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oasis3-to-bids – Conversion of the Open Access Series of Imaging Studies (OASIS-3) to BIDS

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 "Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Disease" set is a retrospective compilation of data for >1000 participants that were collected across several ongoing projects through the WUSTL Knight ADRC over the course of 30 years. Participants include 609 cognitively normal adults and 489 individuals at various stages of cognitive decline ranging in age from 42-95yrs. All participants were assigned a new random identifier and all dates were removed and normalized to reflect days from entry into study. The dataset contains over 2000 MR sessions which include T1w, T2w, FLAIR, ASL, SWI, time of flight, resting-state BOLD, and DTI sequences. Many of the MR sessions are accompanied by volumetric segmentation files produced through Freesurfer processing. PET imaging from 3 different tracers, PIB, AV45, and FDG, totaling over 1500 raw imaging scans and the accompanying post-processed files from the Pet Unified Pipeline (PUP) are also available in OASIS-3.

For more information about the images and the dataset you can read the OASIS-3: Imaging Methods and Data Dictionary.

OASIS 2

We do not currently support the conversion of OASIS-2.

Dependencies

If you installed the core of Clinica, this converter needs no further dependencies.

Downloading OASIS-3

The OASIS-3 to BIDS converter requires the user to have downloaded the OASIS-3 (also called Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Disease) imaging and clinical data.

To do so, visit the OASIS website, click on DATASETS then OASIS-3. For the first access, you have to scroll down to click on Apply To Access OASIS Data in the bottom of the next "Data Use Agreement" section and follow the procedure. Then, you can download the data via the OASIS3 project repository in NITRC.

Regular OASIS3 data

Access the XNAT Imaging Download page after logging in with your OASIS3-accepted NITRC account. You will find a download interface with different options, such as shown below.

Screenshot 2021-07-15 at 10 48 45

  1. Select Sessions : select the sessions you want to work with.

    MAKE SURE TO SELECT THE OASIS3_data_files SESSION, WHICH CONTAINS THE CLINICAL DATA NECESSARY FOR THE CONVERSION.

  2. Select Image Data :

    a. Scan Format : select both BIDS and NIFTI. Otherwise, you will be missing data.

    b. Scan Types : select only the modalities you desire. Do note that if it is not amongst the modality handled by this converter, it will not be converted.

    c. Additional Resources : select BIDS.

    d. Assessments : do not select anything.

  3. Download Data :

    a. ⚠️ select "Simplify downloaded archive structure" and not the other options.

    b. Use the XNAT Desktop Client if you can to be more efficient than downloading through the web browser.

    c. Click "Submit" to download.

  4. After download completion, ensure that the OASIS3_data_files files are in a separate directory which will be your CLINICAL_DATA_DIRECTORY.

    Tip

    You do not have to modify the original folder name before using the converter.

ADRC Clinical Data

In previous versions of clinica (<v0.12.0) we used the "ADRC" metadata file which contained slightly different values for the Age at Entry parameter. This might explain slight differences in your results if you try to compare a OASIS3 dataset metadata based on age then versus now.

TAU PET Imaging

Historically, the Tau PET scans for the OASIS3 longitudinal belonged to a different project, which required additional data request. Nowadays, data usage is granted together with the regular OASIS3 project.

To download Tau PET scans, one must follow the same steps described above (no need to re-download the OASIS3_data_files), on the OASIS3_AV1451 and OASIS3_AV1451L download pages.

You can access the Tau PET projects directly from the OASIS3 Imaging download window by clicking one of the highlighted elements in the following screenshot: OASIS3_TAU.PNG

There, click on Download Images OASIS3_download.PNG

And repeat steps 1 to 4.

Supported modalities

Please note that the converter currently processes the clinical data and the following modalities : T1W / T2star / Flair / DWI / fMRI / PET : FDG, PIB, TAU

Support for additional modalities may be implemented later.

For participants with multiple T1-weighted images available, the average of the motion-corrected co-registered individual images resampled to 1-mm isotropic resolution is given priority.

Using the converter

The converter can be run with the following command line:

clinica convert oasis3-to-bids [OPTIONS] DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY BIDS_DIRECTORY

where:

  • DATASET_DIRECTORY is the path to the original OASIS-3 imaging directory, which content should look like:

    DATASET_DIRECTORY
├── OAS30001_MR_d0757
│   ├── anat1
│   │   ├── sub-OAS30001_ses-d0757_acq-TSE_T2w.json
│   │   └── sub-OAS30001_ses-d0757_acq-TSE_T2w.nii.gz
│   ├── anat2
│   │   ├── ...
│   ├── ...
│   ├── dwi1
│   │   ├── sub-OAS30001_ses-d0757_dwi.bval
│   │   ├── sub-OAS30001_ses-d0757_dwi.bvec
│   │   ├── sub-OAS30001_ses-d0757_dwi.json
│   │   └── sub-OAS30001_ses-d0757_dwi.nii.gz
│   ├── func1
│   │   ├── sub-OAS30001_ses-d0757_task-rest_run-01_bold.json
│   │   └── sub-OAS30001_ses-d0757_task-rest_run-01_bold.nii.gz
│   ├── func2
│   │   ├── ...
│   ├── swi1
│   │   ├── sub-OAS30001_ses-d0757_minIP.json
│   │   └── sub-OAS30001_ses-d0757_minIP.nii.gz
│   └── swi2
│       ├── ...
└── ...
└── OAS30002_AV45_d2340
    ├── BIDS
    │   └── dataset_description.json
    ├── OAS30002_AV45_PUPTIMECOURSE_d2340
    │   └── SNAPSHOTS
    │       ├── OAS30002_AV45_d2340_m0_t.jpg
    │       ├── ...
    └── pet1
        ├── BIDS
        │   ├── sub-OAS30002_ses-d2340_acq-AV45_pet.json
        │   └── sub-OAS30002_ses-d2340_acq-AV45_pet.tsv
        └── NIFTI
            └── sub-OAS30002_ses-d2340_acq-AV45_pet.nii.gz
└── ...

  • CLINICAL_DATA_DIRECTORY is the path to the directory containing the clinical CSV files.

  • BIDS_DIRECTORY is the path to the output directory where the BIDS-converted version of OASIS-3 will be stored.

Note

In order to improve the readability, the BIDS subject ID is different from the original OASIS-3 ID and is defined as follows:

sub-OASIS3+ original numerical ID of the subject

Example

If the original subject ID is OAS30001, since the numerical ID is 0001, the final BIDS ID will be sub-OASIS30001.

Optional parameters common to all converters

  • -- subjects_list / - sl : path to a text file containing a list of specific subjects to extract. The expected format is one subject per line :
  001_S_0001
  002_S_0002
  • -- n_procs / - np : Number of cores used to run in parallel. (default: (Number of available CPU minus one))

Citing this converter in your paper

Example of paragraph:

The OASIS-3 data have been curated and converted to the Brain Imaging Data Structure (BIDS) format [Gorgolewski et al., 2016] using Clinica [Routier et al.; Samper-González et al., 2018].

Tip

Easily access the papers cited on this page on Zotero.

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