clabtoolkit 0.3.3__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- clabtoolkit/__init__.py +5 -0
- clabtoolkit/bidstools.py +2260 -0
- clabtoolkit/config/bids.json +147 -0
- clabtoolkit/config/config.json +58 -0
- clabtoolkit/config/lobes.json +112 -0
- clabtoolkit/config/stats_mapping.json +140 -0
- clabtoolkit/config/viz_views.json +268 -0
- clabtoolkit/connectivitytools.py +0 -0
- clabtoolkit/dicomtools.py +941 -0
- clabtoolkit/dwitools.py +1999 -0
- clabtoolkit/freesurfertools.py +5378 -0
- clabtoolkit/imagetools.py +2734 -0
- clabtoolkit/misctools.py +5204 -0
- clabtoolkit/morphometrytools.py +2970 -0
- clabtoolkit/networktools.py +351 -0
- clabtoolkit/parcellationtools.py +3239 -0
- clabtoolkit/pipelinetools.py +1187 -0
- clabtoolkit/plottools.py +682 -0
- clabtoolkit/qcqatools.py +1305 -0
- clabtoolkit/segmentationtools.py +356 -0
- clabtoolkit/surfacetools.py +2785 -0
- clabtoolkit/visualizationtools.py +5575 -0
- clabtoolkit-0.3.3.dist-info/METADATA +212 -0
- clabtoolkit-0.3.3.dist-info/RECORD +28 -0
- clabtoolkit-0.3.3.dist-info/WHEEL +5 -0
- clabtoolkit-0.3.3.dist-info/licenses/AUTHORS.rst +13 -0
- clabtoolkit-0.3.3.dist-info/licenses/LICENSE +16 -0
- clabtoolkit-0.3.3.dist-info/top_level.txt +1 -0
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{
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"bids_entities": {
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"raw_entities": {
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"sub": "Participant",
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"ses": "Session",
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"task": "Task",
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"acq": "Acquisition",
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"run": "Run",
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"mod": "Modality",
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"dir": "PhaseEncodingDirection",
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"rec": "Reconstruction",
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"echo": "Echo",
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"part": "Part",
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"ce": "ContrastEnhancement"},
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"derivatives_entities": {
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"space": "Space",
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"hemi": "Hemisphere",
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"res": "Resolution",
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"den": "Density",
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"model": "Model",
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"from": "RegistrationSource",
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"to": "RegistrationTarget",
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"mode": "RegistrationMode",
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"atlas": "Atlas",
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"scale": "Scale",
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"seg": "Segmentation",
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"desc": "Description"
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},
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"raw_suffix": ["bold",
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"T1w",
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"T2w",
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"dwi",
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"fmap",
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"flair",
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"pet",
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"asl",
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"T1rho",
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"T1map",
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"T2map",
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"T2starmap",
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"FLAIR",
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"inplaneT1",
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"inplaneT2",
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"PDw",
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"PDmap",
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"angio",
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"defacemask",
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"R1map",
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"R2map",
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"R2starmap",
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"PDT2",
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"FLASH",
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"MTR",
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"MTRmap",
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"MTsat",
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"UNIT1",
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"MWFmap",
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"MTVmap",
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"Chimap",
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"S0map",
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"M0map",
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"MEGRE",
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"MESE",
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"MP2RAGE",
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"MPM",
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"MTS",
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"VFA",
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"IRT1",
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"bold",
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"cbv",
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"events",
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"physio",
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"stim",
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"phase",
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"phasediff",
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"phase1",
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"phase2",
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"magnitude1",
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"magnitude2",
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"magnitude",
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"fieldmap",
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"epi",
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"m0scan",
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"TB1AFI",
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"TB1TFL",
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"TB1RFM",
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"RB1COR",
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"TB1DAM",
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"TB1EPI",
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"TB1SRGE",
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"TB1map",
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"RB1map",
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"noRF",
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"sbref",
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"meg",
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"eeg",
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"ieeg"],
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"derivatives_suffix": ["mask",
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"probseg",
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"dseg",
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"diffmodel",
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"fa",
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"md",
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"rd",
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"ad",
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"vf",
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"cl",
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"cs",
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"cp",
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"evals",
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"evecs",
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"gfa",
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"msd",
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"rtop",
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"rttp",
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"peaks",
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"b0",
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"tdi",
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"tractography",
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"xfm"],
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"bids_folders": [
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"anat",
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"func",
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"dwi",
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"fmap",
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"perf",
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"meg",
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"pet"
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],
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"extensions": [
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".nii.gz",
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".nii",
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".json",
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".bvec",
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".bval",
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".tsv",
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".lut",
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".tck",
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".gii",
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".csv",
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".mat",
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".trk",
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".annot"
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]
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}
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}
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{
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"metrics_units": {
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"thickness": "mm",
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"area": "cm2",
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"volume": "cm3",
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"curv": "mm-1",
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"sulc": "au",
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"lgi": "au",
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"euler": "au",
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"sulcal_depth": "mm",
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"sulcal_width": "mm",
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"fold_opening": "mm",
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"sulcal_length": "mm",
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"fa": "au",
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"md": "mm2/s",
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"cs": "au",
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"cp": "au",
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"cl": "au",
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"trace": "mm2/s",
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"ad": "mm2/s",
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"rd": "mm2/s",
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"fwfa": "au",
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"fwmd": "mm2/s",
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"fwvf": "au",
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"gfa": "au",
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"rtop": "au",
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"rtpp": "au",
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"rtap": "au",
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"msd": "mm2/s",
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"icvf": "au",
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"ecvf": "au",
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"isovf": "au",
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"mean_kurtosis": "au",
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"radial_kurtosis": "au",
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"axial_kurtosis": "au",
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"fiso": "au",
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"restricted_fraction": "au",
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"hindered_fraction": "au",
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"fiber_orientation_distribution": "au",
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"noddi_fiso": "au",
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"noddi_ficvf": "au",
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"noddi_ecvf": "au",
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"ndi": "au",
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"axon_diameter": "μm",
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"mvf": "au",
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"charm_fraction": "au",
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"charm_dpar": "mm2/s",
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"charm_dperp": "mm^2/s",
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"wmti_fraction_restricted": "au",
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"wmti_fraction_hindered": "au",
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"wmti_fraction_free": "au",
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"dbsi_cellularity": "au",
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"dbsi_extracellular_water_fraction": "au",
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"diamond_fraction_intra": "au",
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"diamond_fraction_extra": "au",
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"diamond_fraction_csf": "au"
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}
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}
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{
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"desikan_w_cingulate": {
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"lobes": {
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"frontal": [
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"caudalmiddlefrontal",
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"lateralorbitofrontal",
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"medialorbitofrontal",
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"parsopercularis",
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"parsorbitalis",
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"parstriangularis",
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"precentral",
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"rostralmiddlefrontal",
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"superiorfrontal",
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"frontalpole"
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],
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"parietal": [
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"inferiorparietal",
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"isthmuscingulate",
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"postcentral",
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"precuneus",
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"superiorparietal",
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"supramarginal"
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],
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"cingulate": [
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"rostralanteriorcingulate",
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"caudalanteriorcingulate",
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"posteriorcingulate",
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"isthmuscingulate"
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],
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"temporal": [
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"bankssts",
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"entorhinal",
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"fusiform",
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"inferiortemporal",
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"middletemporal",
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"parahippocampal",
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"superiortemporal",
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],
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"occipital": [
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"cuneus",
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"lateraloccipital",
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"lingual",
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"pericalcarine"
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],
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"insula": ["insula"]
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},
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"colors": {
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"frontal": "#0c4999",
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"parietal": "#076020",
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"cingulate": "#783692",
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"temporal": "#d2711a",
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"occipital": "#7e1221",
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"insula": "#ffc020"
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}
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},
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"desikan": {
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"lobes":{
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"frontal": [
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"caudalanteriorcingulate",
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"caudalmiddlefrontal",
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"lateralorbitofrontal",
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"medialorbitofrontal",
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"precentral",
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"rostralmiddlefrontal",
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"parietal": [
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"occipital": [
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"insula": ["insula"]
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},
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"colors": {
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"frontal": "#0c4999",
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"parietal": "#076020",
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"temporal": "#d2711a",
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"occipital": "#7e1221",
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}
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}
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{ "global":
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{
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"brain-brain-intracraneal": {
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"key": "Estimated Total Intracranial Volume",
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"alternate_keys": ["EstimatedTotalIntraCranialVol", "eTIV"],
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"divisor": 1000
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},
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"brain-brain-wholebrain": {
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"key": "Brain Segmentation Volume",
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"alternate_keys": ["BrainSegVol", "BrainSeg"],
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"divisor": 1000
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},
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|
13
|
+
"gm-brain-graymatter": {
|
|
14
|
+
"key": "Total gray matter volume",
|
|
15
|
+
"alternate_keys": ["TotalGrayVol", "TotalGray"],
|
|
16
|
+
"divisor": 1000
|
|
17
|
+
},
|
|
18
|
+
"wm-brain-whitematter": {
|
|
19
|
+
"key": "Total cerebral white matter volume",
|
|
20
|
+
"alternate_keys": ["CerebralWhiteMatterVol", "CerebralWhiteMatter"],
|
|
21
|
+
"divisor": 1000
|
|
22
|
+
},
|
|
23
|
+
"vent-lh-lateral": {
|
|
24
|
+
"key": "Left-Lateral-Ventricle",
|
|
25
|
+
"index": 3,
|
|
26
|
+
"divisor": 1000
|
|
27
|
+
},
|
|
28
|
+
"vent-lh-inferior": {
|
|
29
|
+
"key": "Left-Inf-Lat-Vent",
|
|
30
|
+
"index": 3,
|
|
31
|
+
"divisor": 1000
|
|
32
|
+
},
|
|
33
|
+
"vent-rh-lateral": {
|
|
34
|
+
"key": "Right-Lateral-Ventricle",
|
|
35
|
+
"index": 3,
|
|
36
|
+
"divisor": 1000
|
|
37
|
+
},
|
|
38
|
+
"vent-rh-inferior": {
|
|
39
|
+
"key": "Right-Inf-Lat-Vent",
|
|
40
|
+
"index": 3,
|
|
41
|
+
"divisor": 1000
|
|
42
|
+
}
|
|
43
|
+
},
|
|
44
|
+
|
|
45
|
+
"aseg": {
|
|
46
|
+
"thal-lh-thalamus": {
|
|
47
|
+
"key": "Left-Thalamus-Proper",
|
|
48
|
+
"alternate_keys": ["Left-Thalamus"],
|
|
49
|
+
"seg_id": 10,
|
|
50
|
+
"divisor": 1000
|
|
51
|
+
},
|
|
52
|
+
"thal-rh-thalamus": {
|
|
53
|
+
"key": "Right-Thalamus-Proper",
|
|
54
|
+
"alternate_keys": ["Right-Thalamus"],
|
|
55
|
+
"seg_id": 49,
|
|
56
|
+
"divisor": 1000
|
|
57
|
+
},
|
|
58
|
+
"subc-lh-caudate": {
|
|
59
|
+
"key": "Left-Caudate",
|
|
60
|
+
"seg_id": 11,
|
|
61
|
+
"divisor": 1000
|
|
62
|
+
},
|
|
63
|
+
"subc-rh-caudate": {
|
|
64
|
+
"key": "Right-Caudate",
|
|
65
|
+
"seg_id": 50,
|
|
66
|
+
"divisor": 1000
|
|
67
|
+
},
|
|
68
|
+
"subc-lh-putamen": {
|
|
69
|
+
"key": "Left-Putamen",
|
|
70
|
+
"seg_id": 12,
|
|
71
|
+
"divisor": 1000
|
|
72
|
+
},
|
|
73
|
+
"subc-rh-putamen": {
|
|
74
|
+
"key": "Right-Putamen",
|
|
75
|
+
"seg_id": 51,
|
|
76
|
+
"divisor": 1000
|
|
77
|
+
},
|
|
78
|
+
"subc-lh-pallidum": {
|
|
79
|
+
"key": "Left-Pallidum",
|
|
80
|
+
"seg_id": 13,
|
|
81
|
+
"divisor": 1000
|
|
82
|
+
},
|
|
83
|
+
"subc-rh-pallidum": {
|
|
84
|
+
"key": "Right-Pallidum",
|
|
85
|
+
"seg_id": 52,
|
|
86
|
+
"divisor": 1000
|
|
87
|
+
},
|
|
88
|
+
"hipp-lh-hippocampus": {
|
|
89
|
+
"key": "Left-Hippocampus",
|
|
90
|
+
"seg_id": 17,
|
|
91
|
+
"divisor": 1000
|
|
92
|
+
},
|
|
93
|
+
"hipp-rh-hippocampus": {
|
|
94
|
+
"key": "Right-Hippocampus",
|
|
95
|
+
"seg_id": 53,
|
|
96
|
+
"divisor": 1000
|
|
97
|
+
},
|
|
98
|
+
"amyg-lh-amygdala": {
|
|
99
|
+
"key": "Left-Amygdala",
|
|
100
|
+
"seg_id": 18,
|
|
101
|
+
"divisor": 1000
|
|
102
|
+
},
|
|
103
|
+
"amyg-rh-amygdala": {
|
|
104
|
+
"key": "Right-Amygdala",
|
|
105
|
+
"seg_id": 54,
|
|
106
|
+
"divisor": 1000
|
|
107
|
+
}
|
|
108
|
+
},
|
|
109
|
+
"cortex":
|
|
110
|
+
{
|
|
111
|
+
"area": {
|
|
112
|
+
"column": "SurfArea",
|
|
113
|
+
"source": "statsfile",
|
|
114
|
+
"unit": "mm²",
|
|
115
|
+
"index": 2,
|
|
116
|
+
"std_index": null
|
|
117
|
+
},
|
|
118
|
+
"volume": {
|
|
119
|
+
"column": "GrayVol",
|
|
120
|
+
"source": "statsfile",
|
|
121
|
+
"unit": "mm³",
|
|
122
|
+
"index": 3,
|
|
123
|
+
"std_index": null
|
|
124
|
+
},
|
|
125
|
+
"thickness": {
|
|
126
|
+
"column": "ThickAvg",
|
|
127
|
+
"source": "statsfile",
|
|
128
|
+
"unit": "mm",
|
|
129
|
+
"index": 4,
|
|
130
|
+
"std_index": 5
|
|
131
|
+
},
|
|
132
|
+
"curv": {
|
|
133
|
+
"column": "MeanCurv",
|
|
134
|
+
"source": "statsfile",
|
|
135
|
+
"unit": "mm⁻¹",
|
|
136
|
+
"index": 6,
|
|
137
|
+
"std_index": null
|
|
138
|
+
}
|
|
139
|
+
}
|
|
140
|
+
}
|