DTI-TK Installation

Follow ALL the steps below (unless noted as optional) to ensure DTI-TK working properly.

If you have compiled DTI-TK from source, skip the steps 1 and 2.

1. Download the binary package (in tar.gz format) for your platform (either Linux i386 or MacOSX). The links to the binary packages can be found in the Downloads page.

2. Move the downloaded file to your location of choice, then uncompress and extract the contents of the package. (Skip to step 3, if you know how to do this). (:showhide init=hide div=extraction:)

The following command can be used to uncompress and extract the package at once:

tar xvfz ${file}

Replace ${file} with the filename of the binary package. As an example, if the filename of the binary package is "dtitk_linux_binary.tar.gz", then the command to use will be

tar xvfz dtitk_linux_binary.tar.gz

If you download the binary package using a web browser, such as Safari, it may uncompress the file automatically. In that case, you only need to extract the contents of the package and the appropriate command to use will be

tar xvf ${file}

Use the same example as above, after the uncompression, the file will be "dti_linux_binary.tar". The command for extraction will be

tar xvf dti_linux_binary.tar

2.1 Mac OS specific instructions (:showhide init=hide div=configure_path:)

For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error ... can't be opened because it is from an unidentified developer.

One can override this through the graphical user interface (GUI) but it becomes tedious quickly to do this for all DTI-TK binary executables.

Thankfully, this can also be achieved through the command line interface (CLI) as described here, allowing the possibility of scripting the process for multiple binary executables.

As an example, the command to remove the error for VolumeInfo looks like the following, assuming you are in the ${DTITK_ROOT}/bin directory:

sudo xattr -dr com.apple.quarantine VolumeInfo

Note that, for security reasons, this will require you to enter the password of the system administrator.

3. Add the path to the DTI-TK and define the DTITK_ROOT variable. (:showhide init=hide div=configure_path:)

The following is written for the bash shell. If you are using a different shell environment, adapt the commands accordingly.

To make temporary changes for the purpose of testing

export DTITK_ROOT=${DIR}/dtitk
export PATH=${PATH}:${DTITK_ROOT}/bin:${DTITK_ROOT}/utilities:${DTITK_ROOT}/scripts

IMPORTANT:

If you download the binary package, replace ${DIR} with the full pathname of the directory where you've unpacked the binary package. e.g., if the full pathname to the directory is "/Users/huiz/unix", then the command to use will be

export DTITK_ROOT=/Users/huiz/unix/dtitk

If you compile DTI-TK from source, replace ${DIR} with the full pathname of your installation directory.

To add the path to the DTI-TK permanently

Include the above command to your .bash_profile file (or equivalent on your unix system). The instruction for Mac is available here and for Linux here. If you use tcsh instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now mandatory.

4. Verify the installation (:showhide init=hide div=verify:)

First check the path is set correctly

which VolumeInfo

Use the example as above (for downloaded binary packages), if the installation is done correctly, the command should return the following

/Users/huiz/unix/dtitk/bin/VolumeInfo

This shows that we have placed the DTI-TK under the directory "/Users/huiz/unix/".

Next check if the binary works as expected

VolumeInfo

If the binary works correctly, you should see

Usage: VolumeInfo filename

(This is typical of most DTI-TK commands. If you do not supply any arguments to the command, it will print out its usage instructions. In this example, the instruction means that you need to provide a single argument.)

If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with pre-compiled binaries. If your system is not among them, you can either switch to a supported platform or will need to compile from the source code.

The optional steps are as follows:

5. Sun Grid Engine (SGE) support for cluster-computing (:showhide init=hide div=sge:)

If your computing infrastructure includes/implements SGE-based cluster-computing support, you can optionally enable DTI-TK to utilize this feature. The environment variable that needs to be defined in your .bash_profile file is DTITK_USE_QSUB. Setting the variable to 1 will enable the SGE support. To disable this feature, simply setting the variable to 0.

export DTITK_USE_QSUB=1

6. Support for animal brains (:showhide init=hide div=species:)

Animals, such as monkeys, have brain size very different from human. DTI-TK accounts for this difference using DTITK_SPECIES environment variable. This variable is default to "HUMAN". You need to set this variable if you want to apply DTI-TK to an animal study. The supported animals include "MONKEY" and "RAT". You can add additional animal support easily by editing the file dtitk_common.sh under the scripts directory.

Here is an example of setting the DTI-TK for a monkey study.

export DTITK_SPECIES="MONKEY"

From PmWiki

Documentation: DTI-TK Installation

DTI-TK Installation