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Re: [Seg3D] Seg3D2.1.1 on Ubuntu 14.04 crashes when attempting to resample mask

Chronological Thread 
  • From: ayla <>
  • To:
  • Cc: Gordon Duffley <>
  • Subject: Re: [Seg3D] Seg3D2.1.1 on Ubuntu 14.04 crashes when attempting to resample mask
  • Date: Tue, 28 Jul 2015 16:35:44 -0700

Gordon - can you do me a huge favour and summarize all this into a GitHub bug report? I'll look into the bug once I'm back from vacation.

On Mon, Jul 27, 2015 at 9:31 AM, Paul Holcomb <> wrote:

Thanks for the reply, Gordon. I used the "hardinfo" utility to grab my machine specs (attached). Hope it helps!


On Mon, Jul 27, 2015 at 12:23 PM Gordon Duffley <> wrote:
I just tried again on my much less powerful OS X laptop, running 2.2.0, and the operations completed without any problem. I’m not sure what the problem could be. Respond with your full machine specs and Ayla might have a better idea of what’s going.


On Jul 27, 2015, at 9:18 AM, Paul Holcomb <> wrote:

Oops! Typo on my previous email. I'm using Seg3D2.2.1, not Seg3D2.1.1. Sorry for the confusion, Gordon, and yes, that's exactly what I meant about the transform and resample. This same issue happens in 2.2.0 as well, on both Ubuntu 14.04 and Windows 7. However, if I crop the data down to just include my tiny mask instead of using the large (mostly zero) mask, and then transform and resample, it works fine. Maybe there is an internal limit to the size of the matrices that the resample tool can handle?

On Mon, Jul 27, 2015 at 11:12 AM Gordon Duffley <> wrote:
Hi Paul,

Using Seg3D2.1.5 on opensuse13.2, those operations completed on your
data without any problems if I understood them correctly. I used the
transform module to move the x and y origin by a single unit, then
resampled back onto the original grid. I have attached the resulting
mask. With regards to doing it yourself, it might be time to upgrade
your version of Seg3D. I am running 2.2.1 on another machine and it is
very stable.


On Mon, 2015-07-27 at 13:34 +0000, Paul Holcomb wrote:
> Dear all,
> I'm having an issue with Seg3D2 on Ubuntu with the attached file. I
> need to shift the mask 1 pixel in x and y, and then resample it back
> into the original volume. Using transform works fine, but when I
> attempt to resample (by shift-clicking and dragging into the original
> object layer or using the resample tool) the resample gets to about
> 68% and then Seg3D immediately closes. Any thoughts or suggestions
> would be greatly appreciated.
> Thanks,
> Paul Holcomb

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