Thanks very much, Doug! That version works perfectly.

Just out of curiosity now, is there potentially a way to create a binarized mask in the other way that I mentioned?

That is, to generate a mask that cuts maintains the middle 95% of the data (i.e. +- 2SDs of the signal mean) as a way to remove extreme values from the final mask?

Thanks again, Bimal

On June 9, 2016 at 1:47:14 PM, Douglas N Greve (greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu) wrote:

That was a bug which I have not fixed. Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize

On 06/09/2016 03:53 PM, Lakhani, Bimal wrote:

Good afternoon,

I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 64bit, but when I use the option — rmax, I am getting an error that says the —rmax option is not recognized. It is made weirded because —rmin works perfectly.

Here is the command line and the following error:

boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz' --rmax 1.95 --o '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’

ERROR: Option --rmax unknown

Thanks very much! Bimal

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