NITRC ShapeWorks Forum: help

RE: Problem with running the code

Félix Renard — Thu, 01 Aug 2013 12:06:33 GMT

Hi,

I am new user of ShapeWorks. I try to use the Linux executable. It works for the Torus exemple. It also works on my data for the different preprocessing of ShapeWorksGroom.
Nevertheless when I use the ShapeWorksRun, I receive this following errors:
itk::ExceptionObject (0xf4803610)
Location: "bool itk::ParticleRegionDomain::ApplyConstraints(itk::ParticleRegionDomain::PointType&) const [with unsigned int VDimension = 3u, itk::ParticleRegionDomain::PointType = itk::Point]"
File: /media/Shared/ShapeWorksCode/ShapeWorksNITRC/source/code/ITKParticleSystem/itkParticleRegionDomain.h
Line: 78
Description: itk::ERROR: ParticleImplicitSurfaceDomain(0x936c338): Point [-87.6903, 56.9256, 71.3354] is outside of the specified Domain, with bounding box [-125.69, 96.9256, 120.335] - [-50.6903, -13.0744, 30.3354]

Will I need to build the source code?
Would you please help me to figure out these problems?

Thanks!
Best regards,
Félix

Source code

Alex Poon — Tue, 22 Jan 2013 2:36:56 GMT

Do you offer any 64-bit Windows version of your work? My data may be too huge for a 32-bit machine. Otherwise I can compile it myself if I have the source code.

Cheers.

RE: first-time user asking for help

Long Pun — Mon, 21 Jan 2013 0:20:23 GMT

Did anyone ever encounter a problem with the [b]center[/b] and [b]auto_crop[/b] command? While running these command with my binary volumes, I came across a "failure to allocate memory" error. Checking the prompt, I saw something like:

Reading xxx.mha...
ImageRegion (00B9F708)
Dimension: 3
Index: [213 213 46]
Size: [4294967083, 4294967083, 4294967025]

What is in the [b]Index[/b] field matches my volume size, but the field in "[b]Size[/b]" does not make any sense, and is different from what I saw in the torus example. I guess it miscalculate something. Any ideas?

RE: first-time user asking for help

Long Pun — Wed, 16 Jan 2013 2:40:10 GMT

Talking of the Torus example, I didn't seem to see it anywhere.
=========
Oh I found it. Hidden so well...

RE: first-time user asking for help

Manasi Datar — Mon, 14 Jan 2013 14:54:03 GMT

Hi Long

i thought we updated the XML parameter files in the Torus example with all the parameters. But i'll double-check that, and also work on the documentation.

Meanwhile, the parameter you are looking for is: < transform_file > filename < / transform_file >
of course, no spaces in the tag :)

HTH
Thanks for your patience !
Regards
manasi

RE: first-time user asking for help

Long Pun — Mon, 14 Jan 2013 12:38:53 GMT

Me again. This time "missing transform file parameter" for the command "center". What parameter does it take? I cannot find it in manual.

Cheers,
Long

RE: first-time user asking for help

Long Pun — Mon, 14 Jan 2013 12:26:26 GMT

To Manasi,

Thanks a lot! After (learning and) rewriting my xml file I finally got the thing running. It would have taken me forever if it wasn't you.

By the way, I think the developers should really consider rewriting the manual... much of the things inside had changed.

And for anyone who clicked at the attachment above, you may see an error page. This is normal, since the xml file seems to have a syntax error. This error shows up in my xml editor, the file cannot be displayed correctly in web browser, but works for the purpose.

Thanks again Manasi!

Regards,
Long

RE: first-time user asking for help

Manasi Datar — Mon, 14 Jan 2013 1:30:15 GMT

Hi Long

The parameter file you attached is not in XML format !
Please look at the attached file for details...

HTH
Regards
manasi

RE: first-time user asking for help

Long Pun — Sun, 13 Jan 2013 23:05:20 GMT

Hi Manasi,

No it doesn't. I suspect I made some mistakes in writing up my .xml, so I uploaded it here.

The data files are named ID5x.mha, in the same folder as the .xml.

Thanks a lot Manasi. You are a star :)

Regards,
Long

RE: first-time user asking for help

Manasi Datar — Sun, 13 Jan 2013 14:35:04 GMT

Hi Long

A command line like: ShapeWorksGroom preprocess.xml
will not work unless at least one filter is specified. Please try a command line like: ShapeWorksGroom preprocess.xml isolate
and let me know if that does not work...

Please not that this version of ShapeWorks is not a professional piece of code, and may not have exceptions/error messages defined for every situation.

HTH
Regards
manasi