4.2 - Add scalar and tensor volume fails

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4.2 - Add scalar and tensor volume fails

chir.set@free.fr
Hello,

This concerns loading a DICOM CT series presented on CDROM.

I use 'Add scalar and tensor volume' in the 'Data Module', and browse to the
directory containing the DICOM files. One file is selected and the option
'Single file' is next unchecked. Only the selected file gets loaded and shown,
not the whole series, and it is loaded slowly. The expected behaviour is a
fast loading of the whole series, as in 3.6 and 4.1 . Experienced in stable
4.2.2 and nightly 4.2.0-2012-12-12 r21516.

Is it a new feature ? a deprecated feature ? a bug ? Should I file a bug ? Is
there some other way to quickly load a whole CT DICOM series ?

Thank you.

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Re: 4.2 - Add scalar and tensor volume fails

Julien Finet
Hi,

Can you list the contents of the directory where the selected file is selected ( what are the file names ?)
Do you confirm that by default the "Single File" check box is unchecked ?

Thanks,
Julien.


On Fri, Dec 14, 2012 at 10:28 AM, <[hidden email]> wrote:
Hello,

This concerns loading a DICOM CT series presented on CDROM.

I use 'Add scalar and tensor volume' in the 'Data Module', and browse to the
directory containing the DICOM files. One file is selected and the option
'Single file' is next unchecked. Only the selected file gets loaded and shown,
not the whole series, and it is loaded slowly. The expected behaviour is a
fast loading of the whole series, as in 3.6 and 4.1 . Experienced in stable
4.2.2 and nightly 4.2.0-2012-12-12 r21516.

Is it a new feature ? a deprecated feature ? a bug ? Should I file a bug ? Is
there some other way to quickly load a whole CT DICOM series ?

Thank you.

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Re: 4.2 - Add scalar and tensor volume fails

Steve Pieper
You may also want to look at the DICOM module as a way to organize your data and access files by patient/study/series:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM#Tutorials

-Steve


On Fri, Dec 14, 2012 at 12:10 PM, Julien Finet <[hidden email]> wrote:
Hi,

Can you list the contents of the directory where the selected file is selected ( what are the file names ?)
Do you confirm that by default the "Single File" check box is unchecked ?

Thanks,
Julien.


On Fri, Dec 14, 2012 at 10:28 AM, <[hidden email]> wrote:
Hello,

This concerns loading a DICOM CT series presented on CDROM.

I use 'Add scalar and tensor volume' in the 'Data Module', and browse to the
directory containing the DICOM files. One file is selected and the option
'Single file' is next unchecked. Only the selected file gets loaded and shown,
not the whole series, and it is loaded slowly. The expected behaviour is a
fast loading of the whole series, as in 3.6 and 4.1 . Experienced in stable
4.2.2 and nightly 4.2.0-2012-12-12 r21516.

Is it a new feature ? a deprecated feature ? a bug ? Should I file a bug ? Is
there some other way to quickly load a whole CT DICOM series ?

Thank you.

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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr
In reply to this post by Julien Finet

Le vendredi 14 décembre 2012 12:10:34 vous avez écrit :

Hi, Can you list the contents of the directory where the selected file is selected ( what are the file names ?) Do you confirm that by default the "Single File" check box is unchecked ? Thanks, Julien.



The files in the directory are named as a series of ct00???? where ???? ranges from 0000 to ?999. They are standard DICOM files of 512 kb each, and the directory contains only these DICOM files.

I confirm that the "Single file" option is _un_checked. I do this last before OK.

 

Thanks for considering.

 

 


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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr
In reply to this post by Steve Pieper

Le vendredi 14 décembre 2012 12:18:46 vous avez écrit :

You may also want to look at the DICOM module as a way to organize your data and access files by patient/study/series:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM#Tutorials

-Steve

Importing the directory containing the DICOM files always stops at some point, 37%... 72% ... 89% and Slicer4 no longer responds.

 

SET

 


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Re: 4.2 - Add scalar and tensor volume fails

Steve Pieper
Hi Set -

Is the data still on the CD at this point?  Does the same happen if the files are copied to a faster drive first?

Don't send us any patient identifiable data, but if you can help us reproduce the issue on our machines we could hope to get a fix.  Perhaps the same issue happens with data from a public site[1] ?

[1] http://www.osirix-viewer.com/datasets/

-Steve


On Fri, Dec 14, 2012 at 12:39 PM, <[hidden email]> wrote:

Le vendredi 14 décembre 2012 12:18:46 vous avez écrit :

You may also want to look at the DICOM module as a way to organize your data and access files by patient/study/series:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM#Tutorials

-Steve

Importing the directory containing the DICOM files always stops at some point, 37%... 72% ... 89% and Slicer4 no longer responds.

 

SET

 



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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr
Le vendredi 14 décembre 2012 14:44:31 Steve Pieper a écrit :

Hi Set -

Is the data still on the CD at this point?  Does the same happen if the files
are copied to a faster drive first?

Don't send us any patient identifiable data, but if you can help us reproduce
the issue on our machines we could hope to get a fix.  Perhaps the same issue
happens with data from a public site[1] ?

[1] http://www.osirix-viewer.com/datasets/

-Steve


1. The data is already on a fast drive. I always rip the CD to an iso file,
which is then mounted using fuseiso utility.

2. I could load the dataset in MACOESSIX/CT1 abdomen/AVEC I.V. - 5305
 from the link you posted. The ZIP file contains 2 other datasets which cannot
be loaded at all. As for the loaded dataset, image spacing is inaccurate, and
the spinboxes in the 'Volume Module' accept only integers, hence the visual
aspect remains distorted.

3. I'll anonymize a problematic series tomorrow and post you a link to
retrieve the data.

4. I must emphasize that 3.6 works flawlessly on the same data, and 4.1 can
load whole series of any CT study I have to deal with. These sometimes
contains 1200 images and I work on a 16 GB x86_64 machine with a 6 core CPU.
So this is not harware limit.

Thank you.

SET

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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr
In reply to this post by Steve Pieper

Le vendredi 14 décembre 2012 14:44:31 Steve Pieper a écrit :

Hi Set -

Is the data still on the CD at this point?  Does the same happen if the files are copied to a faster drive first?

Don't send us any patient identifiable data, but if you can help us reproduce the issue on our machines we could hope to get a fix.  Perhaps the same issue happens with data from a public site[1] ?

[1] http://www.osirix-viewer.com/datasets/

-Steve

Hi All,

 

The link below points to anonymized data of an angio-CT scan produced with the 'Create DICOM Series module'.

 

Same results with the original series and the anonymized one.

 

http://vasc.free.fr/slicer/anon.zip

 

MD5 digest : 236f36921c44d70c3b9a4df3ebcdd395

 

Thanks for considering.

 

SET

 




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Re: 4.2 - Add scalar and tensor volume fails

Steve Pieper
Hi -

Thanks for sharing the anonymized data and helping us debug. 

Regarding the anon.zip file you provided, I had no trouble loading this in slicer 4.2.2 using the Add Data interface.  I also tried with the DICOM module and didn't run into any issues either.  I'm not sure why this would be different on your machine - I agree it's not a hardware issue, and I was also able to load the data on a windows machine with 4 gigabytes of ram (windows 7 x64).  Are you sure the anonymized version behaves the same as the original for you?

Regarding the MACOESSIX dataset, I can load that using the Add Data interface, but not with the DICOM module - I looked into this and filed a bug report with some details [1].  The DICOM files in that zip file are Secondary Capture (screen shot) images and don't have geometry information about the slice spacing.  If you load that data via the Add Data interface, it has the wrong aspect ratio because the the lower level reader guesses 1mm per slice.  The DICOM module refuses to load them without valid geometry.

I was able to replicate the issue you reported about not being able to set the spacing field in the Volumes module.  I filed a bug report on that one too.

[1] http://na-mic.org/Bug/view.php?id=2831
[2] http://na-mic.org/Bug/view.php?id=2832

-Steve





On Sat, Dec 15, 2012 at 4:17 AM, <[hidden email]> wrote:

Le vendredi 14 décembre 2012 14:44:31 Steve Pieper a écrit :

Hi Set -

Is the data still on the CD at this point?  Does the same happen if the files are copied to a faster drive first?

Don't send us any patient identifiable data, but if you can help us reproduce the issue on our machines we could hope to get a fix.  Perhaps the same issue happens with data from a public site[1] ?

[1] http://www.osirix-viewer.com/datasets/

-Steve

Hi All,

 

The link below points to anonymized data of an angio-CT scan produced with the 'Create DICOM Series module'.

 

Same results with the original series and the anonymized one.

 

http://vasc.free.fr/slicer/anon.zip

 

MD5 digest : 236f36921c44d70c3b9a4df3ebcdd395

 

Thanks for considering.

 

SET

 





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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr

Le lundi 17 décembre 2012 14:16:55 Steve Pieper a écrit :

Hi -

Thanks for sharing the anonymized data and helping us debug. 

Regarding the anon.zip file you provided, I had no trouble loading this in slicer 4.2.2 using the Add Data interface.  I also tried with the DICOM module and didn't run into any issues either.  I'm not sure why this would be different on your machine - I agree it's not a hardware issue, and I was also able to load the data on a windows machine with 4 gigabytes of ram (windows 7 x64).  Are you sure the anonymized version behaves the same as the original for you?

Regarding the MACOESSIX dataset, I can load that using the Add Data interface, but not with the DICOM module - I looked into this and filed a bug report with some details [1].  The DICOM files in that zip file are Secondary Capture (screen shot) images and don't have geometry information about the slice spacing.  If you load that data via the Add Data interface, it has the wrong aspect ratio because the the lower level reader guesses 1mm per slice.  The DICOM module refuses to load them without valid geometry.

I was able to replicate the issue you reported about not being able to set the spacing field in the Volumes module.  I filed a bug report on that one too.

[1] http://na-mic.org/Bug/view.php?id=2831
[2] http://na-mic.org/Bug/view.php?id=2832

-Steve


Hi,

 

I confirm that both the nominative and anonymized data behave similarly on my PC. Anyway, I still use 3.6 regularly and check on 4.x when possible. I just hope it gets better than 3.6 soon.

 

Thank you.

 


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Re: 4.2 - Add scalar and tensor volume fails

Julien Finet
Hi, please make sure you are using a 64bits version of slicer.

Julien.

On Dec 17, 2012, at 2:32 PM, [hidden email] wrote:

Le lundi 17 décembre 2012 14:16:55 Steve Pieper a écrit :

Hi -

Thanks for sharing the anonymized data and helping us debug. 

Regarding the anon.zip file you provided, I had no trouble loading this in slicer 4.2.2 using the Add Data interface.  I also tried with the DICOM module and didn't run into any issues either.  I'm not sure why this would be different on your machine - I agree it's not a hardware issue, and I was also able to load the data on a windows machine with 4 gigabytes of ram (windows 7 x64).  Are you sure the anonymized version behaves the same as the original for you?

Regarding the MACOESSIX dataset, I can load that using the Add Data interface, but not with the DICOM module - I looked into this and filed a bug report with some details [1].  The DICOM files in that zip file are Secondary Capture (screen shot) images and don't have geometry information about the slice spacing.  If you load that data via the Add Data interface, it has the wrong aspect ratio because the the lower level reader guesses 1mm per slice.  The DICOM module refuses to load them without valid geometry.

I was able to replicate the issue you reported about not being able to set the spacing field in the Volumes module.  I filed a bug report on that one too.

[1] http://na-mic.org/Bug/view.php?id=2831
[2] http://na-mic.org/Bug/view.php?id=2832

-Steve


Hi,

 

I confirm that both the nominative and anonymized data behave similarly on my PC. Anyway, I still use 3.6 regularly and check on 4.x when possible. I just hope it gets better than 3.6 soon.

 

Thank you.

 

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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr

Le lundi 17 décembre 2012 14:54:39 Julien Finet a écrit :

Hi, please make sure you are using a 64bits version of slicer.

Julien.


Well the Linux 4.x builds are only available as 64 bits from slicer.org.

 

SET




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Re: 4.2 - Add scalar and tensor volume fails

chir.set@free.fr
In reply to this post by Steve Pieper

If it may help, here are the error messages when trying to load the anonymized data in anon.zip using 'Add scalar and tensor volume' in 'Data Module' :

 

 

ERROR: In /home/kitware/Dashboards/Package/Slicer-422/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367

vtkMRMLVolumeArchetypeStorageNode (0x57506d0): ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName = /tmp/anon/IMG4.dcm]

Number of files listed in the node = 0.

File reader says it was able to read 1098 files.

File reader used the archetype file name of /tmp/anon/IMG4.dcm [reader 0th file name = /tmp/anon/IMG1.dcm]

 

 

 

ERROR: In /home/kitware/Dashboards/Package/Slicer-422/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 317

vtkMRMLVolumeArchetypeStorageNode (0x5721b90): ReadData: Failed to instantiate a file reader

 

 

ERROR: In /home/kitware/Dashboards/Package/Slicer-422/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367

vtkMRMLVolumeArchetypeStorageNode (0x5728d20): ReadData: Cannot read file as a volume of type Volume[fullName = /tmp/anon/IMG4.dcm]

Number of files listed in the node = 0.

File reader says it was able to read 1098 files.

File reader used the archetype file name of /tmp/anon/IMG4.dcm [reader 0th file name = /tmp/anon/IMG1.dcm]

 

*******************************************************************************************************

 

When trying to load identified data, the following error is generated :

 

ERROR: In /home/kitware/Dashboards/Package/Slicer-422/Libs/vtkITK/vtkITKArchetypeDiffusionTensorImageReaderFile.cxx, line 138

vtkITKArchetypeDiffusionTensorImageReaderFile (0x6a85530): There is more than one file, use the vtkITKArchetypeImageSeriesReader instead

 

*******************************************************************************************************

 

[ Just learned the existence of the 'Log messages window' in another thread.]

 

Thanks.

 

 


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