bbrc-bx 0.1.9

BarcelonaBeta + XNAT = bx

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 aseg results for an experiment/entire project

bx freesurfer6 aparc <resource_id>

• Download a table with FreeSurfer aparc results for an experiment/entire project

bx freesurfer6 hippoSfVolumes <resource_id>

• Download a table with FreeSurfer hippoSfVolumes results 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 jack <resource_id>
bx signature dickerson <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.