Add AtlasPack atlases (#330)

* Add AtlasPack and write out top-level files. * Update expected outputs. * Feed in source_file. * Add the right atlas files. * Fix the atlas names again. * Document the outputs. * Fix the boilerplate and description. * Update base image version. * Use atlas as its own source file. * Add function to extract entities. * Fix connection. * Update cbf.py * Update cbf.py * Whoops. * Update gecbf.py * Fix outputs. * Don't expect dataset description. * Log the thing. * Update bids.py * Revert. * Document the differences between sets of atlases.
PennLINC · Oct 10, 2023 · 629a4dd · 629a4dd
1 parent 55c378a
commit 629a4dd
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diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM pennlinc/aslprep_build:0.0.2
+FROM pennlinc/aslprep_build:0.0.3
 
 # Install aslprep
 COPY . /src/aslprep

diff --git a/aslprep/cli/run.py b/aslprep/cli/run.py
@@ -147,7 +147,8 @@ def main():
             packagename="aslprep",
         )
         write_derivative_description(
-            config.execution.bids_dir, config.execution.output_dir / "aslprep"
+            config.execution.bids_dir,
+            config.execution.output_dir / "aslprep",
         )
 
         if failed_reports and not config.execution.notrack:

diff --git a/...a/atlases/atlas-ciftiSubcortical_dseg.tsv → aslprep/data/atlases/atlas-HCP_dseg.tsv b/...a/atlases/atlas-ciftiSubcortical_dseg.tsv → aslprep/data/atlases/atlas-HCP_dseg.tsv
diff --git a/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-1000Parcels17Networks_dseg.tsv b/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-1000Parcels17Networks_dseg.tsv
diff --git a/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-100Parcels17Networks_dseg.tsv b/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-100Parcels17Networks_dseg.tsv
diff --git a/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-200Parcels17Networks_dseg.tsv b/aslprep/data/atlases/atlas-Schaefer2018v0143_desc-200Parcels17Networks_dseg.tsv