Simple fMRI Example

Quick start.

Go into the directory example.rawfmri. This example has simulated fMRI data for 8 subjects, two sessions each.

cd example.rawfmri

Look at the arguments in the file readargs.R. You don’t need to change any of these arguments. Options in the file readargs.R are read by npoint as a convenience, instead of having to type them all out.

cmdargs <- c("-m","mask_4mm.nii.gz", "--set1", "setfilenames1.txt",
             "--set2", "setfilenames2.txt",             
             "--setlabels1", "setlabels1.csv",
             "--setlabels2", "setlabels2.csv",             
             "--model", "fmrimodel.R",
             "--output", "sgedata/sim.",
             "--debug", "debug.Rdata",
             "--sgeN", "10")

These arguments specify a mask (mask_4mm.nii.gz), which has a value of 1 in each voxel we will model. In the directory, there is also a file called oneslice_4mm.nii.gz. If you are on a laptop, or are otherwise very limited in time, you might want to change the mask to be oneslice_4mm.nii.gz, which will reduce computation time by limiting analysis to only one slice of the brainmask.

There are two sets of input files, corresponding to time 1 fMRI data and time 2 fMRI data. The input files are all registered to an MNI template resampled to 4mm isotropic voxels (mni_4mm.nii.gz). If you look at the content of setfilenames1.txt and setfilenames2.txt you will see the names of these input files in the fmri subdirectory. Each fMRI file has 150 volumes, and there are 8 subjects at each time point. Therefore, each setlabel file (setlabels1.csv and setlabels2.csv) has 8*150=1200 lines. Each line has two explanatory variables (High and Low), the number of the volume (TR), the subject number and the number of the time point. The TR and time point are not used by this model.

To generate the jobs for this example, type:


This program reads in all the fMRI data and splits it up into R jobs that can be run in parallel. These will be written in the subdirectory sgedata, as specified by the --output flag. In this subdirectory are two scripts of particular interest. The script runme.local uses the UNIX utility make to run the model on the machine you are logged in to. The script runme.sge submits the job to the default SGE cluster using qsub. Note that if SGE is not correctly configured, runme.sge will not work.

To run the model on each voxel in the mask, type either:


or, if you have an SGE cluster


When everything has completed, you will have four statistical parameter maps with the results:

What it means.

This is an example on simulated data that runs a mixed effects model on the raw simulated fMRI data. There are two explanatory variables of interest, High and Low. The file is a map of the t statistics for the contrast High > Low.

To understand this, let us look at the code that actually runs the model, which is in the file fmrimodel.R. This is specified using the --model flag (in the readargs.R file above).


processVoxel <-function(v) {
    Y <- voxeldat[,v]
    e <- try(mod <- lme(Y ~ High+Low, random=~1|subject, method=c("ML"), na.action=na.omit, corr=corAR1(form=~1|subject), control=lmeControl(returnObject=TRUE,singular.ok=TRUE)))
    if(inherits(e, "try-error")) {
        mod <- NULL
    if(!is.null(mod)) {
        contr <- c(0, 1,-1)
        out <- anova(mod,L=contr)
        t.stat <- (t(contr)%*%mod$coefficients$fixed)/sqrt(t(contr)%*%vcov(mod)%*%contr)
        p <- 1-pt(t.stat,df=out$denDF)
        retvals <- list(summary(mod)$tTable["High", "t-value"],
                        summary(mod)$tTable["Low", "t-value"], t.stat, p)
    } else {
    # If we are returning 4 dimensional data, we need to be specify how long
    # the array will be in case of errors
        retvals <- list(999,999,999,999)
    names(retvals) <- c("tstat-High", "tstat-Low", "", "")

The processVoxel function is run for each voxel number v. Thus, Y is the BOLD signal at each voxel. This code specifies a mixed effects model with two explanatory variables, High and Low. The design matrix is made available to the processVoxel function environment. There is a random effect of intercept per subject. We handle autocorrelation in the model using an autoregressive model of order 1 (AR1). Note that this may not be adequate for real fMRI data sets. The point here is not to forget that it is necessary to think about autocorrelation when you are modeling the raw fMRI time course.

If the model runs without error, then we compute the p-value of the contrast (where High > Low). Variables that we wish to save are collected in a vector, and named. The output variables are assembled into files with the prefix specified by the --output flag and the variable names.

For more information on mixed effects modeling of fMRI data in R, see the document A Tutorial on Modeling fMRI Data Using a General Linear Model. However, the processVoxel function can run any model that can be run on a single voxel. This includes structural equation models, growth models, and so on. This function can also compare several models and output the best according to some criteria.

Building and debugging models.

When developing your own processVoxel function, it is helpful to run interactively on a few specific voxels. Similarly, if there are errors at a voxel it may be helpful to interactively interrogate the model output. The --debugfile flag specifies that the design matrix and voxel data should be written to an R file that can be used for model development and debugging.

If you have run npoint as directed above, you will have a file called debug.Rdata in the sgedata directory.

You can start R from within the sgedata directory, load this file, and see what is defined.

[1] "designmat"          "imagecoordtovertex" "mask.arrayindices" 
[4] "voxeldat"

The designmat data structure contains the design matrix, and voxeldat is a structure that holds all the voxels in the mask. The imagecoordtovertex uses the mask.arrayindices structure to transform image coordinates to vertex numbers. For example, suppose you want to find the time course corresponding to voxel x=20,y=42, z=22 in the mni_4mm.nii.gz image. You would call imagecoordtovertex as follows.

v <- imagecoordtovertex(20,42,22)
[1] 16733

To access the voxel time course (for all subjects and runs) and attach to the design matrix:

Y <- voxeldat[,v]