Merge pull request #1059 from bpinsard/fix/dwi_sbref

fix(bids-config): Add dwi root sbref, missing dwi entities to path patterns
bids-standard · May 5, 2024 · ac3a896 · ac3a896
2 parents 6aaa5f2 + e803cbd
commit ac3a896
Showing 1 changed file with 8 additions and 6 deletions.
diff --git a/bids/layout/config/bids.json b/bids/layout/config/bids.json
@@ -119,7 +119,8 @@
         "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_chunk-<index>]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_chunk-<index>]_{suffix<sbref>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{suffix<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{suffix<epi|m0scan>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func|meg|beh>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",
@@ -128,7 +129,7 @@
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<channels>}{extension<.tsv|.json>|.tsv}",
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<coordsystem>}{extension<.json>|.json}",
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<headshape>}{extension<.pos>|.pos}",
-        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_acq-{acquisition<calibration|crosstalk>}_{suffix<meg>|meg}{extension<.fif|.dat>}",    
+        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_acq-{acquisition<calibration|crosstalk>}_{suffix<meg>|meg}{extension<.fif|.dat>}",
         "sub-{subject}[/ses-{session}]/{datatype<motion>|motion}/sub-{subject}[_ses-{session}]_task-{task}_tracksys-{tracksys}[_acq-{acquisition}][_run-{run}]_{suffix<motion|channels>|motion}{extension<.tsv|.json>|.tsv}",
         "sub-{subject}[/ses-{session}]/{datatype<eeg>|eeg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<eeg>}{extension<.edf|.vhdr|.vmrk|.eeg|.set|.fdt|.bdf|.json>}",
         "sub-{subject}[/ses-{session}]/{datatype<nirs>|nirs}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<nirs>}{extension<.snirf|.json>}",
@@ -159,17 +160,18 @@
         "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<pet>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_recording-{recording}_{suffix<blood>}{extension<.tsv|.json>}",
         "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}]_task-{task}[_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}{extension<.tsv|.json>}",
-        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>}",      
+        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>}",
         "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<asl|m0scan>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<aslcontext>}{extension<.tsv|.json>}",
         "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_run-{run}]_{suffix<asllabeling>}{extension<.jpg>}",
-        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_recording{recording}]_{suffix<physio|stim>}{extension<.tsv|.json>}",  
+        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_recording{recording}]_{suffix<physio|stim>}{extension<.tsv|.json>}",
         "[task-{task}_][acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_][part-{part}_][chunk-{chunk}_]{suffix<T1w|T2w|T2star|T2starw|FLAIR|FLASH|PD|PDw|PDT2|inplaneT[12]|angio>}{extension<.json>|.json}",
         "[task-{task}_][acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][run-{run}_][mod-{modality}_]{suffix<defacemask>}{extension<.json>|.json}",
         "task-{task}[_acq-{acquisition}][_run-{run}]_{suffix<nirs>}{extension<.json>}",
         "task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}{extension<.json>|.json}",
         "task-{task}_tracksys-{tracksys}[acq-{acquisition}_][run-{run}_]{suffix<motion>}{extension<.tsv|.json>}",
-        "[acq-{acquisition}_]{suffix<dwi>}{extension<.json>|.json}",
+        "[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_][part-{part}_][chunk-<index>_]{suffix<dwi>}{extension<.bval|.bvec|.json>|.json}",
+        "[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_][part-{part}_][chunk-<index>_]{suffix<sbref>}{extension<.json>|.json}",
         "[acq-{acquisition}_][dir-{direction}_][run-{run}_]{suffix<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
         "[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{suffix<epi|m0scan>}{extension<.json>|.json}",
         "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.json>|.json}",
@@ -185,7 +187,7 @@
         "[task-{task}_][trc-{tracer}_][rec-{reconstruction}_][run-{run}_]{suffix<pet>}{extension<.json>|.json}",
         "[task-{task}_][trc-{tracer}_][rec-{reconstruction}_][run-{run}_]recording-{recording}_{suffix<blood>}{extension<.json>|.json}",
         "task-{task}[_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}{extension<.json>|.json}",
-        "[task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>|.json}",      
+        "[task-{task}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>|.json}",
         "[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_]{suffix<asl|m0scan>}{extension<.json>|.json}",
         "[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_]{suffix<aslcontext>}{extension<.json>|.json}",
         "[acq-{acquisition}_][rec-{reconstruction}_][dir-{direction}_][run-{run}_][recording-{recording}_]{suffix<physio|stim>}{extension<.json>|.json}"