Hi,
I'm also using R to look at some FreeSurfer data, mostly to play with significance values. To do this, I convert them to ascii (mris_convert) and load them into R with the read.table function. When I am done, I write a new ascii file, mris_convert it back to a *.w or *.sig, and load it into tksurfer. The function to write the file is trivial, but here it is for completeness:
## more FreeSurfer specific stuff. ## the modified significance values in a text file called "fdr.txt" ## posindex is a global variable tracking which pvalues were ## positive in the original sig file ## (recall that FS stores sig values as log10(sig), with the ## sign indicating direction of effect) ## vindex is a global variable tracking the vertex number ## associated with a given sig value write.fs.output <- function(){ fdr <- dget('fdr.txt') fdr <- log10(fdr) fdr[posindex] <- fdr[posindex] * -1 cat("0.000\n", length(fdr), "\n", file="AA-TT_cmfdr.ascii") for (i in 1:length(fdr)){ cat(vindex[i], fdr[i], "\n", sep="\t", file="AA-TT_fdr.ascii", append=TRUE) } }