[ITK-users] Command line use of N4 in MacOS terminal

[Nicholas Tustison]

Hi Erik,

It sounds like this is an ANTs-specific issue.  If you have any further 
questions, I would recommend asking at that forum.

https://github.com/stnava/ANTs/issues <https://github.com/stnava/ANTs/issues>

The command line interface that you reference is ANTs-specific and
should have brackets around it e.g.,

-c [50x50x50x50,0.0001]

I don’t know about the rescale problem.  Does it happen on any image 
or just that specific T2?

Anyway, meet me over on the ANTs forum if you have further questions/
issues.

Nick


> On Jan 20, 2015, at 12:04 PM, Erik Olsson <Erik.Olsson at neuro.gu.se> wrote:
> 
> 
> 
> Hi,
> 
> I have recently started to use N4 as a command line installation and the bias field correction works great in general. 
> 
> I am trying to figure out how to configure the flags for best performance on our T2 MRI images and when trying the rescale intensities I get the error message "segmentation fault 11" for both options ( -r 1   as well as -r 0). I also have a problem with the convergence flag -c, all works fine when I leave this flag out but when trying for example -c 50x50x50x50,0.0001 it stops after 1 iteration (Current level = 1
>   Iteration 1 (of 50).   Current convergence value = 0.000816419 (threshold = 0.001). It does not seem like my specification of the threshold is read but the default value is used. Do you have an example of a typical setting for the -c flag other than the default values?
> 
> best regards
> Erik
> 
> Erik Olsson
> PhD 
> 
> Institute of Psychiatry and Neurochemistry 
> Department of Neuroscience & physiology
> The Sahlgrenska academy
> Gothenburg University
> Sweden
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