Merged in the wrong branch earlier for QA (#67)

* serving from across the host file system
* comparison works for sure
* scan niivue preview added to full report
* update avg and warp to occur during main pipeline
* generating svg's for comparison w/ good ole nipype
* renamed svg outputs
* rotating heads are back
* add entrypoint for qa reports
* standardize commands
* refactored from defaced dir to bids dir to make qa usage more clear
* clean up toml and fix import
* Add missing --use_template_anat argument to fix AttributeError
* add badge to readme

Author: bendhouseart

README.md

@@ -12,6 +12,7 @@ This software can be installed via source or via pip from PyPi with `pip install
 
 | CI  | Status |   
 |---------| ------ |
+| `Run on test data` | [![Run on test data](https://github.com/openneuropet/petdeface/actions/workflows/run_on_test_data.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/run_on_test_data.yaml) |
 | `docker build . -t petdeface` | ![docker_build](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiYzdXV0tYSkQzTVNkcG04cHA2S055UXlKRlZTU1VONThUMVRoZVcwU3l1aHFhdVBlNDNaRGVCYzdWM1Q0WjYzQ1lRU2ZTSHpmSERPWFRkVXVyb3k3RTZBPSIsIml2UGFyYW1ldGVyU3BlYyI6IjRCZFFIQnNGT2lKcDA1VG4iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
 | `docker push` | ![docker push icon](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoia0c1bEJYUGI2SXlWYi9JMm1tcGtiYWVTdVd3bmlnOUFaTjN4QjJITU5PTVpvQnN3TlowajhxNmhHY2RwQ2Z5SU93OExqc2xvMzFnTHFvajlqVk1MV2FzPSIsIml2UGFyYW1ldGVyU3BlYyI6Ikl6SzRyc1RabzBnSkplTjciLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
 | `Python 3.14 >= 3.10` | [![Check Python Compatibility](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml) |

petdeface/petdeface.py

@@ -1371,6 +1371,14 @@ def cli():
         required=False,
         default=[],
     )
+    parser.add_argument(
+        "--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,
+        choices=["t1", "mni", "pet"],
+        required=False,
+        default=None,
+    )
     parser.add_argument(
         "--open-browser",
         "--open_browser",