[slicer-users] FW:Help - DICOM does not load in Slicer 3.6

Saurabh Gupta 402549 Saurabh_402549 at infosys.com
Thu Jul 8 07:58:10 EDT 2010


However, sometimes the DICOM files do not load and I get this error :-

ERROR: In ..\..\..\Slicer3\Libs\MRML\vtkMRMLVolumeArchetypeStorageNode.cxx, line 330
vtkMRMLVolumeArchetypeStorageNode (189C71F0): ReadData: Cannot read file, fullName = D:/DICOM/subj006reg001/01.DCM, number of files listed in the node = 0, the ITK reader says it was able to read 0 files, the reader used the archetype file name of D:/DICOM/subj006reg001/01.DCM

I have attached the new dataset with this mail.

-----Original Message-----
From: Saurabh Gupta 402549
Sent: Thursday, July 08, 2010 2:21 PM
To: 'Mark Anderson'; slicer-users at bwh.harvard.edu
Subject: RE: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6

Thanks Mark

I checked the file names and instance number and found they did not tally. So I changed the filenames accordingly. They loaded on Slicer with certain trivial errors.

1. DICOM to NRRD conversion works fine with the following information and error:-

**** Information ****
Found SharedObject Module

**** Information ****
SharedObjectModule

**** Information ****
Dicom to Nrrd Converter command line:

slicer:1B5C86E0 --processinformationaddress 195CF0C8 --inputDicomDirectory D:/DICOM/subj006reg001 --outputDirectory D:/DICOM --outputVolume 2.nrrd

**** Information ****
Dicom to Nrrd Converter standard output:

0018|9089 [FD] [Diffusion Gradient Orientation]
D:/DICOM/2.nrrd
ORIGINAL\PRIMARY\AXIAL\CT
=================== numberOfSlicesPerVolume:59
ImageOrientationPatient (0020:0037): LPS Orientation Matrix
1 -0 0
0 1 0
-0 0 1

SpacingMatrix
0.84 0 0
0 0.84 0
0 0 3

NRRDSpaceDirection
0.84 0 0
0 0.84 0
0 0 3

 Warning: vendor type not valid

**** Error ****
ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1622
vtkCommandLineModuleLogic (1855AE18): Dicom to Nrrd Converter standard error:

Unrecognized vendor.

2. On loading DICOM files through Add Volume (though it loads)

**** Error ****

ERROR: In ..\KWWidgets\vtkKWApplication.cxx, line 1301
vtkSlicerApplication (07D67008): TclTk error: invalid command name "vtkTemp807"
invalid command name "vtkTemp807"
    while executing
"vtkTemp807 Render"
    ("after" script)

3. On loading 2.nrrd through Add Data (though it loads)

**** Error ****
ERROR: In ..\KWWidgets\vtkKWApplication.cxx, line 1301
vtkSlicerApplication (07D67008): TclTk error: invalid command name "vtkTemp10337"
invalid command name "vtkTemp10337"
    while executing
"vtkTemp10337 Render"
    ("after" script)

4. On loading DICOM files again

****Error ****
ERROR: In ..\KWWidgets\vtkKWApplication.cxx, line 1301
vtkSlicerApplication (07D67008): TclTk error: invalid command name "vtkTemp10912"
invalid command name "vtkTemp10912"
    while executing
"vtkTemp10912 Render"
    ("after" script)


So basically by changing the file names, the DICOM files are loading. The image is having size (512,512,59), with origin at (215, 195.1, -1332.5) and the image spacing (0.84, 0.84, 3). But I don't know if that matters much.

Thanks everyone for all the help and the problem looks partially resolved. I think I can work ahead with this.

Saurabh

-----Original Message-----
From: slicer-users-bounces at bwh.harvard.edu [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Mark Anderson
Sent: Thursday, July 08, 2010 12:03 AM
To: slicer-users at bwh.harvard.edu
Subject: Re: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6

Hi Saurabh:
     I noticed that many of the InstanceNumber tags in the image headers
did not match the image number.
e.g 053.DCM has InstanceNumber 28 - this should be 53.
     Also, the SliceLocation started at -1332.5 for the first image.
When I renamed the images to match
the InstanceNumber and reset the slice locations starting at 0.0 and set
3mm apart, the datset
loads in slicer and overlays on the corresponding Dicom to Nrrd  dataset
correctly.

Mark

On 07/07/2010 11:10 AM, Saurabh Gupta 402549 wrote:
> Thanks all for your pains and help
>
> I have reported the bug. You can check it at http://na-mic.org/Mantis/view.php?id=903.
>
> @Isaiah - Yes, you are right. I intend to crop those images and prepare two stacks of femur bone. I wished to get the vtk and stl files for the femur pair. I hope I can do it in Slicer, if the problem is resolved.
>
> Saurabh
>
> -----Original Message-----
> From: slicer-users-bounces at bwh.harvard.edu [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Isaiah Norton
> Sent: Wednesday, July 07, 2010 8:25 PM
> To: slicer-users at bwh.harvard.edu
> Subject: Re: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>
> FYI the converter works and produces a 30mb file, but in Slicer the
> image is way out of frame so the image must be centered or assigned a
> different origin.
>
> I don't see any glaring slice-spacing issues when I scroll or look at a
> volume rendering. It looks like maybe a cross section of two femurs if I
> had to guess - but I'm usually looking only at the head CTs :)
>
>
> On 07/07/2010 10:42 AM, Nicole Aucoin wrote:
>
>> When I open up the tk console (control-t), I see another error message:
>> Can't read file /spl/tmp/nicole/dicomtest/001.DCM
>> Uncaught exception:
>> /projects/birn/nicole/Slicer3.6/Slicer3/Libs/vtkITK/vtkITKArchetypeImageSeriesReader.cxx:610:
>> itk::ERROR: vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot
>> open /spl/tmp/nicole/dicomtest/001.DCM.
>>
>> Looking at the source code, it's a generic catch all exceptions message.
>> The error could be coming from the itk::ImageSeriesReader, or from
>> getting the IJK to RAS direction vector.
>> Clicking on ignore image orientation and single file don't make a
>> difference, and I get the same error on windows32 and linux64 machines.
>> Running the Dicom To Nrrd Converter module on it, I get something more
>> useful:
>> Dicom to Nrrd Converter standard output:
>>
>> C:/cygwin/home/nicole/Data/dicomTest.nrrd
>> ORIGINAL\PRIMARY\AXIAL\CT
>> =================== numberOfSlicesPerVolume:59
>> Dicom images are ordered in a volume interleaving way.
>> ImageOrientationPatient (0020:0037): LPS Orientation Matrix
>> 1 -0 0
>> 0 1 0
>> -0 0 1
>>
>> SpacingMatrix
>> 0.84 0 0
>> 0 0.84 0
>> 0 0 3
>>
>> NRRDSpaceDirection
>> 0.84 0 0
>> 0 0.84 0
>> 0 0 3
>>
>> Warning: vendor type not valid
>>
>>
>> So, unfortunately, the short answer is: Slicer doesn't support this
>> vendor's DICOM format.
>>
>> Nicole
>>
>> Saurabh Gupta 402549 wrote:
>>
>>
>>> Yes, I got the same error message. Now, not sure what to do.
>>>
>>> *From:* Yanling Liu [mailto:vrnova at gmail.com]
>>> *Sent:* Wednesday, July 07, 2010 7:32 PM
>>> *To:* Saurabh Gupta 402549
>>> *Cc:* Magnotta, Vincent A; slicer-users at bwh.harvard.edu
>>> *Subject:* Re: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>>>
>>> No, I can not load them in Slicer. Based on the error message it
>>> sounds like a ITK problem.
>>>
>>> vtkMRMLVolumeArchetypeStorageNode (0x85a5f10): ReadData: Cannot read
>>> file, fullName = /home/yliu/Downloads/subj006reg001/001.DCM, number of
>>> files listed in the node = 0, the ITK reader says it was able to read
>>> 0 files, the reader used the archetype file name of
>>> /home/yliu/Downloads/subj006reg001/001.DCM
>>>
>>> On Wed, Jul 7, 2010 at 9:54 AM, Saurabh Gupta 402549
>>> <Saurabh_402549 at infosys.com<mailto:Saurabh_402549 at infosys.com>>   wrote:
>>>
>>> Thanks Yanling
>>>
>>> @Yanling - Can you load them in Slicer ?
>>>
>>> So any idea, anyone, as to what the problem could be ?
>>>
>>> Saurabh
>>>
>>> *From:* Yanling Liu [mailto:vrnova at gmail.com<mailto:vrnova at gmail.com>]
>>> *Sent:* Wednesday, July 07, 2010 7:22 PM
>>>
>>>
>>> *To:* Saurabh Gupta 402549
>>> *Cc:* Magnotta, Vincent A; slicer-users at bwh.harvard.edu
>>> <mailto:slicer-users at bwh.harvard.edu>
>>> *Subject:* Re: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>>>
>>> Yep, ImageJ and ITK-SNAP can load you data successfully.
>>>
>>> On Wed, Jul 7, 2010 at 9:37 AM, Saurabh Gupta 402549
>>> <Saurabh_402549 at infosys.com<mailto:Saurabh_402549 at infosys.com>>   wrote:
>>>
>>> Hi Yanling
>>>
>>> Yes I have opened the DICOM images on MicroDicom, a DICOM viewer. It
>>> shows all the images perfectly and also lists the various DICOM tags.
>>> So I think the dataset is fine. I am attaching the dataset with this
>>> email.
>>>
>>> Saurabh
>>>
>>> *From:* Yanling Liu [mailto:vrnova at gmail.com<mailto:vrnova at gmail.com>]
>>> *Sent:* Wednesday, July 07, 2010 7:02 PM
>>> *To:* Saurabh Gupta 402549
>>> *Cc:* Magnotta, Vincent A; slicer-users at bwh.harvard.edu
>>> <mailto:slicer-users at bwh.harvard.edu>
>>> *Subject:* Re: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>>>
>>> Just curious, have you tried to use other programs such as ImageJ to
>>> open the DICOM dataset? It would be nice to make sure no problem in
>>> the dataset.
>>>
>>> Yanling
>>>
>>> On Wed, Jul 7, 2010 at 9:26 AM, Saurabh Gupta 402549
>>> <Saurabh_402549 at infosys.com<mailto:Saurabh_402549 at infosys.com>>   wrote:
>>>
>>> Hi Vince
>>>
>>> I renamed the directory. I even renamed the files to follow sequential
>>> order from 001.DCM ... but still it's giving the same error. I can't
>>> see any description when I select a file in the Add Volume Selection
>>> Box that pops up.
>>>
>>> Regards
>>> Saurabh
>>>
>>>
>>> -----Original Message-----
>>> From: Magnotta, Vincent A [mailto:vincent-magnotta at uiowa.edu
>>> <mailto:vincent-magnotta at uiowa.edu>]
>>> Sent: Wednesday, July 07, 2010 6:19 PM
>>> To: Saurabh Gupta 402549; slicer-users at bwh.harvard.edu
>>> <mailto:slicer-users at bwh.harvard.edu>
>>> Subject: RE: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>>>
>>> Try renaming the directory that contains the DICOM files. The .dcm
>>> extension on the directory may be causing problems.
>>>
>>> Vince
>>>
>>> -----Original Message-----
>>> From: Saurabh Gupta 402549<Saurabh_402549 at infosys.com
>>> <mailto:Saurabh_402549 at infosys.com>>
>>> Sent: Wednesday, July 07, 2010 5:29 AM
>>> To: slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>
>>> <slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>>
>>> Subject: [slicer-users] FW:Help - DICOM does not load in Slicer 3.6
>>>
>>>
>>>
>>> From: Saurabh Gupta 402549
>>> Sent: Wednesday, July 07, 2010 3:39 PM
>>> To: 'slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>'
>>> Subject: DICOM does not load in Slicer 3.6
>>>
>>> Hi
>>>
>>> I tried adding DICOM files as volume in Slicer 3.6 and it gives this
>>> error :-
>>>
>>> ERROR: In
>>> ..\..\..\Slicer3\Libs\MRML\vtkMRMLVolumeArchetypeStorageNode.cxx, line 330
>>> vtkMRMLVolumeArchetypeStorageNode (18AD5198): ReadData: Cannot read
>>> file, fullName = D:/DICOM/subj006reg001.dcm/GE2FVHF4.DCM, number of
>>> files listed in the node = 0, the ITK reader says it was able to read
>>> 0 files, the reader used the archetype file name of
>>> D:/DICOM/subj006reg001.dcm/GE2FVHF4.DCM
>>>
>>> Is there a way, I can resolve it ?
>>>
>>> Thanks
>>> Saurabh
>>>
>>>
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