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        "author": "Greg Operto",
        "author_email": "goperto@barcelonabeta.org",
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        "description": "# bx\n\n[![pipeline status](https://gitlab.com/xgrg/bx/badges/master/pipeline.svg)](https://gitlab.com/xgrg/bx/commits/master)\n[![coverage report](https://gitlab.com/xgrg/bx/badges/master/coverage.svg)](https://gitlab.com/xgrg/bx/commits/master)\n[![downloads](https://img.shields.io/pypi/dm/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)\n[![python versions](https://img.shields.io/pypi/pyversions/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)\n[![pypi version](https://img.shields.io/pypi/v/bbrc-bx.svg)](https://pypi.org/project/bbrc-bx/)\n\nBarcelonaBeta + XNAT = BX\n\nThe 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)).\n\n\n## Example:\n\n![example](https://gitlab.com/xgrg/tweetit/raw/master/resources/004-Collecting-FreeSurfer-data-from-XNAT.gif)\n\n## Usage\n\n```\nbx <command> <subcommand> <resource_id> --config /path/to/.xnat.cfg --dest /tmp\n```\n\n`resource_id` may be a reference to a whole XNAT project, some specific imaging\nsession (as found in the table returned by `bx id PROJECT_ID`) or a 'list' of\nsessions (a list of existing lists may be obtained by `bx lists show`).\n\n\n### **`ANTS`**:\n\nANTS - Advanced Normalization Tools\n\n    Available subcommands:\n     `files`:           download all `ANTS` outputs\n     `snapshot`:        download a snapshot from the `ANTS` pipeline\n     `report`:          download the validation report issued by `ANTSValidator`\n     `tests`:           creates an Excel table with all automatic tests outcomes from `ANTSValidator`\n\n    Usage:\n     bx ants <subcommand> <resource_id>\n\n### **`ARCHIVING`**:\n\nArchiving - used to collect automatic tests from `ArchivingValidator`\n\n    Available subcommands:\n     `tests`:           creates an Excel table with all automatic tests outcomes from `ArchivingValidator`\n\n    Usage:\n     bx archiving <subcommand> <resource_id>\n\n### **`ASHS`**:\n\nASHS (Hippocampal subfield segmentation)\n\n    Available subcommands:\n     `files`:           download all `ASHS` outputs (segmentation maps, volumes, everything...)\n     `volumes`:         creates an Excel table with all hippocampal subfield volumes\n     `snapshot`:        download a snapshot from the `ASHS` pipeline\n     `report`:          download the validation report issued by `ASHSValidator`\n     `tests`:           creates an Excel table with all automatic tests outcomes from `ASHSValidator`\n\n    Usage:\n     bx ashs <subcommand> <resource_id>\n\n### **`BAMOS`**:\n\nBAMOS (Bayesian MOdel Selection for white matter lesion segmentation)\n\n    Available subcommands:\n     `files`:           download all `BAMOS` outputs\n     `volumes`:         create an Excel table with global lesion volumes\n     `layers`:          download `layer` (i.e. depth) maps\n     `lobes`:           download lobar segmentation maps\n     `stats`:           create an Excel table with lesions stats per lobe and depth\n     `snapshot`:        download a snapshot from the `BAMOS` pipeline\n     `report`:          download the validation report issued by `BAMOSValidator`\n\n    Usage:\n     bx bamos <subcommand> <resource_id>\n\n    References:\n    - Sudre et al., IEEE TMI, 2015\n\n### **`BRAAK`**:\n\nExtract morphometric/metabolic measurements based on Braak staging.\n\n    Morphometric values are based on regional volumes or cortical thickness\n    as estimated individually by FreeSurfer with respect to each specific stage\n     (namely, Braak_I_II, Braak_III_IV and Braak_V_VI). For each of them, the\n    mean value in all the regions related to the specific stage is returned.\n\n    Metabolic data refer to FDG update associated with each stage as defined\n    by their corresponding ROIs. Masks of each stage were defined based on the\n    CerebrA atlas (Manera et al.).\n\n    Available subcommands:\n     `volumes`:         creates an Excel table with regional volumes for each stage\n     `thickness`:       creates an Excel table with cortical thickness for each stage\n     `fdg`:             creates an Excel table with the FDG uptake for each stage\n\n    Usage:\n     bx braak <subcommand> <resource_id>\n\n    References:\n    - Braak et al., Acta Neuropathol. 2006\n    - Sch\u00f6ll et al., Neuron. 2016\n    - Manera et al.,  Scientific Data. 2020\n\n### **`CAT12`**:\n\nCAT12 - Gray/white matter segmentation\n\n    Available subcommands:\n     `files`:           download all `CAT12` outputs (segmentation maps, warp fields, everything...)\n     `volumes`:         creates an Excel table with GM/WM/CSF volumes\n     `snapshot`:        download a snapshot from the segmentation results\n     `report`:          download the validation report issued by `CAT12Validator`\n     `tests`:           creates an Excel table with all automatic tests outcomes from `CAT12Validator`\n\n    Usage:\n     bx cat12 <subcommand> <resource_id>\n\n### **`DONSURF`**:\n\nDONSURF - Diffusion ON SURFace\n\n    Available subcommands:\n     `files`:           download all `recon-all` outputs (segmentation maps, files, everything...)\n     `aparc`:           create an Excel table with all `aparc` measurements\n     `snapshot`:        download a snapshot from the `recon-all` pipeline\n     `report`:          download the validation report issued by bbrc-validator\n     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator\n\n    Usage:\n     bx donsurf <subcommand> <resource_id>\n\n### **`DTIFIT`**:\n\nProcessing of Diffusion-weighted Imaging data\n\n    Available subcommands:\n    `maps`:             download parametric maps (FA, MD, AxD, RD)\n    `files`:            download all outputs from the `DTIFIT` pipeline (up to parametric maps)\n    `report`:           download the validation report issued by `DTIFITValidator`\n    `snapshot`:         download a snapshot with FA map, RGB tensor and TOPUP distortion correction map\n\n    Usage:\n     bx dtifit <subcommand> <resource_id>\n\n### **`FREESURFER6`**:\n\nFreeSurfer v6.0.0\n\n    Available subcommands:\n     `files`:           download all `recon-all` outputs (segmentation maps, files, everything...)\n     `aseg`:            create an Excel table with all `aseg` measurements\n     `aparc`:           create an Excel table with all `aparc` measurements\n     `hippoSfVolumes`:  save an Excel table with hippocampal subfield volumes (if available)\n     `snapshot`:        download a snapshot from the `recon-all` pipeline\n     `report`:          download the validation report issued by bbrc-validator\n     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator\n\n    Usage:\n     bx freesurfer6 <subcommand> <resource_id>\n\n### **`FREESURFER6HIRES`**:\n\nFreeSurfer v6.0.0 (-hires option)\n\n    Available subcommands:\n     `files`:           download all `recon-all` outputs (segmentation maps, files, everything...)\n     `aseg`:            create an Excel table with all `aseg` measurements\n     `aparc`:           create an Excel table with all `aparc` measurements\n     `hippoSfVolumes`:  save an Excel table with hippocampal subfield volumes (if available)\n     `snapshot`:        download a snapshot from the `recon-all` pipeline\n     `report`:          download the validation report issued by bbrc-validator\n     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator\n\n    Usage:\n     bx freesurfer6hires <subcommand> <resource_id>\n\n### **`FREESURFER7`**:\n\nFreeSurfer v7.1.1\n\n    Available subcommands:\n     `files`:           download all `recon-all` outputs (segmentation maps, files, everything...)\n     `aseg`:            create an Excel table with all `aseg` measurements\n     `aparc`:           create an Excel table with all `aparc` measurements\n     `hippoSfVolumes`:  save an Excel table with hippocampal subfield volumes (if available)\n     `snapshot`:        download a snapshot from the `recon-all` pipeline\n     `report`:          download the validation report issued by bbrc-validator\n     `tests`:           create an Excel table with all automatic tests outcomes from bbrc-validator\n\n    Usage:\n     bx freesurfer7 <subcommand> <resource_id>\n\n### **`ID`**:\n\nReturn generic information like subject/session labels, parent project.\n\n    Usage:\n     bx id <resource_id>\n\n### **`LISTS`**:\n\nManage experiment lists curated by BarcelonaBeta.\n\n    Available subcommands:\n     `show`:            display all existing lists (usage: bx lists show)\n\n    Usage:\n     bx lists <subcommand>\n\n### **`NIFTI`**:\n\nDownload NIfTI images from a given sequence (`SeriesDesc`).\n\n    Available subcommands:\n     `usable`:          download `usable` images (default)\n     `all`:             download all images found\n    User is then asked for sequence name (ex: T1, T2, DWI). Has to match with\n    the one in XNAT (wildcards accepted).\n\n    Usage:\n     bx nifti <subcommand> <resource_id>\n\n### **`FDG`**:\n\n18F-fluorodeoxyglucose PET imaging data\n\n    Available subcommands:\n     `landau`:          creates an Excel table with the Landau's metaROI signature\n     `maps`:            download the normalized FDG maps\n     `tests`:           collect all automatic tests outcomes from `FDGQuantiticationValidator`\n\n    Usage:\n     bx fdg <subcommand> <resource_id>\n\n    Reference:\n    - Landau et al., Ann Neurol., 2012\n\n### **`FTM`**:\n\n18F-flutemetamol PET imaging data\n\n    Available subcommands:\n     `centiloids`:      creates an Excel table with centiloid scales\n     `maps`:            download the normalized FTM maps\n     `tests`:           collect all automatic tests outcomes from `FTMQuantiticationValidator`\n\n    Usage:\n     bx ftm <subcommand> <resource_id>\n\n    References:\n     - Klunk et al, Alzheimers Dement., 2015\n\n### **`SCANDATES`**:\n\nCollect acquisition dates from imaging sessions.\n\n    Usage:\n     bx scandates <resource_id>\n\n### **`SIGNATURE`**:\n\nDownload composite measurements labeled as 'signatures' of Alzheimer's Disease\n\n    Available subcommands:\n     `jack`:            based on FreeSurfer's cortical thickness and local cortical gray matter volumes\n     `dickerson`:       based on Dickerson's cortical signatures (see references below)\n\n    Usage:\n     bx signature <subcommand> <resource_id>\n\n    Jack's AD signature is calculated in two versions,\n    weighted and not weighted. Weighted means that the formula has been\n    applied by normalizing each ROI value by local surface area (as explained\n    in the papers).\n    Not-weighted versions correspond to mean values across regions.\n\n    Examples:\n\n    `bx signature jack` will return Jack's signature, based on thickness and grayvol values.\n    `bx signature dickerson` will return AD and aging signatures, based only on\n    thickness values as they do not have any \"grayvol\" version.\n\n    References:\n    - Jack et al., Alzheimers Dement. 2017\n    - Dickerson et al., Neurology, 2011\n    - Bakkour et al., NeuroImage, 2013\n\n### **`SPM12`**:\n\nSPM12 - Gray/white matter segmentation\n\n    Available subcommands:\n     `files`:           download all `SPM12` outputs (segmentation maps, warp fields, everything...)\n     `volumes`:         creates an Excel table with GM/WM/CSF volumes\n     `snapshot`:        download a snapshot from the segmentation results\n     `report`:          download the validation report issued by `SPM12Validator`\n     `tests`:           creates an Excel table with all automatic tests outcomes from `SPM12`\n     `rc`:              downloads rc* files (DARTEL imports)\n\n    Usage:\n     bx spm12 <subcommand> <resource_id>\n\n\n## Dependencies\n\nRequires [`bbrc-pyxnat>=1.4.2`](https://gitlab.com/pyxnat/pyxnat/tree/bbrc) and\nthe librairies listed in `requirements.txt`.\n\n\n## Install\n\n```\npip install bbrc-bx\n```\n\n## Development\n\nPlease contact us for details on how to contribute.\n\n[![BarcelonaBeta](https://www.barcelonabeta.org/sites/default/files/logo-barcelona-beta_0.png)](https://www.barcelonabeta.org/)",
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