aligned-mri

studyforrest.org Dataset

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Pre-aligned MRI data

This repository contains data derived from the raw data releases of the studyforrest.org project. In particular these are:

• BOLD fMRI timeseries aligned to subject-specific template images and using transformations available from https://github.com/psychoinformatics-de/studyforrest-data-templatetransforms

For more information about the project visit: http://studyforrest.org

File name conventions

Each directory in the subject directories corresponds to one template image space. Data in sub* directories are participant-specific (not aligned across participants). However, templates with the same name have corresponding input data.

Each directory contains one or more image files with more-or-less self-explanatory names, identifying the corresponding participant and scan.

Lastly, the code/ directory contains the source code for computing all files contained, as well as a number of validation analyses.

How to obtain the dataset

This repository is a DataLad dataset. It provides fine-grained data access down to the level of individual files, and allows for tracking future updates. In order to use this repository for data retrieval, DataLad is required. It is a free and open source command line tool, available for all major operating systems, and builds up on Git and git-annex to allow sharing, synchronizing, and version controlling collections of large files. You can find information on how to install DataLad at handbook.datalad.org/en/latest/intro/installation.html.

Get the dataset

A DataLad dataset can be cloned by running

datalad clone <url>

Once a dataset is cloned, it is a light-weight directory on your local machine. At this point, it contains only small metadata and information on the identity of the files in the dataset, but not actual content of the (sometimes large) data files.

Retrieve dataset content

After cloning a dataset, you can retrieve file contents by running

datalad get <path/to/directory/or/file>`

This command will trigger a download of the files, directories, or subdatasets you have specified.

DataLad datasets can contain other datasets, so called subdatasets. If you clone the top-level dataset, subdatasets do not yet contain metadata and information on the identity of files, but appear to be empty directories. In order to retrieve file availability metadata in subdatasets, run

datalad get -n <path/to/subdataset>

Afterwards, you can browse the retrieved metadata to find out about subdataset contents, and retrieve individual files with datalad get. If you use datalad get <path/to/subdataset>, all contents of the subdataset will be downloaded at once.

Keep data up-to-date

DataLad datasets can be updated. The command datalad update will fetch updates and store them on a different branch (by default remotes/origin/master). Running

datalad update --merge

will pull available updates and integrate them in one go.

Find out what has been done

DataLad datasets contain their history in the git log. By running git log (or a tool that displays Git history) in the dataset or on specific files, you can find out what has been done to the dataset or to individual files by whom, and when.

More information

More information on DataLad and how to use it can be found in the DataLad Handbook at handbook.datalad.org. The chapter "DataLad datasets" can help you to familiarize yourself with the concept of a dataset.