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Merge pull request #594 from tsalo/filter-part-entity
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MAINT: Select magnitude images in collect_data for BIDS 1.5.0
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@effigies
effigies authored Mar 30, 2022
2 parents a747eb6 + 81c1378 commit 92cad70
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Showing 3 changed files with 32 additions and 14 deletions.
34 changes: 26 additions & 8 deletions niworkflows/data/nipreps.json
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Expand Up @@ -49,6 +49,22 @@
"name": "echo",
"pattern": "[_/\\\\]+echo-([0-9]+)"
},
{
"name": "flip",
"pattern": "[_/\\\\]+flip-([0-9]+)"
},
{
"name": "inv",
"pattern": "[_/\\\\]+inv-([0-9]+)"
},
{
"name": "mt",
"pattern": "[_/\\\\]+mt-(on|off)"
},
{
"name": "part",
"pattern": "[_/\\\\]+part-(mag|phase|real|imag)"
},
{
"name": "recording",
"pattern": "[_/\\\\]+recording-([a-zA-Z0-9]+)"
Expand Down Expand Up @@ -136,25 +152,27 @@
}
],
"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}",
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"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<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"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|dwi|epiref|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}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_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}][_desc-{desc}]_{suffix<bold>}{extension<.html|.svg>|.svg}"
]
}
10 changes: 5 additions & 5 deletions niworkflows/utils/bids.py
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Expand Up @@ -200,11 +200,11 @@ def collect_data(

queries = {
"fmap": {"datatype": "fmap"},
"bold": {"datatype": "func", "suffix": "bold"},
"sbref": {"datatype": "func", "suffix": "sbref"},
"flair": {"datatype": "anat", "suffix": "FLAIR"},
"t2w": {"datatype": "anat", "suffix": "T2w"},
"t1w": {"datatype": "anat", "suffix": "T1w"},
"bold": {"datatype": "func", "suffix": "bold", "part": ["mag", None]},
"sbref": {"datatype": "func", "suffix": "sbref", "part": ["mag", None]},
"flair": {"datatype": "anat", "suffix": "FLAIR", "part": ["mag", None]},
"t2w": {"datatype": "anat", "suffix": "T2w", "part": ["mag", None]},
"t1w": {"datatype": "anat", "suffix": "T1w", "part": ["mag", None]},
"roi": {"datatype": "anat", "suffix": "roi"},
}
bids_filters = bids_filters or {}
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2 changes: 1 addition & 1 deletion setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ install_requires =
numpy
packaging
pandas
pybids >= 0.11.1, < 0.15
pybids ~= 0.14.1
PyYAML
scikit-image
scipy
Expand Down

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