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

[Erik Olsson]

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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