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[DOC] Modify download instructions for OASIS-to-BIDS data (#1324)
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AliceJoubert authored Oct 10, 2024
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<!-- markdownlint-disable MD046 -->
# `oasis-to-bids` – Conversion of the Open Access Series of Imaging Studies (OASIS) to BIDS

!!! quote "Description reproduced from the [OASIS' webpage](https://sites.wustl.edu/oasisbrains)"
!!! warning
We do not currently support the conversion of OASIS-2.

??? quote "Description reproduced from the [OASIS' webpage](https://sites.wustl.edu/oasisbrains)"
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).
Expand All @@ -22,13 +25,14 @@ If you installed the core of Clinica, this converter needs no further dependenci

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](https://sites.wustl.edu/oasisbrains/), 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`.
To do so, visit the OASIS website page [specific to OASIS-1](https://sites.wustl.edu/oasisbrains/home/oasis-1/), and go to `Download Instructions`.

!!! note
You do not have to modify the original folder name or rename the clinical data file before using the converter.
- Download clinical data by clicking on `OASIS-1 : Demographic and Clinical Data`, then `CSV File with Demographic, and Clinical Data`.
- Download image data by clicking on `OASIS-1 : Raw Data Download` then any archive link.

!!! warning
We do not currently support the conversion of OASIS-2.
All subjects to be converted should be placed in the same folder, which means the archives downloaded from the website should be unzipped in the same folder.


## Modalities supported

Expand All @@ -38,7 +42,6 @@ To convert the imaging data to BIDS, the list of subjects is obtained from the d

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

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├── ...
```

- `CLINICAL_DATA_DIRECTORY` is the path to the directory containing the [CSV](../glossary.md#csv) file called `oasis_cross-sectional.csv`.
- `CLINICAL_DATA_DIRECTORY` is the path to the directory containing the excel file called `oasis_cross-sectional-5708aa0a98d82080.xlsx`.

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

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