I always know that it is possible to call to FSL programs in BrainFX. After all, FSL has a command line interface, and how do we call CamBA program in CamBAfx? Command line. Yes, there are differences beween the environment setup for FSL and CamBA, but solving them is not rocket science. Once you know how to create a specialized, isolated environment to run CamBA on every machine, the same technique can be used to run FSL.
We created BrainFX in support of our Neuroscience research work. Increasingly, we find that we are using FSL to run the preliminary stages for structural analysis of the brain. Thus, we wants to explore whether we can run FSL inside BrainFX with the view of creating hybrid FSL and CamBA pipelines. Unfortunately, the powers-that-be is not willing to take my word for it, so a little demonstrator is in order.
After playing with FSL and BrainFX for a few hours, I managed to cook up such a demonstrator. It is a basic one, i.e., proving that BrainFX can reach out to BET. Let’s face it, BET is one of the easiest program in FSL to co-opt with BrainFX, and the demonstrator did nothing but read in a NifTI image, process it with BET then write the output, bypassing all the options you can set with BET. Nonetheless, it shows that it is possible to run BET with BrainFX.
I must stress that these work are very preliminary. It simply demonstrates that there are no-unsurmountable hurdle in getting BrainFX to work with FSL. The next plan is to get FSL programs that we need running in BrainFX, before branching into mixing FSL with CamBA. There will be a lot of decision to be made before both FSL and CamBA can coexists under BrainFX’s umbrella.
Maintaining the tradition of calling something integrated into genericFX as fx, we named the FSL integration into BrainFX FSLfx.
Please note that we are not integrating FSL and CamBA. They are integrated separately into BrainFX. In fact, it is possible to create a CamBA-like GUI for FSL in such a way that it live and breath FSL, without losing any funtionalities that makes the GUI unique. What we do plan to do is to marry FSL and CamBA to produce offsprings (pipelines) that are more powerful than their parents separately.
We will keep you informed on our progress. Right now the most important task is to get blessing from FSL team.
December 26, 2007 at 3:46 pm |
[Editor Note: comment moved to here from "About".]
Assaf Says:
December 26, 2007 at 10:31 am edit
Hi,
I’m trying to compile FSL with Eclipse , and would appreciate any help you might have.
Also, is the project frozen or are there more developments ahead?
Thanks,
- Assaf Razon
Tel-Aviv University
December 26, 2007 at 4:04 pm |
I haven’t compiled FSL in Eclipse as I have no need to. If I were to do it, I will create an ant script to automatically setup FSL variables etc that is needed for successful compilation, as listed under thier “how to compile from source distribution” page. This will allow me to run the compilation under “Run->Run External As”.
If you are simply using FSL, I cannot see any advantage of doing so. I can see the advantage if you are planning to contribute to FSL. If that is what you wish, talk to the FSL folks. They will be able to help you there.
As far as the FSL with BrainFX is concerned. It’s completed. The idea is to allow calling FSL from Command Line via BrainFX. That’s completed since we can now call from command line. The next stage is to put FSL modules into pipelines.
If what you want is to run inidivual FSL modules on multiple datasete, then we have a set of pipelines for this. They were developed for testing, and is simply an encapsulated version of FSL programs’ command line. There is no maintainer for them. Also, note that you are able to do most of the thing in FSL’s UI anyway.
It will be on an “as-needed” basis to support our work at the Brain Mapping Unit. Currently, we only did TBSS for FSL3.3 and froze it there. If you want to see what we did, go to sourceforge.net/projects/cambafx and download special-editions/1.3.2/tbss_se-1.3.2.zip. Note that you must follow instruction in Help on how to setup FSL properly. There are several reasons why we are not distributing FSL with TBSSfx: (1)No rights to redistribute, [fatal] (2)FSL is simply too large at 1+GB, (3)users need to choose the correct variant of FSL [compounding the problem in (2) ] and (4) FSL packages includes a lot of GNU programs, to distrbute FSL packages as it is means we are also distributing those GNU programs, that post a responsibillity on us to look up and carry the source code for those GNU program which we simply do not have the time to do.
TBSSfx simply automate the 5 steps TBSS process and nothing else. There is no plan to upgrade it to FSL4.0