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.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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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