[slicer-users] Activate Logs

Madan Rao rao.lms at gmail.com
Fri Jun 18 22:58:12 EDT 2010


Hello,

EM Segmenter crash is usually due to either:

(1). if the image data is not in short form. (2). or the memory allocation
is not done due to low RAM.

If your image is in float or unsigned short type you need to cast it to
short before you can run EM module.

hope this helps.

AM Mohan Rao

On Sat, Jun 19, 2010 at 4:39 AM, Andriy Fedorov <fedorov at bwh.harvard.edu>wrote:

> Fidel,
>
> I am sure EM Segmenter developers will get to you with the
> suggestions, but since this has not happened yet, let me try to help
> you based on my limited understanding of this problem.
>
> >> On Thu, Jun 17, 2010 at 13:23, FIDEL ALFARO ALMAGRO <
> falfaro13 at alumno.uned.es> wrote:
> >> - I am using version 3.4 (There is no EM Segment Template Builder Module
> >> in version 3.6 and the tutorial to do segmentation is only valid for
> that
> >> module).
> >>
>
> In fact, there is a template builder module in 3.6:
>
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6
>
> It is correct that 3.4 tutorial will probably not be valid for 3.6,
> but EM Segmenter tutorial for 3.6 should be in the works, if not
> available already. Stuart, Kilian -- can you comment on this?
>
> >> - I am trying to reproduce exactly the same circumstances that appear in
> >> that tutorial (AutomatinSegmentation_SoniaPujol.pdf), but using my own
> >> data, and trying to segment a brain tumor.
> >>
>
> EM Segmenter does segmentation based on the assumptions regarding the
> intensity distribution in the classes you want to segment, and based
> on the prior knowledge about the spatial location of these regions.
>
> As you understand, tumors can often have inhomogeneous intensity,
> irregular shape and nearly arbitrary location. Therefore, this
> particular approach may not be applicable in your situation. The
> specifics depend on the details like the type of tumor you want to
> segment and the image modality (modalities) you have available. Can
> you share a screenshot, or provide some more information?
>
> Having said that, I agree with you that EM Segmenter should not crash.
> But in order to resolve this problem you need to switch to 3.6, since
> I am not sure we work on bugfixes for 3.4.
>
>
> >> - The data are big (over 40 GB), so I cannot pass them, and apart from
> >> that, I do not know if I am allowed to pass that information (Probably,
> I
> >> am not).
> >>
>
> This is understandable.
>
> >> That is why I wanted to have the log... In order to inform you about the
> >> "exception" that caused the application to crash.
> >>
> >> So... What are my options now?
> >>
>
> Trying to understand the cause of the problem from the log is the last
> thing I would try. First, you need to have reason to believe the
> approach you use is appropriate for your problem, and you have
> exhausted readily available alternatives.
>
> I would do the following: (in the order of priorities)
>
> 1) provide more details about the tumor and available modalities
> (screenshots?)
> 2) consider alternative approaches to segment the tumor, which do not
> rely on prior information:
>  * Fast Marching segmentation: (interactive -- easy to get an idea if
> it will work or not)
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6
>  * Robust statistics segmentation: (non-interactive)
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:RobustStatisticsSeg-Documentation-3.6
>  * other segmentation tools in Slicer
> 3) give a try to EM Segmenter in 3.6
>
> Please let us know about your experience with Slicer tools for your
> task, and more details so that we could help you better.
>
> AF
>
>
> >> Thanks,
> >>
> >> Fidel.
> >>
> >>> Fidel,
> >>>
> >>> I am not sure there is such a permanent log. I agree it would be great
> >>> to have it.
> >>>
> >>> Meanwhile, you might have better luck if you help us to understand the
> >>> source of the problem:
> >>>
> >>> * do you also have this problem with Slicer 3.6?
> >>> * what module do you use?
> >>> * what are the parameter settings?
> >>> * can you share an anonymized dataset with us to reproduce the problem?
> >>>
> >>> AF
> >>>
> >>>
> >>>
> >>> On Thu, Jun 17, 2010 at 12:47, FIDEL ALFARO ALMAGRO
> >>> <falfaro13 at alumno.uned.es> wrote:
> >>>> Yes, I was asking for a "permanent" log file, in case of an unexpected
> >>>> application crash. I guess that this log is quite useful, but will
> >>>> disappear as well when the application crashes.
> >>>>
> >>>> Is there anything like that?
> >>>>
> >>>> Thanks.
> >>>>
> >>>> Fidel.
> >>>>
> >>>>> There is an error log that's available by either clicking the X in
> the
> >>>>> bottom right hand corner of the GUi or by going to Window-->Error Log
> >>>>> in
> >>>>> the menubar.
> >>>>>
> >>>>> Are you asking for something beyond this?
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Stuart
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> I am trying to run a brain tumor segmentation on 3D slicer
> >>>>>> 3.4-2010-04-15,
> >>>>>> but the application crashes without giving any information to the
> >>>>>> user.
> >>>>>> Is
> >>>>>> there any possibility to activate any kind of "logs" to see what is
> >>>>>> happening in order to solve it?
> >>>>>>
> >>>>>> Thanks and best regards.
> >>>>>>
> >>>>>> Fidel.
> >>>>>>
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