afni.nimh.nih.gov

Rick,

Thanks very much! I had originally tried what you suggested, but my activation regions are coming to be outside the brain. This is a mismatch. (I have attached the figure.)

Here are the parameters that I used while saving (in R):

y <- nifti(x, pixdim = c(3,3.5,3.5,6), qform.code = 4, sform.code = 4, intent.code = 5, xyzt.units = c("mm", "mm", "mm"), datatype = 16)
##
## no idea why pixdim[1] = 0 and the codes do not get picked up
## 

y@sform_code <- 0
y@qform_code  <- 4
y@intent_code <- 5
y@pixdim[1] <- 3
y@xyzt_units <- 2 # 2 stands for mm
writeNIfTI(nim = y, file = "Bstand2-int-FAST-death-negative", verbose = TRUE)

I will put the new file up also, with a slightly different name, in case the old one gets wiped out by this upload.

Many thanks again, and I am sorry for all the trouble.

Best wishes,
Ranjan