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- studyforrest.org Dataset
- ************************
- |license| |access|
- 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.
- .. _Git: http://www.git-scm.com
- .. _git-annex: http://git-annex.branchable.com/
- .. |license|
- image:: https://img.shields.io/badge/license-PDDL-blue.svg
- :target: http://opendatacommons.org/licenses/pddl/summary
- :alt: PDDL-licensed
- .. |access|
- image:: https://img.shields.io/badge/data_access-unrestricted-green.svg
- :alt: No registration or authentication required
|
