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- High-resolution structural images were used to generate the cortical surfaces
- using FreeSurfer (v5.3.0, freely available at http://surfer.nmr.mgh.harvard.edu,
- [Dale et al., 1999]). Additional high-resolution T2w images were included
- in the reconstruction (recon-all -T2 t2file).
- The surface quality was checked by inspecting the slice screenshots of QATool
- (v1.1, freely available at http://ftp.nmr.mgh.harvard.edu/fswiki/QATools, [no
- source paper linked]). The QATool was adopted to take sreenshots of the
- high-resoluton pial surface.
- DataLad datasets and how to use them
- ====================================
- This repository is a DataLad (https://www.datalad.org/) 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 (https://www.datalad.org/)
- 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
- (https://git-annex.branchable.com/) to allow sharing, synchronizing, and version
- controlling collections of large files. You can find information on how to install
- DataLad at http://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.
- Stay 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.
- More information
- ================
- More information on DataLad and how to use it can be found in the DataLad Handbook at http://handbook.datalad.org/en/latest/index.html. The chapter “DataLad datasets” can help you to familiarize yourself with the concept of a dataset.
- References
- ----------
- Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based analysis. I.
- Segmentation and surface reconstruction. Neuroimage 9, 179-194.
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