Contents

  1. Initial Setup
  2. Adding a data file
  3. Getting a data file
  4. Tagging a data file
    1. Display metadata
    2. Assign metadata
    3. List all files with a given tag
    4. Retrieve all files with a given tag

This page describes how to deal with adding and tagging data files in the freesurfer source code repository.

Initial Setup

Based in the information included in the Freesurfer_github page, the remotes of your freesurfer repo working directory should look something like: 

git remote -v 
 
  datasrc       file:///space/freesurfer/repo/annex.git (fetch)
  datasrc       file:///space/freesurfer/repo/annex.git (push)
  origin        git@github.com:zkaufman/freesurfer.git (fetch)
  origin        git@github.com:zkaufman/freesurfer.git (push)
  upstream      git@github.com:freesurfer/freesurfer.git (fetch)
  upstream      git@github.com:freesurfer/freesurfer.git (push)

Adding a data file

The following example assumes we want to add a data file called 'testdata.tar.gz' to the 'distribution' directory: 



Getting a data file


To retrieve the contents of a data file: 
## Retrieve a specific file
git annex get mri_em_register/testdata.tar.gz

## Retrieve everything under the current directory (not recommended)
git annex get .


Tagging a data file


The data files have been broken down into the following 3 categories, and it is essential that data files get the proper tag(s) so that our servers and diskspace is not overwhelmed when only a known subset of the data is required.: 
  1. Those being required for build time checks (tagged makecheck) 
  2. Those required for a local installation (tagged makeinstall) 
  3. Everything else (untagged) 


Display metadata


To show all the metadata associated with a file: 
git annex metadata mri_em_register/testdata.tar.gz


Assign metadata


To assign a tag to an existing datafile.  
git annex metadata mri_em_register/testdata.tar.gz -s fstags=makecheck
git annex sync
We can also append tags: 
git annex metadata mri_em_register/testdata.tar.gz -s fstags+=makeinstall
git annex sync


List all files with a given tag


git annex find --metadata fstags=makecheck


Retrieve all files with a given tag


Get only the data files required for build time checks (1.9 GB) 
git annex get --metadata fstags=makecheck .
Get only the data files required for local installation (4.3 GB) 
git annex get --metadata fstags=makeinstall .