Merge pull request #331 from Australian-Imaging-Service/t1w-preproc

added t1w preprocess pipeline

.github/workflows/release.yml

@@ -59,6 +59,7 @@ jobs:
       env:
         PUSH: "${{ steps.deployable.outputs.PUSH }}"
       run: >
-        pydra2app make xnat ./australian-imaging-service
-        --registry ghcr.io --check-registry --clean-up --tag-latest --loglevel info 
-        --release pipelines-metapackage $RELEASE $PUSH
+        pipeline2app make xnat ./specs/australian-imaging-service/mri/human/neuro/t1w/preprocess.yaml
+        --registry ghcr.io --check-registry --clean-up --loglevel info 
+        --resources-dir ./resources --spec-root ./specs --source-package . $PUSH
+      # --release pipelines-metapackage $RELEASE --tag-latest 

.gitignore

@@ -12,3 +12,4 @@ __pycache__
 test-data
 *.build*
 *.venv
+_version.py

AUTHORS

@@ -2,3 +2,5 @@ Australian Imaging Service Analysis pipelines were developed by
 
 Thomas G. Close (Sydney Imaging, The University of Sydney, Sydney, Australia
                  & Australian National Imaging Facility, Australia)
+Arkiev D'Souza (Sydney Imaging, The University of Sydney, Sydney, Australia
+                 & Australian National Imaging Facility, Australia)                 

README.rst → README.md

@@ -1,5 +1,4 @@
-AIS Analysis Pipelines
-======================
+# AIS Analysis Pipelines
 
 AIS Analysis pipelines is a collection of scripts for generating containerised
 pipelines that can be run by the XNAT Container Service plugin.
@@ -8,6 +7,3 @@ pipelines that can be run by the XNAT Container Service plugin.
 This work is licensed under a
 `Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License <http://creativecommons.org/licenses/by-nc-sa/4.0/>`_
 
-.. image:: https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png
-  :target: http://creativecommons.org/licenses/by-nc-sa/4.0/
-  :alt: Creative Commons License: Attribution-NonCommercial-ShareAlike 4.0 International

conftest.py

@@ -5,7 +5,7 @@
 import typing as ty
 from datetime import datetime
 from dataclasses import dataclass
-from arcana.core.utils.misc import varname2path
+from frametree.core.utils import varname2path
 import pytest
 from click.testing import CliRunner
 import xnat4tests
@@ -57,11 +57,19 @@ class BidsAppTestBlueprint:
 
 
 BIDS_APP_PARAMETERS = {
-    'fmriprep': {'json_edits': "func/.*bold \".SliceTiming[] /= 1000.0\""},
-    'qsiprep': {'qsiprep_flags': '--output-resolution 2.5'}}
-
-
-bids_apps_dir = Path(__file__).parent / "australianimagingservice" / "mri" / "human" / "neuro" / "bidsapps"
+    "fmriprep": {"json_edits": 'func/.*bold ".SliceTiming[] /= 1000.0"'},
+    "qsiprep": {"qsiprep_flags": "--output-resolution 2.5"},
+}
+
+
+bids_apps_dir = (
+    Path(__file__).parent
+    / "australianimagingservice"
+    / "mri"
+    / "human"
+    / "neuro"
+    / "bidsapps"
+)
 test_bids_data_dir = (
     Path(__file__).parent / "tests" / "data" / "mri" / "human" / "neuro" / "bidsapps"
 )
@@ -160,4 +168,4 @@ def upload_test_dataset_to_xnat(project_id: str, source_data_dir: Path, xnat_con
                 xresource.upload_dir(resource_path, method="tar_file")
 
         # Populate metadata from DICOM headers
-        login.put(f'/data/experiments/{xsession.id}?pullDataFromHeaders=true')
+        login.put(f"/data/experiments/{xsession.id}?pullDataFromHeaders=true")