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ENH: Add volspace and volcohort entities to IO config file #891

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ENH: Add volspace and volcohort entities to IO config file #891

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18 changes: 14 additions & 4 deletions niworkflows/data/nipreps.json
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,10 @@
"name": "space",
"pattern": "[_/\\\\]+space-([a-zA-Z0-9\\+]+)"
},
{
"name": "volspace",
"pattern": "[_/\\\\]+volspace-([a-zA-Z0-9\\+]+)"
},
{
"name": "suffix",
"pattern": "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"
Expand Down Expand Up @@ -149,13 +153,18 @@
"name": "cohort",
"pattern": "[_/\\\\]+cohort-0*(\\d+)",
"dtype": "int"
},
{
"name": "volcohort",
"pattern": "[_/\\\\]+volcohort-0*(\\d+)",
"dtype": "int"
Comment on lines 153 to +160
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never noticed this until now, but why are these 0 padded?

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I believe an earlier version of pybids had something like that for run, so it parsed int("1") instead of int("01"). I don't think it was necessary or that it is still there.

}
],
"default_path_patterns": [
"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<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{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}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
"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<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
"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}][_volspace-{volspace}][_volcohort-{volcohort}][_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<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|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
Expand All @@ -166,7 +175,8 @@
"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}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",
"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}][_desc-{desc}]_{suffix<components|mixing>|components}{extension<.json|.tsv|.nii|.nii.gz>|.tsv}",
"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}][_desc-{desc}]_{suffix<decomposition>|decomposition}{extension<.json>|.json}",
"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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}",
"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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<bold>}{extension<.func.gii|.func.json>}",
"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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_volspace-{volspace}][_volcohort-{volcohort}][_res-{resolution}][_den-{density}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.dtseries.json>}",
"sub-{subject}[/ses-{session}]/{datatype<func>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T2starmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|dwiref|epiref|lowb|dseg>}{extension<.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}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
Expand All @@ -177,9 +187,9 @@
"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}/{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}][_volspace-{volspace}][_volcohort-{volcohort}][_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}/{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>}{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}][_volspace-{volspace}][_volcohort-{volcohort}][_desc-{desc}]_{suffix<bold>}{extension<.html|.svg>|.svg}"
]
}
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