BarcelonaBeta + XNAT = bx
Project description
bx
BarcelonaBeta + XNAT = BX
Example:
Usage
bx <command> <subcommand> <resource_id> --config /path/to/.xnat.cfg --dest /tmp [--overwrite]
Commands:
bx nifti <resource_id>
- Download a NIfTI from a given sequence from an experiment/entire project.
SPM12
bx spm12 volumes <resource_id>
- Download a table with grey/white matter and CSF volumes estimated from SPM12 segmentations
bx spm12 files <resource_id>
- Download SPM12 segmentations from an experiment/entire project
bx spm12 report <resource_id>
- Download a quality report from an SPM12 segmentation for an experiment/entire project
bx spm12 tests <resource_id>
- Download a table with results from automatic validation tests from an SPM12 segmentation for an experiment/entire project
bx spm12 snapshot <resource_id>
- Download a snapshot of SPM12 segmentation results for an experiment/entire project
CAT12
bx cat12 volumes <resource_id>
- Download a table with grey/white matter and CSF volumes estimated from CAT12 segmentations
bx cat12 files <resource_id>
- Download CAT12 segmentations from an experiment/entire project
bx cat12 report <resource_id>
- Download a quality report from an CAT12 segmentation for an experiment/entire project
bx cat12 tests <resource_id>
- Download a table with results from automatic validation tests from an CAT12 segmentation for an experiment/entire project
bx cat12 snapshot <resource_id>
- Download a snapshot of CAT12 segmentation results for an experiment/entire project
FreeSurfer6
bx freesurfer6 aseg <resource_id>
- Download a table with FreeSurfer
asegresults for an experiment/entire project
bx freesurfer6 aparc <resource_id>
- Download a table with FreeSurfer
aparcresults for an experiment/entire project
bx freesurfer6 hippoSfVolumes <resource_id>
- Download a table with FreeSurfer
hippoSfVolumesresults for an experiment/entire project
bx freesurfer6 snapshot <resource_id>
- Download a snapshot of SPM12 segmentation results for an experiment/entire project
bx freesurfer6 files <resource_id>
- Download FreeSurfer6 segmentations from an experiment/entire project
ASHS
bx ashs volumes <resource_id>
- Download a table with hippocampal subfield volumes produced by ASHS for an experiment/entire project
bx ashs files <resource_id>
- Download ASHS segmentations from an experiment/entire project
bx ashs snapshot <resource_id>
- Download a snapshot of SPM12 segmentation results for an experiment/entire project
DTIFIT
bx dtifit files <resource_id>
- Download DTIFIT results from an experiment/entire project
bx dtifit snapshot <resource_id>
- Download a snapshot of DTIFIT results for an experiment/entire project
Miscellaneous
bx id <resource_id>
- Download a table including subject IDs, experiment IDs and XNAT IDs for an experiment/entire project
bx mrdates <resource_id>
- Download a table with acquisition dates from an experiment/entire project
Dependencies
Requires pyxnat>=1.2.1.0.post3.
Install
pip install bbrc-bx
Development
Please contact us for details on how to contribute.
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