OASIS2BIDS

oasis-2-bids – Conversion of the Open Access Series of Imaging Studies (OASIS) to BIDS

!!! quote "Description reproduced from the OASIS' webpage" The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).

The "Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults" set consists of a cross-sectional collection of 416 subjects aged 18 to 96.  For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included.  The subjects are all right-handed and include both men and women.  100 of the included subjects over the age of 60 have been clinically diagnosed with very mild to moderate Alzheimer’s disease (AD).  Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.

For more information about the images and the dataset you can read the OASIS Fact Sheet.

Dependencies

If you only installed the core of Clinica, this pipeline needs the installation of the dcm2nii and dcm2niix DICOM to NIfTI converters, and of FreeSurfer. You can find how to install these software packages on the installation page.

Downloading OASIS

The OASIS to BIDS converter requires the user to have downloaded the OASIS-1 (also called Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults) imaging and clinical data. To do so, visit the OASIS website, click on DATASETS then OASIS-1. You can download the imaging data via FTP or XNAT (if you click on Browse Data). Download the clinical data by clicking on Download CSV.

!!! note You do not have to modify the original folder name or rename the clinical data file before using the converter.

!!! warning We do not currently support the conversion of OASIS-2 and OASIS-3.

Modalities supported

Currently, the converter converts only the T1-weighted MRI images and clinical data.

To convert the imaging data to BIDS, the list of subjects is obtained from the downloaded folders. For each subject, among the multiple T1w MR images available, we select the average of the motion-corrected co-registered individual images resampled to 1 mm isotropic voxels, located in the SUBJ_111 subfolder. The clinical data being converted are defined in a spreadsheet (clinical_specifications.xlsx) available with the code of the converter, which the user can modify.

Using the converter

The converter can be run with the following command line:

clinica convert oasis-to-bids  dataset_directory clinical_data_directory bids_directory

where:

• dataset_directory is the path to the original OASIS images's directory;
• clinical_data_directory is the path to the directory where the xls file with the clinical data is located;
• bids_directory is the path to the output directory, where the BIDS-converted version of OASIS will be stored.

!!! note In order to improve the readability, the BIDS subject id is different from the original OASIS id of the subject. Indeed, the BIDS subject id is so defined: sub-OASIS1+ original numerical id of the subject Example: If the original subject id is OAS1_0001_MR1, since the numerical id is 0001, the final BIDS id will be sub-OASIS10001.

Citing this converter in your paper

!!! cite "Example of paragraph:" The OASIS data have been curated and converted to the Brain Imaging Data Structure (BIDS) format [Gorgolewski et al., 2016] using Clinica [Samper-González et al., 2018].

!!! tip Easily access the papers cited on this page on Zotero.