[Insight-users] N4ITK running error

[Shandra Gutierrez Diaz]

Hi Nick and Jon Haitz,

I have tried again with 

>./N4.exe -d  2 -i t81slice.nii.gz -o t81sliceCorrect.nii.gz -s 4 -b [200] -c [50x50x50x50,0]
but still i get the following error.

Running N4 for 2-dimensional images.

terminate called throwing an exceptionAbort trap: 6

The code that I have was downloaded from http://www.insight-journal.org/browse/publication/640  and I just did some slight modifications such as the GetImageDimension and the way to include the libraries, because it was giving errors with the latest version of ITK. But I did not change anything else in the code. 

Best, 
Shandra

On 30/01/2014, at 14:23, Jon Haitz Legarreta wrote:

> Dear Shandra,
> segmentation faults have to do with memory access (you may be trying to access an unallocated space). If the program is of your own making, you may want to check whether you are allocating all necessary memory space through the corresponding variables/pointers.
> 
> Having read what Nicholas says, it looks like you need to specify some dimensions so that the program knows who much memory space it needs to allocate. If you fail to specify those arguments, the program may try to access a null-length memory extension.
> 
> Both if its a program of your own or if it is an ITK example, you can debug step by step to know where the segmentation fault arises, and whether all implied variables seem to be OK.
> 
> HTH,
> JON HAITZ
> 
> 
> 
> On 30 January 2014 14:13, Nicholas Tustison <ntustison at gmail.com> wrote:
> Hi Shandra,
> 
> You didn’t specify any arguments for -c or -b.  If I remember
> correctly, try something like '-b [200] -c [50x50x50x50,0]’.
> 
> Nick
> 
> On Jan 30, 2014, at 8:10 AM, Shandra Gutierrez Diaz <Shandra.GutierrezDiaz at UGent.be> wrote:
> 
>> 
>> Hi, 
>> 
>> I am trying to work with N4ITK (N4BiasFieldCorrectionImageFilter). I have built it succesfully but when running it, it gives error. 
>> >./N4.exe 2 -i t81slice.nii.gz -o t81sliceCorrect.nii.gz -s 4 -c -b 
>> Segmentation fault: 11
>> >./N4.exe -d 2 -i t81slice.nii.gz -o t81sliceCorrect.nii.gz -s 4 -c -b 
>> terminate called throwing an exceptionAbort trap: 6
>> 
>> Has anyone faced the same problem or any clue what can be?
>> Best, 
>> Shandra
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> 
> _____________________________________
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> 
> 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:
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ir. Shandra Gutierrez Diaz
Ghent University
Medical Image and Signal Processing Group
Department of Electronics and Information Systems
Ghent University Hospital - Block B
De Pintelaan 185
B-9000 Ghent
Belgium


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