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updated naming of derivatives for easier parsing
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@GalKepler
GalKepler committed Sep 4, 2024
1 parent 59dc2c1 commit 5b9573d
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions src/kepost/interfaces/bids/static/kepost.json
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@
},
{
"name": "reconstruction_software",
"pattern": "([a-zA-Z0-9]+)"
"pattern": "software-([a-zA-Z0-9]+)"
},
{
"name":"measure",
Expand All @@ -77,11 +77,11 @@
],

"default_path_patterns": [
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/{subtype<tensors>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_filter-{filter}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dwiref>}{extension<.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/{subtype<atlases>}/atlas-{atlas}[_den-{den}][_div-{division}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dseg>}{extension<.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/{subtype<parcellations>}/atlas-{atlas}[_div-{div}][_den-{den}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<parc>}{extension<.csv|.tsv|.pickle|.pkl>|.pkl}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/{subtype<connectomes>}/atlas-{atlas}[_den-{den}][_div-{division}]/filter-{filter<SIFT2|SIFT>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_filter-{filter}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<connectome|assignments>}{extension<.csv|.tsv|.pickle|.pkl|.txt>|.csv}",
"sub-{subject}[/ses-{session}]/{datatype<anat>}/{subtype<atlases|parcellations>}/atlas-{atlas}[_den-{den}][_div-{division}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dwiref|parc|dseg|probseg|5TT>}{extension<.csv|.tsv|.pickle|.pkl|.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/software-{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/subtype-{subtype<tensors>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_filter-{filter}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dwiref>}{extension<.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/software-{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/subtype-{subtype<atlases>}/atlas-{atlas}[_den-{den}][_div-{division}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dseg>}{extension<.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/software-{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/subtype-{subtype<parcellations>}/atlas-{atlas}[_div-{div}][_den-{den}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<parc>}{extension<.csv|.tsv|.pickle|.pkl>|.pkl}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>}/software-{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}/subtype-{subtype<connectomes>}/atlas-{atlas}[_den-{den}][_div-{division}]/filter-{filter<SIFT2|SIFT>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_filter-{filter}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<connectome|assignments>}{extension<.csv|.tsv|.pickle|.pkl|.txt>|.csv}",
"sub-{subject}[/ses-{session}]/{datatype<anat>}/subtype-{subtype<atlases|parcellations>}/atlas-{atlas}[_den-{den}][_div-{division}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_atlas-{atlas}][_den-{den}][_div-{division}][_scale-{scale}][_label-{label}][_meas-{measure}][_roi-{roi}]_{suffix<dwiref|parc|dseg|probseg|5TT>}{extension<.csv|.tsv|.pickle|.pkl|.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}][_atlas-{atlas}][_{roi}][_{den}]_{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}[/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<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_space-{space}][_res-{res}][_desc-{desc}][_part-{part}][_label-{label}]_{suffix<dwi|dwiref|epiref|mask>}{extension<.bval|.bvec|.b|.json|.nii.gz|.nii>|.nii.gz}",
Expand All @@ -103,7 +103,7 @@
"[acq-{acquisition}_][dir-{direction}_][run-{run}_][space-{space}_][desc-{desc}_]{fmap<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
"[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}][_space-{space}][_desc-{desc}]_{fmap<epi>}{extension<.json>|.json}",
"task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}][_desc-{desc}]_{suffix<events>}{extension<.json>|.json}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}[/{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_label-{label}]_{suffix<qc>}{extension<.nii|.nii.gz|.json|.csv|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}[/software-{reconstruction_software<dipy|mrtrix|mrtrix3|fsl|qc>}]/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_label-{label}]_{suffix<qc>}{extension<.nii|.nii.gz|.json|.csv|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_part-{part}]_{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|dwi>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_res-{res}][_desc-{desc}][_den-{den}][_label-{label}]_{suffix<probseg|5TT>}{extension<.csv|.tsv|.pickle|.nii|.nii.gz|.json|.mif>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<tracts|weights>}{extension<.tck|.trk|.fib.gz|.txt>|.tck}"
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