bbrc-bx 0.8
BarcelonaBeta + XNAT = bx

# bx

[![pipeline status](https://gitlab.com/bbrc/xnat/bx/badges/master/pipeline.svg)](https://gitlab.com/bbrc/xnat/bx/commits/master)
[![coverage report](https://gitlab.com/bbrc/xnat/bx/badges/master/coverage.svg)](https://gitlab.com/bbrc/xnat/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

The interested reader may find a description of `bx` in its native ecosystem in [J. Huguet et al.](https://www.frontiersin.org/articles/10.3389/fnins.2021.633438/full), _Frontiers in Neuroscience_ (2021) (doi:[10.3389/fnins.2021.633438](https://www.frontiersin.org/articles/10.3389/fnins.2021.633438/full)).


## 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
```

`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 show`).


### **`ALPS`**:

ALPS - Diffusion Tensor Imaging analysis ALong the Perivascular Space

    Available subcommands:
     `stats`:		create an Excel table with `ALPS` metrics
     `diffusion`:	create an Excel table with `FA` and `MD` diffusion metrics in ALPS ROIs
     `files`:       download all `ALPS` outputs (parametric maps, DTI tensors, transformations, everything...)
     `snapshot`:	download snapshots from the `ALPS` pipeline
     `report`:      download the validation report issued by bbrc-validator
     `tests`:       create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx alps <subcommand> <resource_id>

    References:
      - X. Liu, G. Barisano, et al., Aging and Disease, 2023. DOI: 10.14336/AD.2023.0321-2
      - T. Taoka et al., Magnetic Resonance in Medical Sciences, 2024. DOI: 10.2463/mrms.rev.2023-0175
      - T. Taoka et al. Japanese Journal of Radiology, 2017. DOI: 10.1007/s11604-017-0617-z

### **`ANTS`**:

ANTS - Advanced Normalization Tools

    Available subcommands:
     `files`:		download all `ANTS` outputs
     `snapshot`:	download a snapshot from the `ANTS` pipeline
     `report`:		download the validation report issued by `ANTSValidator`
     `tests`:		creates an Excel table with all automatic tests outcomes from `ANTSValidator`

    Usage:
     bx ants <subcommand> <resource_id>

### **`ARCHIVING`**:

Archiving - Collect automatic tests from MRI or PET session Validators.

    Available subcommands:
     `mri`:		creates an Excel table with all automatic tests outcomes from `ArchivingValidator`
     `pet`:		creates an Excel table with all automatic tests outcomes from `PetSessionValidator`
     `tau`:		creates an Excel table with all automatic tests outcomes from `TauPetSessionValidator`

    Usage:
     bx archiving <subcommand> <resource_id>

### **`ASHS`**:

ASHS (Hippocampal subfield segmentation)

    Available subcommands:
     `files`:		download all `ASHS` outputs (segmentation maps, volumes, everything...)
     `volumes`:		creates an Excel table with all hippocampal subfield volumes
     `snapshot`:	download a snapshot from the `ASHS` pipeline
     `report`:		download the validation report issued by `ASHSValidator`
     `tests`:		creates an Excel table with all automatic tests outcomes from `ASHSValidator`

    Usage:
     bx ashs <subcommand> <resource_id>

    References:
    - Yushkevich PA. et al., Human Brain Mapping, 2014. DOI: 10.1002/hbm.22627

### **`ASL3D`**:

Cerebral perfusion quantification of reconstructed 3D Arterial Spin Labeling MRI.

    Available subcommands:
     `perfusion`:       creates an Excel table with global perfusion values.
     `aal`:             creates an Excel table with regional perfusion values (in AAL atlas).
     `maps`:            download the calibrated perfusion maps
     `files`:           download all 3D-ASL QUANTIFICATION outputs (perfusion maps, files, everything...)
     `snapshot`:        download a snapshot from the 3D-ASL QUANTIFICATION pipeline
     `report`:          download the validation report issued by bbrc-validator
     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx asl3d <subcommand> <resource_id>

    References:
    - Chappell MA. et al., Imaging Neuroscience, 2023. DOI: 10.1162/imag_a_00041

### **`BAMOSARTERIAL`**:

Quantification of BAMOS WMH lesions per brain arterial territories

    Available subcommands:
     `files`:		download all `BAMOS_ARTERIAL` outputs
     `stats`:       create an Excel table with lesions stats per arterial territory
     `snapshot`:    download a snapshot from the `BAMOS_ARTERIAL` pipeline
     `report`:      download the validation report issued by `BAMOSArterialValidator`
     `tests`:       create an Excel table with all automatic tests outcomes from bbrc-validator


    Usage:
     bx bamosarterial <subcommand> <resource_id>

    References:
    - Liu, CF. et al. Scientific Data, 2023. DOI: 10.1038/s41597-022-01923-0

### **`BAMOS`**:

BAMOS (Bayesian MOdel Selection for white matter lesion segmentation)

    Available subcommands:
     `files`:		download all `BAMOS` outputs
     `volumes`:		create an Excel table with global lesion volumes
     `layers`:		download `layer` (i.e. depth) maps
     `lobes`:		download lobar segmentation maps
     `stats`:		create an Excel table with lesions stats per lobe and depth
     `snapshot`:	download a snapshot from the `BAMOS` pipeline
     `report`:		download the validation report issued by `BAMOSValidator`
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator


    Usage:
     bx bamos <subcommand> <resource_id>

    References:
    - Sudre et al., IEEE TMI, 2015

### **`BASIL`**:

BASIL - Bayesian Inference for Arterial Spin Labeling MRI. Arterial Spin Labeling 
(ASL) MRI is a non-invasive method for the quantification of perfusion.

    Available subcommands:
     `perfusion`:	creates an Excel table with global perfusion and arrival-time values.
     `stats`:		creates an Excel table with regional perfusion values (in Harvard-Oxford atlas).
     `aal`:			creates an Excel table with regional perfusion values (in AAL atlas).
     `maps`:		download the calibrated perfusion maps
     `files`:		download all BASIL-ASL outputs (perfusion maps, files, everything...)
     `snapshot`:	download a snapshot from the BASIL-ASL pipeline
     `report`:		download the validation report issued by bbrc-validator
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx basil <subcommand> <resource_id>

    References:
    - Chappell MA., IEEE Transactions on Signal Processing, 2009.
    - Chappell MA. et al., Imaging Neuroscience, 2023. DOI: 10.1162/imag_a_00041

### **`BRAAK`**:

Extract morphometric/metabolic measurements based on Braak staging.

    Morphometric values are based on regional volumes or cortical thickness
    as estimated individually by FreeSurfer with respect to each specific stage
     (namely, Braak_I_II, Braak_III_IV and Braak_V_VI). For each of them, the
    mean value in all the regions related to the specific stage is returned.

    Metabolic data refer to FDG update associated with each stage as defined
    by their corresponding ROIs. Masks of each stage were defined based on the
    CerebrA atlas (Manera et al.).

    Available subcommands:
     `volumes`:		creates an Excel table with regional volumes for each stage
     `thickness`:	creates an Excel table with cortical thickness for each stage
     `fdg`:			creates an Excel table with the FDG uptake for each stage

    Usage:
     bx braak <subcommand> <resource_id>

    References:
    - Braak et al., Acta Neuropathol. 2006
    - Schöll et al., Neuron. 2016
    - Manera et al.,  Scientific Data. 2020

### **`CAT12`**:

CAT12 - Gray/white matter segmentation

    Available subcommands:
     `files`:		download all `CAT12` outputs (segmentation maps, warp fields, everything...)
     `volumes`:		creates an Excel table with GM/WM/CSF volumes
     `snapshot`:	download a snapshot from the segmentation results
     `report`:		download the validation report issued by `CAT12Validator`
     `tests`:		creates an Excel table with all automatic tests outcomes from `CAT12Validator`

    Usage:
     bx cat12 <subcommand> <resource_id>
    
### **`DARTEL`**:

DARTEL - Smoothed, spatially normalized and Jacobian scaled gray matter images in MNI space

    Available subcommands:
     `maps`:		download the MNI-normalized gray matter maps
     `template`:	download cohort-specific DARTEL template
     `report`:		download the validation report issued by `DartelNorm2MNIValidator`
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx dartel <subcommand> <resource_id>

    References:
     Ashburner J., Neuroimage, 2007. DOI: 10.1016/j.neuroimage.2007.07.007
    
### **`SPM12`**:

SPM12 - Gray/white matter segmentation

    Available subcommands:
     `files`:		download all `SPM12` outputs (segmentation maps, warp fields, everything...)
     `volumes`:		creates an Excel table with GM/WM/CSF volumes
     `snapshot`:	download a snapshot from the segmentation results
     `report`:		download the validation report issued by `SPM12Validator`
     `tests`:		creates an Excel table with all automatic tests outcomes from `SPM12`
     `rc`:			downloads rc* files (DARTEL imports)

    Usage:
     bx spm12 <subcommand> <resource_id>
    
### **`DONSURF`**:

DONSURF - Diffusion ON SURFace

    Available subcommands:
     `files`:		download all `recon-all` outputs (segmentation maps, files, everything...)
     `aparc`:		create an Excel table with all `aparc` measurements
     `snapshot`:	download a snapshot from the `recon-all` pipeline
     `report`:		download the validation report issued by bbrc-validator
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx donsurf <subcommand> <resource_id>

    References:
      - Montal V. et al., Alzheimers Dement, 2017. DOI: 10.1016/j.jalz.2017.09.013
    
### **`DTIFIT`**:

DTIFIT - Processing of Diffusion-weighted Imaging data

    Available subcommands:
     `maps`:		download parametric maps (FA, MD, AxD, RD)
     `files`:		download all `*DTIFIT` outputs (including parametric maps)
     `report`:		download the validation report issued by `*DTIFITValidator`
     `snapshot`:	download a snapshot with FA map, RGB tensor and TOPUP distortion correction map
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator


    Usage:
     bx dtifit <subcommand> <resource_id>

### **`FMRIPREP`**:

fMRIPrep - Preprocessing of fMRI data.

    Available subcommands:
     `files`:           download all `FMRIPREP` outputs (preprocessed BOLD, confounds, segmentations, everything...)
     `report`:          download the validation report issued by `FMRIPrepValidator`
     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx fmriprep <subcommand> <resource_id>

    References:
    - Esteban O, et al., Nat Methods 16, 111–116 (2019).

### **`FREESURFER6`**:

FreeSurfer v6.0.0

    Available subcommands:
     `files`:			download all `recon-all` outputs (segmentation maps, files, everything...)
     `aseg`:			create an Excel table with all `aseg` measurements
     `aparc`:			create an Excel table with all `aparc` measurements
     `hippoSfVolumes`:	save an Excel table with hippocampal subfield volumes
     `snapshot`:		download a snapshot from the `recon-all` pipeline
     `report`:			download the validation report issued by bbrc-validator
     `tests`:			create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx freesurfer6 <subcommand> <resource_id>

### **`FREESURFER6HIRES`**:

FreeSurfer v6.0.0 (-hires option)

    Available subcommands:
     `files`:			download all `recon-all` outputs (segmentation maps, files, everything...)
     `aseg`:			create an Excel table with all `aseg` measurements
     `aparc`:			create an Excel table with all `aparc` measurements
     `hippoSfVolumes`:	save an Excel table with hippocampal subfield volumes
     `snapshot`:		download a snapshot from the `recon-all` pipeline
     `report`:			download the validation report issued by bbrc-validator
     `tests`:			create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx freesurfer6hires <subcommand> <resource_id>

### **`FREESURFER7`**:

FreeSurfer v7.1.1

    Available subcommands:
     `files`:			download all `recon-all` outputs (segmentation maps, files, everything...)
     `aseg`:			create an Excel table with all `aseg` measurements
     `aparc`:			create an Excel table with all `aparc` measurements
     `amygNucVolumes`:	save an Excel table with amygdalar volumes
     `brainstem`:		save an Excel table with brainstem substructures volumes
     `thalamus`:		save an Excel table with thalamic nuclei volumes
     `hypothalamus`:	save an Excel table with hypothalamic subunits volumes
     `jack`:			compute the cortical AD signature with FS7 results
     `hippoSfVolumes`:	save an Excel table with hippocampal subfield volumes
     `snapshot`:		download a snapshot from the `recon-all` pipeline
     `report`:			download the validation report issued by bbrc-validator
     `tests`:			create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx freesurfer7 <subcommand> <resource_id>

### **`FREESURFER7EXTRAS`**:

FreeSurfer v7.2.0 (extra segmentation modules)

    Available subcommands:
     `files`:		download all extra segmentation modules outputs (segmentation maps, files, everything...)
     `snapshot`:	download a snapshot from the extra segmentation modules pipeline
     `report`:		download the validation report issued by bbrc-validator
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx freesurfer7extras <subcommand> <resource_id>

### **`ID`**:

Return generic information like subject/session labels, parent project.

    Usage:
     bx id <resource_id>
	 
### **`LCMODEL`**:

LCModel - Quantification and tissue-correction of MR Spectroscopy images.

    Available subcommands:
     `stats`:           creates an Excel table with metabolite concentrations and global signal quality stats
     `correction`:      creates an Excel table with tissue correction parameters
     `files`:           download all LCModel outputs (stats, tissue correction, masks, everything...)
     `snapshot`:        download snapshots from the LCMODEL pipeline
     `report`:          download the validation report issued by `LCModelValidator`
     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx lcmodel <subcommand> <resource_id>

    References:
    - Provencher SW., Magnetic Resonance in Medicine, 1993.

### **`LISTS`**:

Manage experiment lists curated by BarcelonaBeta.

    Available subcommands:
     `show`:		display all existing lists (usage: bx lists show)

    Usage:
     bx lists <subcommand>

### **`MRTRIX3`**:

MRtrix3 - Diffusion MRI tractography and structural connectivity.

    Available subcommands:
     `connectome`:	download the structural connectivity matrices (Desikan-Killiany atlas)
     `files`:		download all `MRTRIX3` outputs (streamlines, segmentations, everything...)
     `report`:		download the validation report issued by `MRtrix3Validator`
     `snapshot`:	download snapshots from the MRTRIX3 pipeline
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx mrtrix3 <subcommand> <resource_id>

    References:
    - Tournier JD et al., NeuroImage 202 (2019).
    
### **`NIFTI`**:

Download NIfTI images from a given sequence (`SeriesDesc`).

    Available subcommands:
     `usable`:		download `usable` images (default)
     `all`:			download all images found
    User is then asked for sequence name (ex: T1, T2, DWI). Has to match with
    the one in XNAT (wildcards accepted).

    Usage:
     bx nifti <subcommand> <resource_id>

### **`PYMENT`**:

Brain Age prediction. 

    Available subcommands:
     `predictions`:	creates an Excel table with raw and bias-corrected predictions
     `files`:		download all `PYMENT` outputs
     `snapshot`:	download snapshots from the `PYMENT` pipeline
     `report`:		download the validation report issued by `PYMENTValidator`
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx pyment <subcommand> <resource_id>

    References:
    - Leonardsen E.H. et al., NeuroImage, 2022
    - Peng H. et al., Medical Image Analysis, 2021

### **`FDG`**:

18F-fluorodeoxyglucose PET imaging data

    Available subcommands:
     `landau`:		creates an Excel table with the Landau's metaROI signature
     `maps`:		download the normalized FDG maps in MNI space
     `files`:		download all outputs from the `FDG_QUANTIFICATION2` pipeline
     `mri`:		    creates an Excel table with details from associated MRI sessions
     `regional`:	creates an Excel table with the regional quantification results
     `aging`:		creates an Excel table with the aging composite ROI
     `snapshot`:	download snapshots from `FDG_QUANTIFICATION2` pipeline
     `report`:		download the validation report issued by `FDGQuantificationValidator`
     `tests`:		collect all automatic tests outcomes from `FDGQuantificationValidator`

    Usage:
     bx fdg <subcommand> <resource_id>

    References:
    - Landau et al., Ann Neurol., 2012

### **`FTM`**:

18F-flutemetamol PET imaging data

    Available subcommands:
     `centiloids`:	creates an Excel table with centiloid scales
     `maps`:		download the normalized FTM maps
     `files`:		download all outputs from the `FTM_QUANTIFICATION2` pipeline
     `mri`:			creates an Excel table with details from associated MRI sessions
     `regional`:	creates an Excel table with the regional quantification results
     `snapshot`:	download snapshots from `FTM_QUANTIFICATION2` pipeline
     `report`:		download the validation report issued by `FTMQuantificationValidator`
     `tests`:		collect all automatic tests outcomes from `FTMQuantificationValidator`

    Usage:
     bx ftm <subcommand> <resource_id>

    References:
     - Klunk et al., Alzheimers Dement., 2015

### **`TAU`**:

18F-RO-948 tau PET imaging data

    Available subcommands:
     `centaurz`:	creates an Excel table with CenTauRz scales
     `files`:		download all outputs from the `CENTAURZ` pipeline
     `mri`:			creates an Excel table with details from associated MRI sessions
     `regional`:	creates an Excel table with the quantification results
     `snapshot`:	download snapshots from `CenTaurZValidator` pipeline
     `report`:		download the validation report issued by `CenTaurZValidator`
     `tests`:		collect all automatic tests outcomes from `CenTaurZValidator`

    Usage:
     bx tau <subcommand> <resource_id>

    References:
     - Villemagne V.L. et al., 2023. DOI: 10.1002/dad2.12454
    
### **`QSMXT`**:

QSMxT - QSM processing and analysis pipeline. Quantitative susceptibility mapping 
(QSM) is an MRI technique for quantifying magnetic susceptibility within biological tissue.

    Available subcommands:
     `stats`:		creates an Excel table with regional QSM values (in FreeSurfer aseg atlas).
     `maps`:		download the reconstructed QSM maps
     `files`:		download all `QSMxT` outputs (QSM maps, segmentations, everything...)
     `report`:		download the validation report issued by `QSMxTValidator`
     `tests`:		create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx qsmxt <subcommand> <resource_id>

    References:
    - Stewart AW et al., Magnetic Resonance in Medicine, 2022.
    
### **`SCANDATES`**:

Collect acquisition dates from imaging sessions.

    Usage:
     bx scandates <resource_id>

### **`SIGNATURE`**:

Download composite measurements labeled as 'signatures' of Alzheimer's Disease

    Available subcommands:
     `jack`:		based on FreeSurfer's cortical thickness and local cortical gray matter volumes
     `dickerson`:	based on Dickerson's cortical signatures (see references below)

    Usage:
     bx signature <subcommand> <resource_id>

    Jack's AD signature is calculated in two versions,
    weighted and not weighted. Weighted means that the formula has been
    applied by normalizing each ROI value by local surface area (as explained
    in the papers).
    Not-weighted versions correspond to mean values across regions.

    Examples:

    `bx signature jack` will return Jack's signature, based on thickness and grayvol values.
    `bx signature dickerson` will return AD and aging signatures, based only on
    thickness values as they do not have any "grayvol" version.

    References:
    - Jack et al., Alzheimers Dement. 2017
    - Dickerson et al., Neurology, 2011
    - Bakkour et al., NeuroImage, 2013

### **`XCPD`**:

XCP-D - Resting State fMRI postprocessing and functional connectivity.

    Available subcommands:
     `conmat`:          download the functional connectivity matrix (Desikan-Killiany atlas)
     `timeseries`:      download the parcellated BOLD time-series (Desikan-Killiany atlas)
     `files`:           download all `XCP_D` outputs (denoised BOLD data, segmentations, everything...)
     `report`:          download the validation report issued by `XCPDValidator`
     `snapshot`:        download snapshots from the XCPD pipeline
     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator

    Usage:
     bx xcpd <subcommand> <resource_id>

    References:
    - Ciric R, et al., Nat Protoc 13 (2018).
    - Mehta K., Salo T. et al., bioRxiv (2023). DOI: 10.1101/2023.11.20.567926

## Dependencies

Requires [`bbrc-pyxnat>=1.6.4`](https://github.com/pyxnat/pyxnat/tree/bbrc) and
the libraries listed in `requirements.txt`.


## 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/)