fMRI studies and AFNI

[kreno]

Anyone here familiar with AFNI? I'm trying to learn it.... how long does it take? Not an easy program - I have some familiarity with Linux, thank god... but other than that it's not easy.

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[panch]

kreno,

it would take about two weeks to become familiar enough to begin to be able to play w/ datasets. that assumes that you have a Linux machine already setup w/ AFNI and some scans to play w/. prolly a month after that to produce something of interest (assuming that you have subjects and data collected).

if you are starting from scratch or you are at a center w/ advanced analysis in fMRI data going on, i would suggest learning freesurfer (an MGH/MIT overlay on AFNI that should allow much more precise data analysis) along w/ AFNI basics.

if you are new to the principles of functional imaging, i would suggest reading some papers or chapters on the fundamentals of functional brain imaging, and the principles and drawbacks of BOLD and other fMRI techniques and block vs event-related design, etc. better yet, if you can get funded, i would suggest taking an fMR workshop class by the likes of MCW, MGH, UCLA or the NIH (also Wash U, Stanford, U Pitt, U Penn, U Chicago (to some extent), among other leaders in the field)

also check out the AFNI documentation pages and the AFNI message board. Dr. Robert Cox, the "godfather" of AFNI is great at recognizing the advantages and disadvantages of his techniques.
http://afni.nimh.nih.gov/afni/

above all, as you master the basic of computer analysis, understand that the most important first step is to design and execute experiments that actually address the question being asked. there's not much more frustrating than chasing an epiphenomenon or ghost of poor initial experimental design.

 

[kreno]

Wow, thanks. Well, yes, I have a linux machine running with AFNI installed....

I'm not starting from scratch; rather, I'm at a lab w/everything involved - I'm just a beginning undergraduate lab associate, and as such my Prof wants me to learn it... problem is that it's not the easiest thing in the world with just minimal guidance.

What is freesurfer? Can you explain exactly what this is?

Yes, thank you about Dr. Cox - I've already used his site and online workbooks, etc, extensively!

 

[panch]

here it goes (sorry, i may be a touch hazy on the details, but the principles are important):

freesurfer is a more overarching fMRI data analysis tool as it allows one to create 3d reconstructions of the structural and functional datasets (read, helping to localize to that subject's brain better), to allow for pooled data-set type of analysis (comparing activation b/w groups), and to allow the creation of a blowup structural brain and functional overlay (allowing for fine detailed localization, perhaps differentiating signal from abutting cortex w/in the same sulcus)

website:
http://surfer.nmr.mgh.harvard.edu/

mind you, i have not played w/ freesurfer myself, i just know it exists and the claims that the writers make are strong (it's the type of data analysis that i would do if i had a good project).

also, this is all based on the presumption that we are measuring anything approaching brain activity w/ the BOLD technique.

but, have fun w/ the work. it will be "hot" for at least the next 5 years, and you'll learn a lot about how we think the brain works (and maybe help to reshape our notions).

 

[sat0ri]

Hey so I'm necrobumping because I'm in the same boat a decade later: I'm an undergraduate and I'm looking to process (and pre-proccess) some human fMRI data. I have some minor but increasing familiarity with MatLab, and would like to do it through there if possible. Does anyone have some recent materials or tutorials on how to do this?

 

[meister]

I wish the admins had listened to me and set it up so threads auto-close after a few weeks of no activity...I mean honestly, 11 years???