Hi all,
I've written a function that can write mgh files from R ( http://www.r-project.org/). Hopefully some of you will find it useful. It's more or less a translation of save_mgh.m.
If you're looking for a function that can read mgh files into R, load.mgh.R is included in a package I wrote which can be found here: http://www.nitrc.org/frs/download.php/4629/cortex_0.1.tar.gz
I recommend using load.mgh.R to read data in, only because save.mgh.R follows the same scheme within R for storing data. I'll include save.mgh.R in this package at some stage.
If you run into problems with either of these let me know & I'll do my best to help.
Code is pasted below between the lines below, copy this into a text file and save as "save.mgh.R"
Example usage (in R):
my.surface <- load.mgh("hpardoe.lh.thickness.fsaverage.mgh") my.surface$x <- rnorm(163842, mean = 3, sd = 0.3) # replaces thickness
values with random noise
save.mgh(vol = my.surface, fname = "test.lh.mgh")
you can then open "test.lh.mgh" in freeview.
Best wishes Heath
---------------------------------------------- save.mgh <-function(vol,fname) {
# R translation of save_mgh.m # written by Heath Pardoe, heath.pardoe@nyumc.org, 09/12/2013
MRI.UCHAR <- 0 MRI.INT <- 1 MRI.LONG <- 2 MRI.FLOAT <- 3 MRI.SHORT <- 4 MRI.BITMAP <- 5 MRI.TENSOR <- 6 slices <- c(1:256)
fid <- file(fname,open = "wb", blocking = TRUE)
width <- vol$ndim1 height <- vol$ndim2 depth <- vol$ndim3
writeBin(as.integer(1),fid,size = 4, endian = "big") writeBin(as.integer(width),fid,size = 4, endian = "big") writeBin(as.integer(height),fid,size = 4, endian = "big") writeBin(as.integer(depth),fid,size = 4, endian = "big") writeBin(as.integer(1),fid,size = 4, endian = "big")
# HP note: I've ignored all the diffusion tensor stuff writeBin(as.integer(MRI.FLOAT),fid,size = 4, endian = "big")
writeBin(as.integer(1),fid,size = 4, endian = "big") # dof = fread(fid, 1, 'int'); ## HP note: ignored ^this line^ from save_mgh.m
UNUSED.SPACE.SIZE <- 256 USED.SPACE.SIZE <- (3*4+4*3*4) # space for ras transform
unused.space.size <- UNUSED.SPACE.SIZE - 2
# ignored all the stuff about "M" - could probably do it if necessary so let me know #if (nargin > 2) ## fwrite(fid, 1, 'short') # ras.good.flag <- 0 # writeBin(1,fid,size = 2, endian = "big") # unused.space.size <- unused.space.size - USED.SPACE.SIZE ## fwrite(fid, sizes(1), 'float32') # xsize ## fwrite(fid, sizes(2), 'float32') # ysize ## fwrite(fid, sizes(3), 'float32') # zsize # # fwrite(fid, M(1,1), 'float32') # x.r # fwrite(fid, M(2,1), 'float32') # x.a # fwrite(fid, M(3,1), 'float32') # x.s
# fwrite(fid, M(1,2), 'float32') # y.r # fwrite(fid, M(2,2), 'float32') # y.a # fwrite(fid, M(3,2), 'float32') # y.s
# fwrite(fid, M(1,3), 'float32') # z.r # fwrite(fid, M(2,3), 'float32') # z.a # fwrite(fid, M(3,3), 'float32') # z.s
# fwrite(fid, M(1,4), 'float32') # c.r # fwrite(fid, M(2,4), 'float32') # c.a # fwrite(fid, M(3,4), 'float32') # c.s #else # fwrite(fid, 0, 'short') # ras.good.flag <- 0 writeBin(as.integer(0),fid,size = 2, endian = "big")
# } #
writeBin(as.integer(rep.int(0,unused.space.size)),fid,size = 1) bpv <- 4 # bytes/voxel nelts <- width * height # bytes per slice writeBin(vol$x,fid, size = 4, endian = "big") close(fid) } ---------------------------------------------