ukb-to-bids – Conversion of the UK Biobank (UKB) to BIDS¶
Description reproduced from the UK Biobank webpage
UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. The database is regularly augmented with additional data and is globally accessible to approved researchers undertaking vital research into the most common and life-threatening diseases. It is a major contributor to the advancement of modern medicine it and has led to the discovery of several scientific advances and numerous treatments to improve human health.
If you installed the core of Clinica, this converter needs the
Downloading UK Biobank¶
The UK Biobank to BIDS converter assumes that the user has already applied to get access to the data and that the imaging and clinical data have already been downloaded locally.
Be careful, the file
clinical_data.csv needs to contain the following informations about the subject: sex, year of birth, age at recruitment, age at sessions (there are two columns as there are two imaging sessions). The names of the columns should be kept as they are when downloaded using
ukbconv using options
Please note that this converter processes the following modalities : - T1W (nifti) - T2 Flair (nifti) - DWI (nifti) - SWI (nifti) - tfMRI (dicom) - rsfMRI (dicom)
Whenever is possible, the converter uses the rawest files found. This decision allows the user to choose the processing needed. When available the converter get the associated json.
|T1W||T1.nii.gz||Defaced and cropped so there is no neck. The rawest image would be the simply defaced one, but brain studies usually are not interested in the region of the neck. No other corrections are included.|
|T2 Flair||T2_FLAIR.nii.gz||Defaced and cropped so there is no neck. The reasons for choosing this image are the same as for T1.|
|DWI||AP/PAnii.gz||It is the rawest images we can get. bvals and bvec are also available.|
|rsfMRI||rsfMRI.dcm||Since the nii.gz version doesn't always include a json and in consideration for it's usage, we convert the dicom.|
|tfMRI||tfMRI.dcm||Same as rsfMRI.|
|SWI||SWI.nii.gz||Combined coil version. We would get a rawer version, but
Using the converter¶
The converter can be run with the following command line:
clinica convert ukb-to-bids [OPTIONS] DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY BIDS_DIRECTORY
DATASET_DIRECTORYis the path to the original UK BIobank imaging directory, whose content should look like:
DATASET_DIRECTORY ├── 1000223_20227_2_0.zip ├── 1000223_20249_2_0.zip ├── 1000223_20250_2_0.zip ├── 1000223_20251_2_0.zip ├── 1000223_20252_2_0.zip ├── 1000223_20253_2_0.zip ├── 3338337_20251_2_0.zip └── 5566112_20253_2_0.zip
CLINICAL_DATA_DIRECTORYis the path to the directory containing the clinical CSV file.
BIDS_DIRECTORYis the path to the output directory where the BIDS-converted version of UK Biobank will be stored.
In order to improve the readability, the BIDS subject ID is different from the original UK Biobank ID and is defined as follows:
sub-UKB+ original numerical ID of the subject
If the original subject ID is
0001, the final BIDS ID will be
Citing this converter in your paper¶
Example of paragraph:
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