From feaecc99b6785cf5349f590c9a6f403158466ee2 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Jan 2026 14:02:48 -0500 Subject: [PATCH 1/6] add seg entity --- niworkflows/data/nipreps.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index 56b86770e5a..d27f1856d3e 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -161,6 +161,10 @@ { "name": "hash", "pattern": "hash-([a-zA-Z0-9+]+)" + }, + { + "name": "segmentation", + "pattern": "[_/\\\\]+seg-([a-zA-Z0-9+]+)" } ], "default_path_patterns": [ @@ -199,7 +203,7 @@ "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dscalar.nii|.json>}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_pvc-{pvc}][_desc-{desc}]_{suffix|timeseries}{extension<.json|.tsv>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_pvc-{pvc}][_seg-{segmentation}][_desc-{desc}]_{suffix|timeseries}{extension<.json|.tsv>|.tsv}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi}][_pvc-{pvc}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_res-{resolution}]_desc-{desc}_{suffix}{extension<.tsv|.json>|.tsv}", "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", From 5be67f3f489c3ee3435801876fb578c08bbc0a38 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 29 Jan 2026 15:50:44 -0500 Subject: [PATCH 2/6] update nipreps.json --- niworkflows/data/nipreps.json | 94 +++++++++++++++-------------------- 1 file changed, 41 insertions(+), 53 deletions(-) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index d27f1856d3e..78575463a0b 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -45,10 +45,6 @@ "name": "proc", "pattern": "[_/\\\\]+proc-([a-zA-Z0-9+]+)" }, - { - "name": "pvc", - "pattern": "[_/\\\\]+pvc-([a-zA-Z0-9+]+)" - }, { "name": "modality", "pattern": "[_/\\\\]+mod-([a-zA-Z0-9+]+)" @@ -95,7 +91,7 @@ }, { "name": "datatype", - "pattern": "[/\\\\]+(func|anat|pet|fmap|dwi|perf|meg|eeg|figures)[/\\\\]+" + "pattern": "[/\\\\]+(func|anat|pet|fmap|dwi|meg|eeg|perf|figures)[/\\\\]+" }, { "name": "extension", @@ -159,57 +155,49 @@ "dtype": "int" }, { - "name": "hash", - "pattern": "hash-([a-zA-Z0-9+]+)" - }, - { - "name": "segmentation", + "name": "seg", "pattern": "[_/\\\\]+seg-([a-zA-Z0-9+]+)" } ], "default_path_patterns": [ - 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"sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg|.png>|.html}" ] } From 6fa39dae4c37041dbef0cfaf6dedc454a8adc653 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 29 Jan 2026 16:10:12 -0500 Subject: [PATCH 3/6] reconcile petprep config from latest nipreps --- niworkflows/data/nipreps.json | 86 +++++++++++++++++++---------------- 1 file changed, 47 insertions(+), 39 deletions(-) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index 78575463a0b..0442046baa6 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -45,6 +45,10 @@ "name": "proc", "pattern": "[_/\\\\]+proc-([a-zA-Z0-9+]+)" }, + { + "name": "pvc", + "pattern": "[_/\\\\]+pvc-([a-zA-Z0-9+]+)" + }, { "name": "modality", "pattern": "[_/\\\\]+mod-([a-zA-Z0-9+]+)" @@ -154,50 +158,54 @@ "pattern": "[_/\\\\]+cohort-0*(\\d+)", "dtype": "int" }, + { + "name": "hash", + "pattern": "hash-([a-zA-Z0-9+]+)" + }, { "name": "seg", "pattern": "[_/\\\\]+seg-([a-zA-Z0-9+]+)" } ], "default_path_patterns": [ - 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"sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}_{suffix|xfm}{extension<.txt|.h5>}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.surf.gii|.shape.gii>}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dscalar.nii|.json>}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_label-{label}]_desc-{desc}_{suffix|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}[_desc-{desc}]_{suffix|xfm}{extension<.txt|.h5>}", + "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix|AROMAnoiseICs}{extension<.csv|.tsv>|.csv}", + 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"sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_hemi-{hemi}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}", + "sub-{subject}[/ses-{session}]/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.json|.nii.gz|.nii>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix}{extension<.json|.nii.gz|.nii>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.tsv|.bval|.bvec|.b>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|dwi}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode|image}[_desc-{desc}]_{suffix|xfm}{extension<.txt|.h5>}", + "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode|image}_{suffix|xfm}{extension<.txt|.h5>}", + "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.json|.tsv>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}_{suffix|xfm}{extension<.txt|.h5>}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.surf.gii|.shape.gii>}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dscalar.nii|.json>}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix|timeseries}{extension<.json|.tsv>|.tsv}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", + "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg|.png>|.html}" ] } From 852ce14886b6d60cfe9bdb54c82230ae6d57a521 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 23 Feb 2026 10:03:57 -0500 Subject: [PATCH 4/6] add deleted rules back --- niworkflows/data/nipreps.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index 0442046baa6..bfe026df7f7 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -176,6 +176,9 @@ "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_label-{label}][_desc-{desc}]_{suffix}{extension<.tsv|.json>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi}[_space-{space}][_cohort-{cohort}][_den-{density}]_desc-{desc}_{suffix|mask}{extension<.label.gii|.json>|.label.gii}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}][_hash-{hash}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}[_desc-{desc}]_{suffix|xfm}{extension<.txt|.h5>}", @@ -195,6 +198,9 @@ "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.json|.tsv>|.tsv}", "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}", "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_pvc-{pvc}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}_{suffix|xfm}{extension<.txt|.h5>}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.surf.gii|.shape.gii>}", From 436e22f0b113680442b5d31d1ed60b42986152ca Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 23 Feb 2026 10:10:38 -0500 Subject: [PATCH 5/6] remove duplicate fmap pattern --- niworkflows/data/nipreps.json | 1 - 1 file changed, 1 deletion(-) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index bfe026df7f7..f9ff73a8bab 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -199,7 +199,6 @@ "sub-{subject}[/ses-{session}]/{datatype|perf}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}", "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", - "sub-{subject}[/ses-{session}]/{datatype|fmap}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_label-{label}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_pvc-{pvc}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}]_from-{from}_to-{to}_mode-{mode|image}_{suffix|xfm}{extension<.txt|.h5>}", From 16f3d3eb74f4f54fc0bc57d39b421eda34449da2 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 24 Feb 2026 11:46:43 -0500 Subject: [PATCH 6/6] add back pattern paths --- niworkflows/data/nipreps.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json index f9ff73a8bab..cb6fe4b1c30 100644 --- a/niworkflows/data/nipreps.json +++ b/niworkflows/data/nipreps.json @@ -207,6 +207,8 @@ "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_seg-{seg}][_label-{label}][_desc-{desc}]_{suffix|timeseries}{extension<.json|.tsv>|.tsv}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi}][_pvc-{pvc}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}", + "sub-{subject}[/ses-{session}]/{datatype|pet}/sub-{subject}[_ses-{session}][_hash-{hash}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_res-{resolution}]_desc-{desc}_{suffix}{extension<.tsv|.json>|.tsv}", "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}", "sub-{subject}/{datatype}/sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_label-{label}][_desc-{desc}]_{suffix}{extension<.html|.svg>|.svg}",