[ITK] [ITK-users] Command line use of N4 in MacOS terminal
Nicholas Tustison
ntustison at gmail.com
Tue Jan 20 17:05:19 EST 2015
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
> _____________________________________
> Powered by www.kitware.com <http://www.kitware.com/>
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php <http://www.kitware.com/products/protraining.php>
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users <http://public.kitware.com/mailman/listinfo/insight-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20150120/934e53a7/attachment.html>
-------------- next part --------------
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users
More information about the Community
mailing list