Metadata-Version: 2.1
Name: bbrc-bx
Version: 0.1.8
Summary: BarcelonaBeta + XNAT = bx
Home-page: https://gitlab.com/xgrg/bx
Author: Greg Operto
Author-email: goperto@barcelonabeta.org
License: UNKNOWN
Download-URL: https://gitlab.com/xgrg/bx/-/archive/v0.1.6/bx-v0.1.6.tar.gz
Description: # bx
        
        [![pipeline status](https://gitlab.com/xgrg/bx/badges/master/pipeline.svg)](https://gitlab.com/xgrg/bx/commits/master)
        [![coverage report](https://gitlab.com/xgrg/bx/badges/master/coverage.svg)](https://gitlab.com/xgrg/bx/commits/master)
        [![downloads](https://img.shields.io/pypi/dm/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)
        [![python versions](https://img.shields.io/pypi/pyversions/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)
        [![pypi version](https://img.shields.io/pypi/v/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)
        
        BarcelonaBeta + XNAT = BX
        
        ## Example:
        
        ![example](https://gitlab.com/xgrg/tweetit/raw/master/resources/004-Collecting-FreeSurfer-data-from-XNAT.gif)
        
        ## 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 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`](https://gitlab.com/pyxnat/pyxnat/tree/bbrc) 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.
        
        [![BarcelonaBeta](https://www.barcelonabeta.org/sites/default/files/logo-barcelona-beta_0.png)](https://www.barcelonabeta.org/)
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
