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Re: [slicer-users] Slicer4 - can't really use it yet

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Re: [slicer-users] Slicer4 - can't really use it yet

Steve Pieper
Hi SET - 

Thanks for sending the log - this confirms for me that you are seeing the same locale issues that have been discussed lately on the slicer-developer list [1].  This is interesting since it means that something similar is happening for you on linux where before we only saw it on mac.  In the log [2] you can clearly see that the floating point numbers are being saved with comma for decimal indicators.  The correct behavior would be for slicer to display something like 0,25 in the gui, but always save it as 0.25 in a data file (that is, using the native locale for display, but the "C" locale for data files).

I want to discuss this with the developers on next Tuesday's hangout, but I hear from mulitlingual friends that other programs (such as Excel) also have problems with internationalization of data, so my preference would be to force all of slicer into the "C" locale until such time as we can figure out how to make sure that we don't end up with bad data.  I suspect the code to selectively enable language features [3] is not working as expected.

For now, SET, maybe you can try explicitly setting the LANG and related environment variables to C in the shell where you launch slicer and see if that allows you to run the program as expected.

-Steve



[2]
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /home/user/src/Slicer4-SuperBuild-Release/ITKv4/Modules/IO/NRRD/src/itkNrrdImageIO.cxx:258:
itk::ERROR: NrrdImageIO(0x25e8f00): ReadImageInformation: Error reading /tmp/Slicer/BEDAD_vtkMRMLScalarVolumeNodeC.nrrd:
[nrrd] nrrdLoad: trouble reading "/tmp/Slicer/BEDAD_vtkMRMLScalarVolumeNodeC.nrrd"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: trouble reading NRRD file
[nrrd] _nrrdFormatNRRD_read: trouble parsing space directions info |(0,625,0,0) (0,0,625,0) (0,0,0,31201172000000005)|
[nrrd] _nrrdReadNrrdParse_space_directions: trouble getting space vector 1 of 3
[nrrd] _nrrdSpaceVectorParse: space dimension is 3, but seem to have 4 coefficients


On Fri, Mar 15, 2013 at 9:59 AM, <[hidden email]> wrote:
Hello,

OS : Linux x86_64 running ARCH

I could finally load a DICOM CT study after building Slicer4 locally (can't do
that with the nightly build available at slicer.org).

I need to crop a volume and perform 'Simple Region Growing' on the cropped
volume.

The segmentation fails immediately with errors.

The cropping runs, but the resulting volume is identical to the original.

I made a desktop recording available here :

https://owncloud.nmset.info/public.php?service=files&token=3939b3ce75ed54ac46b48d43767e6533e2a52db6&file=/Slicer/Slicer00.ogv

Attached also is the stdout of the session, showing where errors happen.

Has anyone managed to successfully perform these steps with Slicer4 on Linux
with DICOM series ? Am I missing some steps ?

Regards.
SET


[Although the attached output refers to a directory named Slicer4-SuperBuild-
Release, it's actually a Debug build.]
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