Aimsgraphmesh: Extended NeighboorhoodSegmentation fault

AIMS library and commands usage

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cmacdow
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Joined: Wed Sep 04, 2013 8:31 am

Aimsgraphmesh: Extended NeighboorhoodSegmentation fault

Postby cmacdow » Thu Sep 05, 2013 3:00 am

Hello, I'm fairly new to this software so I apologize if this topic is covered somewhere else or if it's a simple fix.

I'm having issues while using Aimsgraphmesh to create meshes from .arg files. That process initiates fine in terminal for a bit but after a little while it stops and says : "extended neighborhoodSegmentation fault". Sometimes it also says "neighboorhoodBus error."


Example of the terminal output:

Clearing interface : done
Reading slice : 5
getting interface : done
processing mesh : done
clearing interface : done
reading slice : 20
getting interface : done
processing mesh : [ 1, 1] Extended neighboorhoodSegmentation fault (core dumped)


This occurs when I run it on mac osx 10.6.8 or Ubuntu 12.04 with either 32 or 64 bit versions of brianvisa installed. I've also tried using different brain sections (compiled using brainra into .ima then converted with Aimsgraphconvert to .arg), smaller number of initial brain slices, larger numbers of brain slices, (only the prettiest tissue samples of course).

Any suggestions? Any additionally information I can add that may help?


Thank you in advance

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riviere
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Re: Aimsgraphmesh: Extended NeighboorhoodSegmentation fault

Postby riviere » Sat Sep 07, 2013 5:55 pm

Hello,
Well it still works for me. Maybe there is something in your data that triggers the bug, which doesn't happen for me.
Would it be possible to get a sample of the data you are using as input ?
Maybe I get a few more clues from you:
- Something that seems a bit strange to me: you say you are unsing AimsGraphConvert to get the .arg. Are you using it on a segmented (binarized) image ?
- is the input data a single slice, or several (from your message I understand several, but just to make sure) ?
- in the binarized (segmented) data, does an object touch the image borders ? (I'm not sure there is a protection in the mesher, and it may be a possible crash cause)
Denis

cmacdow
Posts: 2
Joined: Wed Sep 04, 2013 8:31 am

Re: Aimsgraphmesh: Extended NeighboorhoodSegmentation fault

Postby cmacdow » Mon Sep 09, 2013 2:34 am

Thank you for the response, I went through the input data (multiple slices) and removed all the images where the object was close/touching the image borders - now there is no more segmentation fault issue.

Thank you for pointing that out!

- cmacdow

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riviere
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: Aimsgraphmesh: Extended NeighboorhoodSegmentation fault

Postby riviere » Mon Sep 09, 2013 8:49 am

Well, then you have a workaround, but it is still a bug. We'll try to fix this...
Denis


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