xnatutils 0.4.3

Optional Dependencies

The following converters are required for automatic conversions of downloaded images (using the ‘–convert_to’ and ‘–converter’ options)

• dcm2niix (https://github.com/rordenlab/dcm2niix)

• MRtrix 3 (http://mrtrix.readthedocs.io/en/latest/)

Installation

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

brew install python

which python

/usr/local/bin/python

brew doctor

pip --version

easy_install pip

pip install xnatutils

pip install --user xnatutils

pip uninstall progressbar

pip install progressbar2

Authentication

The first time you use one of the utilities you will need to provide the --server (or -s for short) option with the full server address of the XNAT server you would like to connect to. To authenticate with the server you will be prompted to enter your username and password. By default a alias token for these credentials will be stored in a ~/.netrc file with the following format (with permissions set to 600 on the file):

machine <your-server-url>
user <your-alias-token-or-username>
password <your-alias-secret-or-password>

If you don’t want these credentials stored, then pass the ‘–no_netrc’ (or ‘-n’) option.

If you have saved your credentials in the ~/.netrc file, subsequent calls won’t require you to provide the server address or username/password until the token expires (if you don’t want deal with expiring tokens you can just save your username/password in the ~/.netrc file instead, however, please be careful with important passwords). To reset the saved credentials provide --server option again with the full server address including the protocol (e.g. ‘https://’) or edit the ~/.netrc file directly.

To connect to an additional XNAT server, provide the new server address via the --server option. Credentials for this server will be saved alongside the credentials for your previously saved servers. If the --server option is not provided the first server in the file will be used. To used the save credentials for a secondary server you only need to provide as of the secondary server address to --server to distinguish it from the other saved servers. For example given the following saved credentials in a ~/.netrc file:

machine xnat.myuni.edu
user myusername
password mypassword
machine xnat-dev.myuni.edu
user mydevusername
password mydevpassword

then:

$ xnat-ls -s dev MYPROJECT

will be enough to select the development server from the saved credentials list.

Usage

Six commands will be installed

• xnat-get - download scans and resources

• xnat-put - upload scans and resources (requires write privileges to project)

• xnat-ls - list projects/subjects/sessions/scans

• xnat-rename - renames an XNAT session

• xnat-varget - set a metadata field (including “custom variables”)

• xnat-varput - retrieve a metadata field (including “custom variables”)

Please see the help for each tool by passing it the ‘-h’ option.

Help on Regular Expressions

The regular expression syntax used by xnat-get and xnat-ls is fully defined here, https://docs.python.org/2/library/re.html. However, for most basic use cases you will probably only need to use the ‘.’ and ‘*’ operators.

‘.’ matches any character so the pattern:

MRH060_00._MR01

will match

MRH060_001_MR01
MRH060_002_MR01
MRH060_003_MR01
MRH060_004_MR01
MRH060_005_MR01
MRH060_006_MR01
MRH060_007_MR01
MRH060_008_MR01
MRH060_009_MR01

The ‘*’ matches 0 or more repeats of the previous character, which is most useful in conjunction with the ‘.’ character to match string of wildcard characters, e.g.:

MRH060.*

will match all subjects/sessions in the MRH060 project.

Note, that when using regular expressions that use ‘*’ on the command line you will need to enclose them in single quotes to avoid the default wilcard file search, e.g.:

$ xnat-ls 'MRH099.*'

Probably the only other syntax that will prove useful is the ‘(option1|option2|…)’. For example:

MRH060_00(1|2|3)_MR01

will match

MRH060_001_MR01
MRH060_002_MR01
MRH060_003_MR01

For more advanced syntax please refer to the numerous tutorials on regular expressions online.