From 6f81685bfdb19e455a8f8d1020904fa7beede9f0 Mon Sep 17 00:00:00 2001 From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com> Date: Thu, 10 Oct 2024 09:29:14 +0200 Subject: [PATCH] [DOC] Modify download instructions for OASIS-to-BIDS data (#1324) --- docs/Converters/OASIS2BIDS.md | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/docs/Converters/OASIS2BIDS.md b/docs/Converters/OASIS2BIDS.md index 63c6d29ea..85fbf1dc3 100644 --- a/docs/Converters/OASIS2BIDS.md +++ b/docs/Converters/OASIS2BIDS.md @@ -1,7 +1,10 @@ # `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). @@ -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 @@ -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 @@ -67,7 +70,7 @@ DATASET_DIRECTORY ├── ... ``` -- `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.