studyforrest.org Dataset

Template images and image space transformations

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

• participant/scan-specific template images
• transformation between these respective image spaces

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

File name conventions

Each directory in the subject directories and the "templates" directory corresponds to one image template. Templates in sub* directories are participant-specific (not aligned across participants). However, templates with the same name have corresponding input data. Templates in the templates directory have been derived from all participants, and there are typically transformation from participant specific templates into the group template space provided. Group template images carry a grp prefix in their label.

All transformations are the output if FSL tools: either MAT files with 4x4 affine transformation matrices from FLIRT, or FNIRT warp files.

Here is an example of how transformations can be located. The transformation of the template image created from all 3T BOLD images of participant 01 acquired in phase 2 of the project into the group template space for 3T BOLD scans can be found in:

sub-01/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz

Each template directory contains one or more image files with more-or-less self-explanatory names, such as "head", "brain", or "brain_mask". File with such a name in the one of the in_* folders represent the image in the parent folder, aligned and resliced to the target space for this transformation. These images can be used to inspect the quality of the transformation.

Lastly, the code/ directory contains the source code for computing template images and transformation between them.

How to obtain the dataset

This repository contains metadata and information on the identity of all included files. However, the actual content of the (sometime large) data files is stored elsewhere. To obtain any dataset component, git-annex is required in addition to Git.

1. Clone this repository to the desired location.

2. Enter the directory with the local clone and run:

   git annex init
   

   Older versions of git-annex may require you to run the following command immediately afterwards:

   git annex enableremote mddatasrc
   

Now any desired dataset component can be obtained by using the git annex get command. To obtain the entire dataset content run:

git annex get .

Keep data up-to-date

If updates to this dataset are made in the future, update any local clone by running:

git pull

followed by:

git annex get .

to fetch all new files.