A single application to download, bidsify and preprocess public datasets
This is a very early work in progress.
This application is being developed as part of the project "High-resolution spatiotemporal models of the brain across the lifespan for diagnosis and decision-making", funded by a fellowship of the Royal Society (NIF\R1\232460).
pip install "braindataprep @ git+https://github.com/balbasty/braindataprep"Specific datasets may require additional dependencies. To install the dependencies to a specific dataset, use the corresponding tag. For example:
pip install "braindataprep[ixi] @ git+https://github.com/balbasty/braindataprep"To install all possible dependencies, use the all tag:
pip install "braindataprep[all] @ git+https://github.com/balbasty/braindataprep"After installation, the bdp command is available from your shell.
Each known dataset is a specific command, with a set of subcommands.
These datasets can be listed by typing bdp:
Usage: bdp COMMAND
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ BrainDataPrep : Download, Bidsify and Process public datasets ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ ixi Commands related to the IXI dataset │
│ oasis1 Commands related to the OASIS-I dataset │
│ oasis2 Commands related to the OASIS-II dataset │
│ --help,-h Display this message and exit. │
│ --version Display application version. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp ixi COMMAND
Commands related to the IXI dataset
• Project Information eXtraction from Images (IXI)
• Modalities T1w, T2w, PD2, MRA, DTI
• Populations Controls
• Funding EPSRC GR/S21533/02
• License CC BY-SA 3.0
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ download Download source data for the IXI dataset. │
│ bidsify Convert source data into a BIDS-compliant directory │
│ --help,-h Display this message and exit. │
│ --version Display application version. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp ixi download [ARGS] [OPTIONS]
Download source data for the IXI dataset.
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An IXI folder will be created. │
│ --keys Modalities to download │
│ [default: ('meta', 'T1w', 'T2w','PDw', 'angio', 'dwi')] │
│ --if-exists Behaviour if a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --packet Packet size to download, in bytes [default: 8.4 MB] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp ixi bidsify [ARGS] [OPTIONS]
Convert source data into a BIDS-compliant directory
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An IXI/sourcedata folder │
│ must exist. │
│ --keys Only bidsify these keys │
│ [default: ('meta', 'T1w', 'T2w','PDw', 'angio', 'dwi')] │
│ --subs Only bidsify these subjects (all if empty) [default: ()] │
│ --exclude-subs Do not bidsify these subjects [default: ()] │
│ --json Whether to write (only) sidecar JSON files │
│ [choices:yes,no,only] [default: yes] │
│ --if-exists Behaviour when a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis1 COMMAND
Commands related to the OASIS-I dataset
• Project Open Access Series of Imaging Studies (OASIS)
• Subproject Cross-sectional data across the adult lifespan (OASIS-I)
• Modalities T1w
• Populations Controls, Dementia
• Funding NIH: P50 AG05681, P01 AG03991, P01 AG026276, R01 AG021910,
P20 MH071616, U24 RR021382
• Reference https://doi.org/10.1162/jocn.2007.19.9.1498
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ download Download source data for the OASIS-I dataset. │
│ bidsify Convert source data into a BIDS-compliant directory │
│ --help,-h Display this message and exit. │
│ --version Display application version. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis1 download [ARGS] [OPTIONS]
Download source data for the OASIS-I dataset.
Possible keys:
• raw All the raw imaging data
• fs Data processed with FreeSurfer
• meta Metadata
• reliability Repeatability measures data sheet
• facts Fact sheet
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-1 folder will be created. │
│ --keys Data categories to download │
│ [default: ('raw', 'fs', 'meta', 'reliability', 'facts')] │
│ --discs Discs to download [default: (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)] │
│ --if-exists Behaviour if a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --packet Packet size to download, in bytes [default: 8.4 MB] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis1 bidsify [ARGS] [OPTIONS]
Convert source data into a BIDS-compliant directory
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-1/sourcedata folder │
│ must exist. │
│ --keys Only bidsify these keys │
│ [default: ('meta', 'raw', 'avg', 'tal', 'fsl', 'fs', 'fs-all')] │
│ --discs Discs to bidsify. │
│ [default: (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)] │
│ --subs Only bidsify these subjects (all if empty) [default: ()] │
│ --exclude-subs Do not bidsify these subjects [default: ()] │
│ --json Whether to write (only) sidecar JSON files │
│ [choices: yes,no,only] [default: yes] │
│ --if-exists Behaviour when a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis2 COMMAND
Commands related to the OASIS-II dataset
• Project Open Access Series of Imaging Studies (OASIS)
• Subproject Longitudinal MRI Data in Nondemented and Demented Older Adults
(OASIS-II)
• Modalities T1w
• Populations Controls, Dementia
• Funding NIH: P50 AG05681, P01 AG03991, P01 AG026276,
R01 AG021910, P20 MH071616, U24 RR021382
• Reference https://doi.org/10.1162/jocn.2009.21407
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ download Download source data for the OASIS-II dataset. │
│ bidsify Convert source data into a BIDS-compliant directory │
│ --help,-h Display this message and exit. │
│ --version Display application version. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis2 download [ARGS] [OPTIONS]
Download source data for the OASIS-II dataset.
Possible keys:
• raw All the raw imaging data
• fs Data processed with FreeSurfer
• meta Metadata
• reliability Repeatability measures data sheet
• facts Fact sheet
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-2 folder will be created. │
│ --keys Data categories to download [default: ('raw', 'meta')] │
│ --parts Parts to download [default: (1, 2)] │
│ --if-exists Behaviour if a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --packet Packet size to download, in bytes [default: 8.4 MB] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis2 bidsify [ARGS] [OPTIONS]
Convert source data into a BIDS-compliant directory
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-2/sourcedata folder must │
│ exist. │
│ --keys Only bidsify these keys [default: ('meta', 'raw')] │
│ --parts Parts to bidsify. [default: (1, 2)] │
│ --subs Only bidsify these subjects (all if empty) [default: ()] │
│ --exclude-subs Do not bidsify these subjects [default: ()] │
│ --json Whether to write (only) sidecar JSON files │
│ [choices: yes,no,only] [default: yes] │
│ --if-exists Behaviour when a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
OASIS-3: Longitudinal Multimodal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer's Disease
Usage: bdp oasis3 COMMAND
Commands related to the OASIS-III dataset
• Project Open Access Series of Imaging Studies (OASIS)
• Subproject Longitudinal Multimodal Neuroimaging, Clinical, and Cognitive
Dataset for Normal Aging and Alzheimer's Disease (OASIS-III)
• Modalities T1w, T2w, TSE, FLAIR, T2star, angio, pasl, asl, bold,
dwi, swi, fdg, pib, av45, av1451, CT
• Populations Controls, Dementia
• Funding NIH: P30 AG066444, P50 AG00561, P30 NS09857781, P01 AG026276,
P01 AG003991, R01 AG043434, UL1 TR000448, R01 EB009352
• Reference https://doi.org/10.1101/2019.12.13.19014902
╭─ Commands ────────────────────────────────────────────────────────────────────────╮
│ download Download source data for the OASIS-III dataset. │
│ bidsify Convert source data into a BIDS-compliant directory │
│ --help,-h Display this message and exit. │
│ --version Display application version. │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis3 download [ARGS] [OPTIONS]
Download source data for the OASIS-III dataset.
Hierarchy of keys:
• raw : All the raw imaging data
• mri : All the MRI data
• anat : All the anatomical MRI data
• T1w : T1-weighted MRI scans
• T2w : T2-weighted MRI scans
• TSE : Turbo Spin Echo MRI scans
• FLAIR : Fluid-inversion Recovery MRI scans
• T2star : T2-star quantitative scans
• angio : MR angiography scans
• swi : All susceptibility-weighted MRI data
• func : All fthe functional MRI data
• pasl : Pulsed arterial spin labeling
• asl : Arterial spin labelling
• bold : Blood-oxygenation level dependant (fMRI) scans
• fmap : All field maps
• dwi : All diffusion-weighted MRI data
• pet : All the PET data
• fdg : Fludeoxyglucose
• pib : Pittsburgh Compound B (amyloid)
• av45 : 18F Florpiramine (tau)
• av1451 : 18F Flortaucipir (tau)
• ct All the CT data
• derivatives : All derivatives
• fs : Freesurfer derivatives
• pup : PET derivatives
• meta : All metadata
• pheno : Phenotypes
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-2 folder will be created. │
│ --keys Data categories to download [default: ()] │
│ --subs Only bidsify these subjects (all if empty) [default: ()] │
│ --exclude-subs Do not bidsify these subjects [default: ()] │
│ --if-exists Behaviour if a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --user NITRC username │
│ --password NITRC password │
│ --packet Packet size to download, in bytes [default: 8.4 MB] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯
Usage: bdp oasis3 bidsify [ARGS] [OPTIONS]
Convert source data into a BIDS-compliant directory
Hierarchy of keys:
• raw : All the raw imaging data
• mri : All the MRI data
• anat : All the anatomical MRI data
• T1w : T1-weighted MRI scans
• T2w : T2-weighted MRI scans
• TSE : Turbo Spin Echo MRI scans
• FLAIR : Fluid-inversion Recovery MRI scans
• T2star : T2-star quantitative scans
• angio : MR angiography scans
• swi : All susceptibility-weighted MRI data
• func : All fthe functional MRI data
• pasl : Pulsed arterial spin labeling
• asl : Arterial spin labelling
• bold : Blood-oxygenation level dependant (fMRI) scans
• fmap : All field maps
• dwi : All diffusion-weighted MRI data
• pet : All the PET data
• fdg : Fludeoxyglucose
• pib : Pittsburgh Compound B (amyloid)
• av45 : 18F Florpiramine (tau)
• av1451 : 18F Flortaucipir (tau)
• ct All the CT data
• derivatives : All derivatives
• fs : Freesurfer derivatives
• fs-all : Freesurfer derivatives (even non bidsifiable ones)
• pup : PET derivatives
• meta : All metadata
• pheno : Phenotypes
╭─ Parameters ──────────────────────────────────────────────────────────────────────╮
│ PATH,--path Path to root of all datasets. An OASIS-2/sourcedata folder must │
│ exist. │
│ --keys Only bidsify these keys (all if empty) [default: ()] │
│ --exclude-keys Do not bidsify these keys [default: ()] │
│ --subs Only bidsify these subjects (all if empty) [default: ()] │
│ --exclude-subs Do not bidsify these subjects [default: ()] │
│ --json Whether to write (only) sidecar JSON files │
│ [choices: yes,no,only] [default: yes] │
│ --if-exists Behaviour when a file already exists │
│ [choices: skip,overwrite,different,refresh,error] [default: skip] │
│ --log Path to log file │
╰───────────────────────────────────────────────────────────────────────────────────╯