AFNI and SPM are two different software packages that are primarily used for analyzing MRI/fMRI data. Both are free open-source software, but whereas SPM is written in/runs in MATLAB, AFNI is written in C and runs on most unix-like platforms. Both have applications for pre-processing/normalizing MRI scans, performing general linear model analyses on fMRI data, and visualizing results. SPM may be somewhat more versatile, since there are many toolboxes and extensions available to complement the main software suite (e.g. the Conn toolbox). SPM also has functions for performing voxel-based morphometry analyses on anatomical MRI scans, and has extensions for use with EEG/MEG data as well. While there may be comparable functions in AFNI, I am not aware of them. Typically, whether one uses AFNI or SPM is a matter of preference and available software (i.e. access to MATLAB). Hope this helps!

Thanks Mr. Griffis.

hi there Muhammad,

Depends what you want to do. I've used both SPM and AFNI a lot for fMRI. In my opinion AFNI is more versatile in terms of customizing an analysis. It has many more tools and functions for visualizing your data at an astoundingly detailed level. I believe that it's stronger with resting state analyses (see ANATICOR, i.e. Hang Joon Jo, 2010) and with nonlinear registration (i.e. 3dQwarp) and can do many advanced kinds of regressions (one may need 'R' installed, however). Although afni_proc.py has streamlined and standardized many kinds of analyses in AFNI, it perhaps requires more a little more tcsh scripting than your average SPM user uses Matlab scripting. SPM has some analyses available that no other package has (like dynamic causal modeling) and yes it's true there are many extensions that the SPM community has contributed ( http://www.fil.ion.ucl.ac.uk/spm/ext/ ). SPM's also stronger with modalities other than fMRI. However, it doesn't integrate as fluidly with large parallel computing clusters as AFNI does. Also the packages have slightly different 'ideological foci' in that SPM's authors and community is a little heavier on computational modeling than AFNI's, which in turn is a little more focused on very carefully looking at and understanding one's data. Because SPM's community is larger there are a few more workshops available around the world to learn it. Both have active listservs. After using SPM throughout my doctorate, I was quite pleased with AFNI once I got a hang of it during my postdoc. I plan to return to SPM for certain things, however. Like I said, depends on what you want to do.

-Salvatore (Sam)

Dear Sam,

Thanks very much for your full description.

Is there anybody who can help my problem with AFNI ? Basically I wanna use SPM pre-processed data or do pre-process at AFNI same as SPM.

Well both are free fMRI analysis software. AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analysing, and displaying functional MRI (FMRI) data. And SPM (Statistical Parametric Mapping) is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. However, for SPM you need MATLAB to run it. I don't thgink you can do the pre-processing in SPM and use it with AFNI, and why you need to that any way?

FSL, and BrainVoyager are other options.