Make the dcm2niix suffix fallback optional (pull request #214)

Donders-Institute · Jan 15, 2024 · 2c9cc06 · 2c9cc06
1 parent efcd7ac
commit 2c9cc06
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diff --git a/bidscoin/bidseditor.py b/bidscoin/bidseditor.py
@@ -71,7 +71,9 @@
 
 meta: The file extensions of the associated / equally named (meta)data sourcefiles that are copied over as
     BIDS (sidecar) files, such as ['.json', '.tsv', '.tsv.gz']. You can use this to enrich json sidecar files,
-    or add data that is not supported by this plugin"""
+    or add data that is not supported by this plugin
+
+fallback: Appends unhandled dcm2niix suffixes to the `acq` label if 'y' (recommended, else the suffix data is discarded)"""
 
 
 class MainWindow(QMainWindow):

diff --git a/tests/test_data/bidsmap.yaml b/tests/test_data/bidsmap.yaml
@@ -33,17 +33,13 @@ Options:
       args: -b y -z y -i n -l n     # Argument string that is passed to dcm2niix. Tip: SPM users may want to use '-z n' (which produces unzipped nifti's, see dcm2niix -h for more information)
       anon: y                       # Set this anonymization flag to 'y' to round off age and discard acquisition date from the meta data
       meta: [.json, .tsv, .tsv.gz]  # The file extensions of the equally named metadata sourcefiles that are copied over to the BIDS sidecar files
+      fallback: y                   # Appends unhandled dcm2niix suffixes to the `acq` label if 'y' (recommended, else the suffix data is discarded)
     spec2nii2bids:                  # The settings for the spec2nii2bids plugin
       command: spec2nii             # Command to run spec2nii, e.g. "module add spec2nii; spec2nii" or "PATH=/opt/spec2nii/bin:$PATH; spec2nii" or /opt/spec2nii/bin/spec2nii or 'C:\"Program Files"\spec2nii\spec2nii.exe' (note the quotes to deal with the whitespace)
       args:                         # Argument string that is passed to spec2nii (see spec2nii -h for more information)
       anon: y                       # Set this anonymization flag to 'y' to round off age and discard acquisition date from the meta data
       meta: [.json, .tsv, .tsv.gz]  # The file extensions of the equally named metadata sourcefiles that are copied over to the BIDS sidecar files
       multiraid: 2                  # The mapVBVD argument for selecting the multiraid Twix file to load (default = 2, i.e. 2nd file)
-    dcm2niix4petbids:
-      command: dcm2niix4pet
-      args:
-      anon:
-      meta: [.json, .tsv]
 
 
 DICOM: