My goal this summer is to learn both of these systems. I have a background in R programming but I know that learning how to do data processing for fMRI studies is a skill to itself. Does anyone have some solid suggestions for how to do this?
hello carrie
there are lots of available tools for FMRI data processing , for matlab you can look for conn ,Gretna spm and many other tools
for Linux you can try FSL
Thanks Diksha,
Do you know of any tutortials for SPM and FSL? I can get both set up on my laptop, but where to go from there to develop some fluency with the programs is a bit more challenging. I will be working in a lab over the summer, but I want to get into the lab (they use FSL) with some degree of working knowledge.
till now I have not tried SPM and I am also new with FSL .so what I can tell you try to look at fsl wiki and join fsl open discussion form where experts try to solve out even basics queries . please find attaced link for fsl and jiscmail for open discussion
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
https://www.jiscmail.ac.uk/
Carrie, documentation for FSL is really complete and full of practical examples that you can run on your own. Look for FSL course on their website, you will find step-by-step tutorials packed with some test data to download. SPM is a little bit tricky to use, along with AFNI, but if you have some programming skills it won't be difficult to manage these packages as well.
I am starting on AFNI since that will be the first program I work on. I am digging through documentation NIH recommends using WUBI on top of Virtual Box, but WUBI is not supported on Windows 8. Any suggestions?
What I have ended up doing is I installed VirtualBox and created a Linux virtual machine on to which I installed Ubuntu. From there I set up AFNI per the instructions on the NIH website. However, those instructions are outdated and rely on Red Hat... so some of the commands were invalid or did the wrong thing.
In fact, it has you install R base but it is an old version so you have to update R to the new version and then (as a newbie) I couldn't get packages to install. The permissions were wrong. So, since I have experience with R-Studio I installed that, updated, and installed packages, hoping this would also transform into the command line R base. It did! Yay!
Things I have learned that I would have liked to know going into it.
To get out of the VirtualBox default, obnoxious and dysfunctional teeny tiny screen (low resolution, no full-screen) mode you have to install guest additions from the Devices Menu. If you don't do this, it is nearly impossible to change resolutions or adjust your screen size to fully visualize anything. Since I'm learning fMRI this is REALLY important... not to mention working from a 4" x 5" screen gets very frustrating very fast.
Just to get everything on your system (from ground up) installed and updated (including practice data sets) going for AFNI and their Boot Camp tutorials, your virtual computer needs 13 GB... that is just the BARE minimum... if you are doing analysis and manipulation you will need more space. I have a lot of space on my laptop anyway so I just gave it 50 GB, so I have about 35 GB free to work with.
RedHat Command to install:
sudo yum istall package_to_install
Ubuntu Command to install:
sudo apt-get install package_to_install
There is more, and I would re-write the instructions for beginners because there is enough ambiguity and innacuracy in the AFNI site instructions that things go wrong and frequently.
Some of that is just a matter of orienting and learning how to navigate a new system, but a some of it is poor instructions.
http://afni.nimh.nih.gov/bootcamp/howto/linux_setup.html
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