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Expanding derivatives' configuration to validate existing BIDS-apps #881

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c5f9a21
some sort of QA for derivatives' default_path_patterns
GalKepler Aug 2, 2022
7fd2cb2
edited derivatives configuration to validate QSIPrep's outputs
GalKepler Aug 3, 2022
be57b4d
made some changes to consolidate QSIPrep's anatomical outputs
GalKepler Aug 3, 2022
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7 changes: 4 additions & 3 deletions bids/layout/config/derivatives.json
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Expand Up @@ -53,12 +53,13 @@

"default_path_patterns": [
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_from-{from}][_to-{to}][_desc-{desc}][_mode-{mode}]_{suffix<xfm>}{extension<.h5>|.h5}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}][_space-{space}][_desc-{desc}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype{anat}|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix<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}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix<mask|dseg|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}][_space-{space}][_desc-{desc}]_{suffix<bold|cbv|phase|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}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix<mask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}][_desc-{desc}]_{suffix<dwi>}{extension<bval|bvec|.json|.nii.gz|.nii>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix<mask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_space-{space}][_desc-{desc}]_{suffix<dwi|dwiref|epiref|cnr|confounds|dwiqc>}{extension<.bval|.bvec|.b|.json|.nii.gz|.nii|.tsv|.csv>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_res-{res}][_den-{den}][_label-{label}][_desc-{desc}]_{suffix<mask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_desc-{desc}]_{fmap<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}][_space-{space}][_desc-{desc}]_{fmap<epi>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.json>|.json}",
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