readii/io/__init__.py
new file mode 100644
index 0000000..2938c56
--- /dev/null
+++ b/src/readii/io/__init__.py
@@ -0,0 +1 @@
+"""Tools for reading and writing data."""
\ No newline at end of file
diff --git a/src/readii/io/utils/__init__.py b/src/readii/io/utils/__init__.py
new file mode 100644
index 0000000..62c805d
--- /dev/null
+++ b/src/readii/io/utils/__init__.py
@@ -0,0 +1,8 @@
+"""Utilities for the io module."""
+
+from .pattern_resolver import PatternResolver, PatternResolverError
+
+__all__ = [
+		"PatternResolver",
+		"PatternResolverError",
+]
\ No newline at end of file
diff --git a/src/readii/io/utils/pattern_resolver.py b/src/readii/io/utils/pattern_resolver.py
new file mode 100644
index 0000000..15d58a2
--- /dev/null
+++ b/src/readii/io/utils/pattern_resolver.py
@@ -0,0 +1,120 @@
+import re
+from dataclasses import dataclass, field
+from typing import Any, ClassVar, Dict, Tuple
+
+from imgtools.dicom.sort.exceptions import InvalidPatternError  # type: ignore
+from imgtools.dicom.sort.parser import PatternParser  # type: ignore
+
+from readii.utils import logger
+
+
+# Define custom exceptions
+class PatternResolverError(Exception):
+	"""Base exception for errors in pattern resolution."""
+
+	pass
+
+@dataclass
+class PatternResolver:
+	r"""Handles parsing and validating filename patterns.
+	
+	By default, this class uses the following pattern parser:
+
+	>>> DEFAULT_PATTERN: re.Pattern = re.compile(r"%(\w+)|\{(\w+)\}")
+
+	This will match placeholders of the form `{key}` or `%(key)s`.
+	
+	Example
+	-------
+	Given a filename format like `"{subject_id}_{date}/{disease}.txt"`, the pattern parser 
+	will extract the following keys:
+
+	>>> pattern_resolver.keys
+	{'subject_id', 'date', 'disease'}
+
+	And the following formatted pattern:
+
+	>>> pattern_resolver.formatted_pattern
+	%(subject_id)s_%(date)s/%(disease)s.txt
+
+	So you could resolve the pattern like this:
+
+	>>> data_dict = {"subject_id": "JohnDoe", "date": "January-01-2025", "disease": "cancer"}
+
+	>>> pattern_resolver.formatted_pattern % data_dict 
+	'JohnDoe_01-01-2025/cancer.txt'
+
+	A more convenient way to resolve the pattern is to use the `resolve` method:	
+	>>> pattern_resolver.resolve(data_dict))
+	'JohnDoe_01-01-2025/cancer.txt'
+	"""
+
+	filename_format: str = field(init=True)
+
+	DEFAULT_PATTERN: ClassVar[re.Pattern] = re.compile(r"%(\w+)|\{(\w+)\}")
+
+	def __init__(self, filename_format: str) -> None:
+		self.filename_format = filename_format
+
+		try:
+			self.pattern_parser = PatternParser(
+				self.filename_format, pattern_parser=self.DEFAULT_PATTERN
+			)
+			self.formatted_pattern, self.keys = self.parse()  # Validate the pattern by parsing it
+		except InvalidPatternError as e:
+			msg = f"Invalid filename format: {e}"
+			raise PatternResolverError(msg) from e
+		else:
+			logger.debug("All keys are valid.", keys=self.keys)
+			logger.debug("Formatted Pattern valid.", formatted_pattern=self.formatted_pattern)
+
+	def parse(self) -> Tuple[str, list[str]]:
+		"""
+		Parse and validate the pattern.
+
+		Returns
+		-------
+		Tuple[str, List[str]]
+			The formatted pattern string and a list of extracted keys.
+
+		Raises
+		------
+		InvalidPatternError
+			If the pattern contains no valid placeholders or is invalid.
+		"""
+		formatted_pattern, keys = self.pattern_parser.parse()
+		return formatted_pattern, keys
+
+	def resolve(self, context: Dict[str, Any]) -> str:
+		"""Resolve the pattern using the provided context dictionary.
+
+		Parameters
+		----------
+		context : Dict[str, Any]
+			Dictionary containing key-value pairs to substitute in the pattern.
+
+		Returns
+		-------
+		str
+			The resolved pattern string with placeholders replaced by values.
+
+		Raises
+		------
+		PatternResolverError
+			If a required key is missing from the context dictionary.
+		"""
+		if None in context.values():
+			msg = "None is not a valid value for a placeholder in the pattern."
+			none_keys = [key for key, value in context.items() if value is None]
+			msg += f" None keys: {none_keys}"
+			raise PatternResolverError(msg)
+
+		try:
+			return self.formatted_pattern % context
+		except KeyError as e:
+			# missing_key = e.args[0]
+			missing_keys = set(context.keys()) - set(self.keys)
+			msg = f"Missing value for placeholder(s): {missing_keys}"
+			msg += "\nPlease provide a value for this key in the `context` argument."
+			msg += f" i.e `{self.__class__.__name__}.save(..., {e.args[0]}=value)`."
+			raise PatternResolverError(msg) from e
\ No newline at end of file
diff --git a/src/readii/io/writers/README.md b/src/readii/io/writers/README.md
new file mode 100644
index 0000000..703b24e
--- /dev/null
+++ b/src/readii/io/writers/README.md
@@ -0,0 +1,112 @@
+# Understanding How the Writer Works
+
+The Writer system is designed to provide a flexible, reusable, and customizable way to handle file
+writing. Here's how it works at a **base level** and how it can be **extended** with subclasses.
+
+---
+
+## **1. Base Level (BaseWriter)**
+
+The `BaseWriter` is an **abstract base class (ABC)** that defines the core logic and structure for
+writing files. It cannot be used directly but provides a foundation that subclasses can build upon.
+
+### Key Components
+
+1. **Root Directory**:
+   - You must specify a `root_directory` where the files will be saved.
+   - If the directory doesn’t exist and `create_dirs` is `True`, it will be automatically created.
+
+2. **Filename Format**:
+   - You define a `filename_format` that specifies how the file names should be structured.
+   - The format can include placeholders like `{SubjectID}`, `{date}`, or any custom keys.
+      - Format of placeholders is `{key}` or `%key` which allows for both python code and CLI usage.
+   - These placeholders are replaced with actual values provided when calling the `save()` method (actual values passed in as keyword arguments(`**kwargs`)).
+
+     ```python
+       # Example filename_format
+       filename_format = "Patient_{SubjectID}_{date}.txt"
+     ```
+
+3. **Pattern Resolution**:
+   - The `BaseWriter` uses a `PatternResolver`, inherited from `Med-ImageTools` to validate and parse the `filename_format`.
+   - It ensures all placeholders are valid and logs errors if any are missing during file creation.
+
+4. **Core Methods**:
+   - `resolve_path(**kwargs)`: Generates the file path by replacing placeholders in the
+     `filename_format`.
+   - `save(*args, **kwargs)`: Abstract method. Subclasses implement the logic for writing files.
+
+     ```python
+       # Example resolve_path usage for an ImplementedWriter subclass
+       writer = ImplementedWriter(
+           root_directory="output",
+           filename_format="{SubjectID}_data_{date}.txt"
+       )
+       file_path = writer.resolve_path(SubjectID="JohnDoe", date="2024-01-01")
+       print(file_path)
+       # Output: output/JohnDoe_data_2024-01-01.txt
+     ```
+
+5. **Context Management**:
+   - `BaseWriter` can be used as a context manager for setup and teardown logic.
+   - Automatically cleans up empty directories created during file operations.
+
+     ```python
+       with writer:
+           writer.save(...)
+     ```
+
+---
+
+## **2. Subclass Level**
+
+Subclasses of `BaseWriter` provide the actual file writing logic. Each subclass must implement the
+`save()` method to define how files of a specific type are written.
+
+### Subclass Responsibilities
+
+1. **Implement the `save()` Method**:
+   - This method takes in data (e.g., text, images, or other file types) and writes it to disk using
+     the path generated by `resolve_path()`.
+
+     ```python
+       class TextWriter(BaseWriter):
+           def save(self, content: str, **kwargs: Any) -> Path:
+               output_path = self.resolve_path(**kwargs)
+               with output_path.open("w") as file:
+                   file.write(content)
+               return output_path
+     ```
+
+2. **Handle File-Specific Logic**:
+   - Each subclass can validate its data or handle specific requirements, such as compression or
+     formatting.
+
+     ```python
+       class NIFTIWriter(BaseWriter):
+           def save(self, image: sitk.Image, **kwargs: Any) -> Path:
+               output_path = self.resolve_path(**kwargs)
+               sitk.WriteImage(image, str(output_path), useCompression=True)
+               return output_path
+     ```
+
+3. **Use Class-Level Validation**:
+   - Subclasses can define their own validation for file extensions, required placeholders, etc.
+
+---
+
+## **Summary**
+
+1. **BaseWriter**:
+   - Defines the core functionality for handling directories, generating paths, and managing
+     resources.
+   - Requires `save()` to be implemented by subclasses.
+
+2. **PatternResolver**:
+   - Validates and parses filename formats.
+
+3. **Subclasses**:
+   - Provide specific file writing logic (e.g., text files, NIFTI images).
+   - Implement validation, compression, or other requirements.
+
+By extending `BaseWriter`, you can create flexible and reusable file writers for any type of data.
diff --git a/src/readii/io/writers/__init__.py b/src/readii/io/writers/__init__.py
new file mode 100644
index 0000000..9bb3553
--- /dev/null
+++ b/src/readii/io/writers/__init__.py
@@ -0,0 +1 @@
+"""Tools for writing data."""
diff --git a/src/readii/io/writers/base_writer.py b/src/readii/io/writers/base_writer.py
new file mode 100644
index 0000000..411d54e
--- /dev/null
+++ b/src/readii/io/writers/base_writer.py
@@ -0,0 +1,101 @@
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from datetime import datetime, timezone
+from pathlib import Path
+from types import TracebackType
+from typing import Any, Optional
+
+from readii.io.utils import PatternResolver
+from readii.utils import logger
+
+
+@dataclass
+class BaseWriter(ABC):
+	"""Abstract base class for managing file writing with customizable paths and filenames."""
+
+	# Any subclass has to be initialized with a root directory and a filename format
+	root_directory: Path
+	filename_format: str
+
+	# optionally, you can set create_dirs to False if you want to handle the directory creation yourself
+	create_dirs: bool = field(default=True)
+
+	# class-level pattern resolver instance shared across all instances
+	pattern_resolver: PatternResolver = field(init=False)
+
+	def __post_init__(self) -> None:
+		"""Initialize the writer with the given root directory and filename format."""
+		self.root_directory = Path(self.root_directory)
+		if self.create_dirs:
+			self.root_directory.mkdir(parents=True, exist_ok=True)
+		elif not self.root_directory.exists():
+			msg = f"Root directory {self.root_directory} does not exist."
+			raise FileNotFoundError(msg)
+		self.pattern_resolver = PatternResolver(self.filename_format)
+
+	@abstractmethod
+	def save(self, *args: Any, **kwargs: Any) -> Path:  # noqa
+		"""Abstract method for writing data. Must be implemented by subclasses."""
+		pass
+
+	def _generate_datetime_strings(self) -> dict[str, str]:
+		now = datetime.now(timezone.utc)
+		return {
+			"date": now.strftime("%Y-%m-%d"),
+			"time": now.strftime("%H%M%S"),
+			"date_time": now.strftime("%Y-%m-%d_%H%M%S"),
+		}
+
+	def resolve_path(self, **kwargs: Any) -> Path:  # noqa
+		"""Generate a file path based on the filename format, subject ID, and additional parameters."""
+		context = {**self._generate_datetime_strings(), **kwargs}
+		filename = self.pattern_resolver.resolve(context)
+		out_path = self.root_directory / filename
+		if self.create_dirs:
+			out_path.parent.mkdir(parents=True, exist_ok=True)
+		return out_path
+
+	# Context Manager Implementation
+	def __enter__(self) -> "BaseWriter":
+		"""
+		Enter the runtime context related to this writer.
+
+		Useful if the writer needs to perform setup actions, such as
+		opening connections or preparing resources.
+		"""
+		logger.debug(f"Entering context manager for {self.__class__.__name__}")
+		return self
+
+	def __exit__(
+		self: "BaseWriter",
+		exc_type: Optional[type],
+		exc_value: Optional[BaseException],
+		traceback: Optional[TracebackType],
+	) -> None:
+		"""
+		Exit the runtime context related to this writer.
+
+		Parameters
+		----------
+		exc_type : Optional[type]
+				The exception type, if an exception was raised, otherwise None.
+		exc_value : Optional[BaseException]
+				The exception instance, if an exception was raised, otherwise None.
+		traceback : Optional[Any]
+				The traceback object, if an exception was raised, otherwise None.
+		"""
+		if exc_type:
+			logger.exception(
+				f"Exception raised in {self.__class__.__name__} while in context manager.",
+				exc_info=exc_value,
+			)
+		logger.debug(f"Exiting context manager for {self.__class__.__name__}")
+
+		# if the root directory is empty, aka we created it but didn't write anything, delete it
+		if (
+			self.create_dirs
+			and self.root_directory.exists()
+			and not any(self.root_directory.iterdir())
+		):
+			logger.debug(f"Deleting empty directory {self.root_directory}")
+			self.root_directory.rmdir()  # remove the directory if it's empty
diff --git a/src/readii/io/writers/nifti_writer.py b/src/readii/io/writers/nifti_writer.py
new file mode 100644
index 0000000..52f0130
--- /dev/null
+++ b/src/readii/io/writers/nifti_writer.py
@@ -0,0 +1,134 @@
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import ClassVar
+
+import numpy as np
+import SimpleITK as sitk
+
+from readii.io.writers.base_writer import BaseWriter
+from readii.utils import logger
+
+
+class NiftiWriterError(Exception):
+	"""Base exception for NiftiWriter errors."""
+
+	pass
+
+
+class NiftiWriterValidationError(NiftiWriterError):
+	"""Raised when validation of writer configuration fails."""
+
+	pass
+
+
+class NiftiWriterIOError(NiftiWriterError):
+	"""Raised when I/O operations fail."""
+
+	pass
+
+
+@dataclass
+class NIFTIWriter(BaseWriter):
+	"""Class for managing file writing with customizable paths and filenames for NIFTI files."""
+
+	compression_level: int = field(
+		default=9,
+		metadata={
+			"help": "Compression level (0-9). Higher values mean better compression but slower writing."
+		},
+	)
+	overwrite: bool = field(
+		default=False,
+		metadata={
+			"help": "If True, allows overwriting existing files. If False, raises FileExistsError."
+		},
+	)
+
+	# Make extensions immutable
+	VALID_EXTENSIONS: ClassVar[list[str]] = [
+		".nii",
+		".nii.gz",
+	]
+	MAX_COMPRESSION_LEVEL: ClassVar[int] = 9
+	MIN_COMPRESSION_LEVEL: ClassVar[int] = 0
+
+	def __post_init__(self) -> None:
+		"""Validate writer configuration."""
+		super().__post_init__()
+
+		if not self.MIN_COMPRESSION_LEVEL <= self.compression_level <= self.MAX_COMPRESSION_LEVEL:
+			msg = f"Invalid compression level {self.compression_level}. Must be between {self.MIN_COMPRESSION_LEVEL} and {self.MAX_COMPRESSION_LEVEL}."
+			raise NiftiWriterValidationError(msg)
+
+		if not any(self.filename_format.endswith(ext) for ext in self.VALID_EXTENSIONS):
+			msg = f"Invalid filename format {self.filename_format}. Must end with one of {self.VALID_EXTENSIONS}."
+			raise NiftiWriterValidationError(msg)
+
+	def save(self, image: sitk.Image | np.ndarray, PatientID: str, **kwargs: str | int) -> Path:
+		"""Write the SimpleITK image to a NIFTI file.
+
+		Parameters
+		----------
+		image : sitk.Image | np.ndarray
+			The SimpleITK image to save
+		PatientID : str
+			Required patient identifier
+		**kwargs : str | int
+			Additional formatting parameters for the output path
+
+		Returns
+		-------
+		Path
+			Path to the saved file
+
+		Raises
+		------
+		NiftiWriterIOError
+			If file exists and overwrite=False or if writing fails
+		NiftiWriterValidationError
+			If image is invalid
+		"""
+		match image:
+			case sitk.Image():
+				pass
+			case np.ndarray():
+				image = sitk.GetImageFromArray(image)
+			case _:
+				msg = "Input must be a SimpleITK Image or a numpy array"
+				raise NiftiWriterValidationError(msg)
+
+		logger.debug("Saving.", kwargs=kwargs)
+
+		out_path = self.resolve_path(PatientID=PatientID, **kwargs)
+		if out_path.exists():
+			if not self.overwrite:
+				msg = f"File {out_path} already exists. \nSet {self.__class__.__name__}.overwrite to True to overwrite."
+				raise NiftiWriterIOError(msg)
+			else:
+				logger.warning(f"File {out_path} already exists. Overwriting.")
+
+		logger.debug("Writing image to file", out_path=out_path)
+		try:
+			sitk.WriteImage(
+				image, str(out_path), useCompression=True, compressionLevel=self.compression_level
+			)
+		except Exception as e:
+			msg = f"Error writing image to file {out_path}: {e}"
+			raise NiftiWriterIOError(msg) from e
+		else:
+			logger.info("Image saved successfully.", out_path=out_path)
+			return out_path
+
+
+if __name__ == "__main__": # pragma: no cover
+	from rich import print  # noqa
+
+	nifti_writer = NIFTIWriter(
+		root_directory=Path("TRASH", "nifti_writer_examples"),
+		filename_format="{NegativeControl}_{Region}/{SubjectID}_{Modality}.nii.gz",
+		compression_level=9,
+		overwrite=False,
+		create_dirs=True,
+	)
+
+	print(nifti_writer)
diff --git a/tests/io/test_base_writer.py b/tests/io/test_base_writer.py
new file mode 100644
index 0000000..e3bf1f8
--- /dev/null
+++ b/tests/io/test_base_writer.py
@@ -0,0 +1,81 @@
+
+import os
+import pytest
+from pathlib import Path
+from readii.io.writers.base_writer import BaseWriter # type: ignore
+
+class SimpleWriter(BaseWriter):
+    def save(self, content: str) -> Path:
+        file_path = self.resolve_path()
+        with open(file_path, 'w') as f:
+            f.write(content)
+        return file_path
+
+class MediumWriter(BaseWriter):
+    def save(self, content: str, suffix: str = '') -> Path:
+        file_path = self.resolve_path(suffix=suffix)
+        with open(file_path, 'w') as f:
+            f.write(content)
+        return file_path
+
+class ComplexWriter(BaseWriter):
+    def save(self, content: str, metadata: dict) -> Path:
+        file_path = self.resolve_path(**metadata)
+        with open(file_path, 'w') as f:
+            f.write(content)
+        return file_path
+
+@pytest.fixture
+def temp_dir(tmp_path):
+    return tmp_path
+
+def test_simple_writer(temp_dir):
+    writer = SimpleWriter(root_directory=temp_dir, filename_format="{date_time}.txt")
+    with writer:
+        file_path = writer.save("Simple content")
+    assert file_path.exists()
+    assert file_path.read_text() == "Simple content"
+
+def test_medium_writer(temp_dir):
+    writer = MediumWriter(root_directory=temp_dir, filename_format="{date_time}_{suffix}.txt")
+    with writer:
+        file_path = writer.save("Medium content", suffix="test")
+    assert file_path.exists()
+    assert file_path.read_text() == "Medium content"
+
+def test_complex_writer(temp_dir):
+    writer = ComplexWriter(root_directory=temp_dir, filename_format="{date_time}_{user}.txt")
+    with writer:
+        file_path = writer.save("Complex content", metadata={"user": "testuser"})
+    assert file_path.exists()
+    assert file_path.read_text() == "Complex content"
+
+def test_context_manager_cleanup(temp_dir):
+    subdir = temp_dir / "nested"
+    writer = SimpleWriter(root_directory=subdir, filename_format="{date_time}.txt")
+    with writer:
+        assert subdir.exists()
+    assert not subdir.exists()
+
+def test_directory_creation(temp_dir):
+    writer = SimpleWriter(root_directory=temp_dir / "nested", filename_format="{date_time}.txt")
+    with writer:
+        file_path = writer.save("Content")
+    assert file_path.exists()
+    assert file_path.read_text() == "Content"
+    assert (temp_dir / "nested").exists()
+
+def test_directory_not_created_if_exists(temp_dir):
+    existing_dir = temp_dir / "existing"
+    existing_dir.mkdir()
+    writer = SimpleWriter(root_directory=existing_dir, filename_format="{date_time}.txt")
+    with writer:
+        file_path = writer.save("Content")
+    assert file_path.exists()
+    assert file_path.read_text() == "Content"
+    assert existing_dir.exists()
+
+def test_no_create_dirs_non_existent(temp_dir):
+    with pytest.raises(FileNotFoundError):
+        with SimpleWriter(root_directory=temp_dir / "nested_non_existent", filename_format="{date_time}.txt", create_dirs=False) as writer:
+            file_path = writer.save("Content")
diff --git a/tests/io/test_nifti_writer.py b/tests/io/test_nifti_writer.py
new file mode 100644
index 0000000..70eae1b
--- /dev/null
+++ b/tests/io/test_nifti_writer.py
@@ -0,0 +1,73 @@
+import pytest
+import SimpleITK as sitk
+import numpy as np
+from pathlib import Path
+from readii.io.writers.nifti_writer import NIFTIWriter, NiftiWriterValidationError, NiftiWriterIOError # type: ignore
+
+@pytest.fixture
+def sample_image():
+    """Fixture for creating a sample SimpleITK image."""
+    image = sitk.Image(10, 10, sitk.sitkUInt8)
+    return image
+
+@pytest.fixture
+def sample_array():
+    """Fixture for creating a sample numpy array."""
+    array = np.zeros((10, 10), dtype=np.uint8)
+    return array
+
+@pytest.fixture
+def nifti_writer(tmp_path):
+    """Fixture for creating a NIFTIWriter instance."""
+    return NIFTIWriter(
+        root_directory=tmp_path,
+        filename_format="{PatientID}.nii.gz",
+        compression_level=5,
+        overwrite=False,
+        create_dirs=True,
+    )
+
+@pytest.mark.parametrize("image", ["not_an_image", 12345])
+def test_save_invalid_image(nifti_writer, image):
+    """Test saving an invalid image."""
+    with pytest.raises(NiftiWriterValidationError):
+        nifti_writer.save(image=image, PatientID="12345")
+
+@pytest.mark.parametrize("image", ["sample_image", "sample_array"])
+def test_save_valid_image(nifti_writer, request, image):
+    """Test saving a valid image."""
+    image = request.getfixturevalue(image)
+    out_path = nifti_writer.save(image=image, PatientID="12345")
+    assert out_path.exists()
+
+def test_save_existing_file_without_overwrite(nifti_writer, sample_image):
+    """Test saving when file already exists and overwrite is False."""
+    nifti_writer.save(sample_image, PatientID="12345")
+    with pytest.raises(NiftiWriterIOError):
+        nifti_writer.save(sample_image, PatientID="12345")
+
+def test_save_existing_file_with_overwrite(nifti_writer, sample_image):
+    """Test saving when file already exists and overwrite is True."""
+    nifti_writer.overwrite = True
+    nifti_writer.save(sample_image, PatientID="12345")
+    assert nifti_writer.save(sample_image, PatientID="12345").exists()
+
+@pytest.mark.parametrize("compression_level", [0, 5, 9])
+def test_save_with_different_compression_levels(nifti_writer, sample_image, compression_level):
+    """Test saving with different compression levels."""
+    nifti_writer.compression_level = compression_level
+    out_path = nifti_writer.save(sample_image, PatientID="12345")
+    assert out_path.exists()
+
+@pytest.mark.parametrize("filename_format", ["{PatientID}.nii", "{PatientID}.nii.gz"])
+def test_save_with_different_filename_formats(nifti_writer, sample_image, filename_format):
+    """Test saving with different filename formats."""
+    nifti_writer.filename_format = filename_format
+    out_path = nifti_writer.save(sample_image, PatientID="12345")
+    assert out_path.exists()
+
+@pytest.mark.parametrize("key,value", [("Modality", "T1"), ("Region", "Brain")])
+def test_save_with_additional_keys(nifti_writer, sample_image, key, value):
+    """Test saving with additional keys."""
+    out_path = nifti_writer.save(sample_image, PatientID="12345", **{key: value})
+    assert out_path.exists()
diff --git a/tests/io/test_pattern_resolver.py b/tests/io/test_pattern_resolver.py
new file mode 100644
index 0000000..f77da6d
--- /dev/null
+++ b/tests/io/test_pattern_resolver.py
@@ -0,0 +1,23 @@
+import pytest
+from readii.io.utils import PatternResolver, PatternResolverError # type: ignore
+
+@pytest.mark.parametrize("pattern, context, expected", [
+  ("{subject_id}_{date}/{disease}.txt", {"subject_id": "JohnDoe", "date": "2025-01-01", "disease": "cancer"}, "JohnDoe_2025-01-01/cancer.txt"),
+  ("{subject_id}_{date}/{disease}.txt", {"subject_id": "JohnDoe", "date": "2025-01-01"}, PatternResolverError),
+  ("{subject_id}_{date}/{disease.txt", {}, PatternResolverError),
+  # New complex test cases
+  ("{subject_id}_{date}/{disease}/{sample_id}.txt", {"subject_id": "JaneDoe", "date": "2025-01-01", "disease": "flu", "sample_id": "S123"}, "JaneDoe_2025-01-01/flu/S123.txt"),
+  ("{subject_id}_{date}/{disease}/{sample_id}.txt", {"subject_id": "JaneDoe", "date": "2025-01-01", "disease": "flu"}, PatternResolverError),
+  ("{subject_id}_{date}/{disease}/{sample_id}.txt", {"subject_id": "JaneDoe", "date": "2025-01-01", "disease": "flu", "sample_id": ""}, "JaneDoe_2025-01-01/flu/.txt"),
+  ("{subject_id}_{date}/{disease}/{sample_id}.txt", {"subject_id": "JaneDoe", "date": "2025-01-01", "disease": "flu", "sample_id": None}, PatternResolverError),
+  ("{subject_id}_{date}/{disease}/{sample_id}.txt", {"subject_id": "JaneDoe", "date": "2025-01-01", "disease": "flu", "sample_id": "S123", "extra_key": "extra_value"}, "JaneDoe_2025-01-01/flu/S123.txt"),
+])
+def test_resolve(pattern, context, expected):
+  if isinstance(expected, type) and issubclass(expected, Exception):
+    with pytest.raises(expected):
+      resolver = PatternResolver(pattern)
+      resolver.resolve(context)
+  else:
+    resolver = PatternResolver(pattern)
+    result = resolver.resolve(context)
+    assert result == expected