FSLfx

Website is work in progress

FSLfx is a plugin designed to allow FSL to be used in BrainFX.

It is developed and maintained separately and is not affiliated with FMRIB, the creator of FSL.

The objective of developing FSLfx is to support work in the Brain Mapping Unit which aims to create hybrid analysis pipelines using software from different fMRI analysis package. As such, it is not intended as a replacement for FSL’s user interface. It is also not expected to expose all FSL analysis modules to BrainFX. In fact, we expects to expose each FSL analysis modules on an as-needed basis.

We haven’t decided on the license yet. Any license will of course have to be compatible with FSL’s license. The principle consideration will be to permit third party to build on FSLfx work (even if it means FSLfx has to be torn apart) and that they contribute back to FSLfx users community. It is likely to be the General Public License.

At present, we only completed the proof-of-concept work which demonstrate that we can call FSL inside BrainFX. Please stay tuned.

Important Notes:

1. BrainFX FSL Customization

These is the preliminary installation instructions and is expected to change without notice

In CamBAfx:

1. click on Help→Software Update→Find and Install...→Search for new features to install
2. Check “CamBA Discovery Site”
3. Click “Finish” button
4. On the next screen, expands “CamBA Discovery Site”, then expands “FSLfx” and check “FSLfx Batch Processing Workbench Plugin 0.1.0”
5. Click “Next” button
6. Select “I accept the terms in the licensing agreement”
7. Click “Next” button
8. On the next screen, select “Install”
9. When asked whether you want to restart, choose “Yes” to restart, or “Apply Changes”.

Then

1. Download FSL from http://www.fmrib.ox.ac.uk, call this fsl.tar.gz
2. Change directory to <camba>/plugins/uk.ac.ox.fmrib.fsl.linux_0.1.0/software where <camba> is your CamBAfx installation directory.
3. Unzip <fsl.tar.gz>
   <code>tar -zxvf fsl.tar.gz
   The directory fsl should be created.
4. Then either merge <camba>/plugins/uk.ac.ox.fmrib.fsl.linux_0.1.0/software/fsl.sh with your existing ~/.fslconf/fsl.sh where ~ is your home directory, or copy it there.
   The alternative is to replace <camba>/plugins/uk.ac.ox.fmrib.fsl.linux_0.1.0/software/fsl/etc/fslconf/fsl.sh with the one in <camba>/plugins/uk.ac.ox.fmrib.fsl.linux_0.1.0/software/fsl-fslfx.sh
   Both will set FSL to output 4D NifTI uncompressed file. The first approach change the setting for all your FSL programs; the latter only FSLfx’s version of FSL.

Note: “CamBA Discovery site’s URL” is http://discovery.cambafx.org/1.x.

• The design is going to mirror CamBAfx’s layout. It’s more a practical maintenance issue to keep the two layout in sync than a requirement.
• Plugin does not contain FSL suite itself. Users are expected to download FSL themselves. Reasons:
  • FSL exists in a lot of different variant. For example, for Linux, there is a different beween RedHat and Fedora variants. BrainFX is at present, not setup properly to handle this. Chiefly, the plugin name convention does not identify variants. BrainFX is actively considering the pro and con for changing plugin naming convension to org.myplugin.os.vendor as in uk.ac.ox.fmrib.fsl.linux.fedora
  • Even assuming we resolve the plugin name problem, we do not have the resources to hold all versions/variants of FSL.
  • The present Eclipse 3.1 installation system is not tested to see whether it can maintain the execute permission when unzipping the plugin after downloading it. At present, the update site does not maintain execute permission to files when zipping up plugins. [Note: This is solved in Eclipse 3.2]
  • FSL binary packages, what most users will download, are huge (400+MB) after unzipping. It is large because it is designed to be self-contained, i.e., it does not rely on any external program. The only way to trim this down where the trimming makes a dent in size is to write a program to look for and delete program inside FSL bin directory files that already exists on the target computer. At present, no such program is known to exist.

• Built a set of Eclipse plugin to host the FSL program
  • hosting for FSL software
  • Ability to edit ~/fslconf/fsl.sh inside Preference Page.
  • Create a FSL feature to facilitate update of BrainFX over the net
  • Create an installer script/hanlindg library to automate customization of FSL for BrainFX need according to BMU’s Data Standard.
• Build a bridge for BrainFX to communicate with FSL (Implemented as fslfx.sh)

Finally

• Import FSL analysis module as pipeline modules as needed.