Merge pull request #965 from nipreps/dev_petprep

feat: Sync PETPrep requirements

Author: effigies

niworkflows/data/nipreps.json

@@ -28,6 +28,10 @@
       "name": "reconstruction",
       "pattern": "[_/\\\\]+rec-([a-zA-Z0-9+]+)"
     },
+    {
+      "name": "tracer",
+      "pattern": "[_/\\\\]+trc-([a-zA-Z0-9+]+)"
+    },
     {
       "name": "direction",
       "pattern": "[_/\\\\]+dir-([a-zA-Z0-9+]+)"
@@ -41,6 +45,14 @@
       "name": "proc",
       "pattern": "[_/\\\\]+proc-([a-zA-Z0-9+]+)"
     },
+    {
+      "name": "pvc",
+      "pattern": "[_/\\\\]+pvc-([a-zA-Z0-9+]+)"
+    },
+    {
+      "name": "ref",
+      "pattern": "[_/\\\\]+ref-([a-zA-Z0-9+]+)"
+    },
     {
       "name": "modality",
       "pattern": "[_/\\\\]+mod-([a-zA-Z0-9+]+)"
@@ -158,6 +170,8 @@
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_desc-{desc}]_{suffix<dseg>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_desc-{desc}]_{suffix<morph>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_desc-{desc}_{suffix<mask>|mask}{extension<.label.gii|.json>|.label.gii}",
     "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}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|boldmap|dseg>}{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}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
@@ -178,17 +192,19 @@
     "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries>}{extension<.json|.tsv>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<pet|petref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dwi|epi|epiref>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_pvc-{pvc}][_desc-{desc}]_{suffix<pet|petref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_ref-{ref}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_ref-{ref}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_pvc-{pvc}][_ref-{ref}][_desc-{desc}]_{suffix<timeseries|regressors|tacs>|timeseries}{extension<.json|.tsv>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi<L|R>}][_pvc-{pvc}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<pet>}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_ref-{ref}][_res-{resolution}]_desc-{desc}_{suffix<morph>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dwi|epi|epiref>}{extension<.html|.svg>|.svg}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|boldmap>}{extension<.html|.svg>|.svg}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<pet>}{extension<.html|.svg>|.svg}"
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_trc-{tracer}][_ref-{ref}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<pet>}{extension<.html|.svg>|.svg}"
   ]
 }

niworkflows/utils/spaces.py

@@ -41,6 +41,7 @@
     'individual',
     'dwi',
     'asl',
+    'petref',
 ]
 """List of supported nonstandard reference spaces."""