BarcelonaBeta + XNAT = bx
Project description
bx
BarcelonaBeta + XNAT = BX
Example:
Usage
bx <command> <subcommand> <resource_id> --config /path/to/.xnat.cfg --dest /tmp [--overwrite]
resource_id may be a reference to a whole XNAT project, some specific imaging
session (as found in the table returned by bx id PROJECT_ID) or a 'list' of
sessions (a list of existing lists may be obtained by bx lists display).
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
Cortical AD signatures
bx signature thickness <resource_id>
bx signature grayvol <resource_id>
- Download composite measurements labeled as 'signatures' of Alzheimer's Disease as described in Jack et al., Alzheimers Dement. 2017 and Dickerson et al., Neurology, 2011.
PET imaging
bx ftm maps <resource_id>
bx fdg maps <resource_id>
- Download FTM/FDG images provided some user-specified reference region.
bx ftm centiloids <resource_id>
- Collect centiloid scales from amyloid maps for a given session/over an entire project and store them in an Excel file.
bx fdg landau <resource_id>
- Collect AD signatures as described in Landau et al., Ann Neurol., 2012 for a given session / over an entire project and store them in an Excel file.
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
White matter lesions
bx bamos volumes <resource_id>
- Download volumes of white matter lesions as segmented by BaMOS (Sudre et al., IEEE TMI, 2015).
Dependencies
Requires bbrc-pyxnat>=1.4.1 and
the following librairies: requests, six, lxml, nibabel, pydicom,
numpy, pandas, xlutils, tqdm and openpyxl.
Install
pip install bbrc-bx
Development
Please contact us for details on how to contribute.
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bbrc-bx-0.1.8.tar.gz
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