Re: volume loading problem (Liu Yangyang)

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Re: volume loading problem (Liu Yangyang)

Liu Yangyang
Thanks for the reply.

Yes, that is exactly what I did. File -> add volume . and the error message is "Can not load XXX.dcm as a volume.

Regards

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Re: volume loading problem (Liu Yangyang)

swallace
Got the same error message on the same platform using both Slicer 3.4 and
3.5 nightly. DICOM header info isnt loading either; where did you get this
dataset from? Directly off your scanner?


Stuart

>
> Thanks for the reply.
>
>
>
> Yes, that is exactly what I did. File -> add volume . and the error
> message is "Can not load XXX.dcm as a volume.
>
>
> Regards    _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to
> [hidden email] with unsubscribe as the
> subject

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Re: volume loading problem (Liu Yangyang)

pieper
Administrator
Hi Yangyang -

It does appear to be something specific to these particular data files
that prevents them from loading.  The problem is with the dicom
libraries that slicer uses, so I'll forward this on to some people who
can help track it down.  Slicer is careful not to load data for which
the correct geometry cannot be loaded from the header (to avoid
inaccurate measurements).  Thanks for making the files available!

-Steve

p.s. for the record:

The data is available here:

http://isbweb.org/c/isb/pub/files/orig_website/data/vsj/humeral/humeral1.zip

When I try a simple ITK based command line program, the following errors
are generated:

(Slicer3-build) 53 % lib/Slicer3/Plugins/Cast
/Users/pieper/Dropbox/tmp/humeral/hum0001.dcm /tmp/out.nrrd
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.

This indicates that the "fallback" ITK dicom reader is being used.
Slicer specificially disables that fallback reader since it has
historically given incorrect geometry on input files.



On D/29/09 5:17 PM, [hidden email] wrote:

> Got the same error message on the same platform using both Slicer 3.4 and
> 3.5 nightly. DICOM header info isnt loading either; where did you get this
> dataset from? Directly off your scanner?
>
>
> Stuart
>
>>
>> Thanks for the reply.
>>
>>
>>
>> Yes, that is exactly what I did. File ->  add volume . and the error
>> message is "Can not load XXX.dcm as a volume.
>>
>>
>> Regards    _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to
>> [hidden email] with unsubscribe as the
>> subject
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: volume loading problem (Liu Yangyang)

Mathieu Malaterre
On Tue, Dec 29, 2009 at 11:33 PM, Steve Pieper <[hidden email]> wrote:
> The data is available here:
>
> http://isbweb.org/c/isb/pub/files/orig_website/data/vsj/humeral/humeral1.zip

Using ITK from CVS HEAD:

$ make -j8 DicomImageReadWrite && valgrind ./bin/DicomImageReadWrite
~/tmp/hum/hum0001.dcm  bla.dcm bla.mhd bla2.dcm
[  2%] Built target itkvcl
[  4%] Built target itksys
[ 11%] [ 11%] Built target itkzlib
Built target itkjpeg12
[ 13%] Built target itkopenjpeg
[ 20%] Built target itkjpeg8
[ 24%] Built target itkjpeg16
[ 24%] Built target itkpng
[ 28%] [ 31%] Built target ITKEXPAT
Built target ITKNrrdIO
[ 31%] Built target ITKznz
[ 31%] Built target ITKDICOMParser
[ 33%] [ 37%] [ 37%] Built target ITKMetaIO
Built target itkgdcm
Built target ITKniftiio
[ 55%] Built target itkvnl
[ 77%] Built target itkv3p_netlib
[ 84%] Built target itkvnl_algo
[ 86%] Built target itkvnl_inst
[ 93%] Built target ITKCommon
[ 93%] Built target ITKSpatialObject
[100%] Built target ITKIO
[100%] Built target DicomImageReadWrite
==16434== Memcheck, a memory error detector.
==16434== Copyright (C) 2002-2008, and GNU GPL'd, by Julian Seward et al.
==16434== Using LibVEX rev 1884, a library for dynamic binary translation.
==16434== Copyright (C) 2004-2008, and GNU GPL'd, by OpenWorks LLP.
==16434== Using valgrind-3.4.1-Debian, a dynamic binary
instrumentation framework.
==16434== Copyright (C) 2000-2008, and GNU GPL'd, by Julian Seward et al.
==16434== For more details, rerun with: -v
==16434==
==16434==
==16434== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8 from 1)
==16434== malloc/free: in use at exit: 0 bytes in 0 blocks.
==16434== malloc/free: 18,909 allocs, 18,909 frees, 3,484,036 bytes allocated.
==16434== For counts of detected errors, rerun with: -v
==16434== All heap blocks were freed -- no leaks are possible.


I cannot reproduce the issue you are describing here. Are you doing
anything specific for Slicer ?

2cts
--
Mathieu
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Re: volume loading problem (Liu Yangyang)

pieper
Administrator
Hi Mathieu -

Thanks for your help with this - you are just the person we need ;)

Slicer is currently using ITK 3.16 - did something change in the ITK
HEAD that would affect this?  If so, great!

Note also that slicer uses the 'stock' gdcm that ships with ITK - is
that the key difference?

Best regards,
Steve

 From a slicer build directory I get the following:

% ./Slicer3 --launch lib/Slicer3/Plugins/Cast hum0001.dcm out.nrrd
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
... skip a few progress messages...
No DICOM magic number found, but file appears to be DICOM.
Proceeding without caution.
...



On D/30/09 10:49 AM, Mathieu Malaterre wrote:

> On Tue, Dec 29, 2009 at 11:33 PM, Steve Pieper<[hidden email]>  wrote:
>> The data is available here:
>>
>> http://isbweb.org/c/isb/pub/files/orig_website/data/vsj/humeral/humeral1.zip
>
> Using ITK from CVS HEAD:
>
> $ make -j8 DicomImageReadWrite&&  valgrind ./bin/DicomImageReadWrite
> ~/tmp/hum/hum0001.dcm  bla.dcm bla.mhd bla2.dcm
> [  2%] Built target itkvcl
> [  4%] Built target itksys
> [ 11%] [ 11%] Built target itkzlib
> Built target itkjpeg12
> [ 13%] Built target itkopenjpeg
> [ 20%] Built target itkjpeg8
> [ 24%] Built target itkjpeg16
> [ 24%] Built target itkpng
> [ 28%] [ 31%] Built target ITKEXPAT
> Built target ITKNrrdIO
> [ 31%] Built target ITKznz
> [ 31%] Built target ITKDICOMParser
> [ 33%] [ 37%] [ 37%] Built target ITKMetaIO
> Built target itkgdcm
> Built target ITKniftiio
> [ 55%] Built target itkvnl
> [ 77%] Built target itkv3p_netlib
> [ 84%] Built target itkvnl_algo
> [ 86%] Built target itkvnl_inst
> [ 93%] Built target ITKCommon
> [ 93%] Built target ITKSpatialObject
> [100%] Built target ITKIO
> [100%] Built target DicomImageReadWrite
> ==16434== Memcheck, a memory error detector.
> ==16434== Copyright (C) 2002-2008, and GNU GPL'd, by Julian Seward et al.
> ==16434== Using LibVEX rev 1884, a library for dynamic binary translation.
> ==16434== Copyright (C) 2004-2008, and GNU GPL'd, by OpenWorks LLP.
> ==16434== Using valgrind-3.4.1-Debian, a dynamic binary
> instrumentation framework.
> ==16434== Copyright (C) 2000-2008, and GNU GPL'd, by Julian Seward et al.
> ==16434== For more details, rerun with: -v
> ==16434==
> ==16434==
> ==16434== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8 from 1)
> ==16434== malloc/free: in use at exit: 0 bytes in 0 blocks.
> ==16434== malloc/free: 18,909 allocs, 18,909 frees, 3,484,036 bytes allocated.
> ==16434== For counts of detected errors, rerun with: -v
> ==16434== All heap blocks were freed -- no leaks are possible.
>
>
> I cannot reproduce the issue you are describing here. Are you doing
> anything specific for Slicer ?
>
> 2cts
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Re: volume loading problem (Liu Yangyang)

Mathieu Malaterre
Hi Steve,

On Wed, Dec 30, 2009 at 7:06 PM, Steve Pieper <[hidden email]> wrote:
> Hi Mathieu -
>
> Thanks for your help with this - you are just the person we need ;)
>
> Slicer is currently using ITK 3.16 - did something change in the ITK HEAD
> that would affect this?  If so, great!

I do not see why this file could be a problem. The only nasty thing is
if GDCM is trying to unterpret a private tag.

> Note also that slicer uses the 'stock' gdcm that ships with ITK - is that
> the key difference?

No GDCM 1.2.x shipped with ITK should be perfeclty fine.

Simply updating itk::GDCMImageIO should -hopefully- fix the issue.

HTH
--
Mathieu
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Re: volume loading problem (Liu Yangyang)

madanrao
Hi,

You can open and save the dicom images to png form using ImageJ and view them with Slicer. Use Castimage module if you want them in nrrd.

AM Mohan Rao

On Thu, Dec 31, 2009 at 12:30 AM, Mathieu Malaterre <[hidden email]> wrote:
Hi Steve,

On Wed, Dec 30, 2009 at 7:06 PM, Steve Pieper <[hidden email]> wrote:
> Hi Mathieu -
>
> Thanks for your help with this - you are just the person we need ;)
>
> Slicer is currently using ITK 3.16 - did something change in the ITK HEAD
> that would affect this?  If so, great!

I do not see why this file could be a problem. The only nasty thing is
if GDCM is trying to unterpret a private tag.

> Note also that slicer uses the 'stock' gdcm that ships with ITK - is that
> the key difference?

No GDCM 1.2.x shipped with ITK should be perfeclty fine.

Simply updating itk::GDCMImageIO should -hopefully- fix the issue.

HTH
--
Mathieu
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