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

Isaiah Norton inorton at partners.org
Wed Jul 7 10:55:24 EDT 2010


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
>>
>>
>> **************** CAUTION - Disclaimer *****************
>> This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended
>> solely
>> for the use of the addressee(s). If you are not the intended
>> recipient, please
>> notify the sender by e-mail and delete the original message. Further,
>> you are not
>> to copy, disclose, or distribute this e-mail or its contents to any
>> other person and
>> any such actions are unlawful. This e-mail may contain viruses.
>> Infosys has taken
>> every reasonable precaution to minimize this risk, but is not liable
>> for any damage
>> you may sustain as a result of any virus in this e-mail. You should
>> carry out your
>> own virus checks before opening the e-mail or attachment. Infosys
>> reserves the
>> right to monitor and review the content of all messages sent to or
>> from this e-mail
>> address. Messages sent to or from this e-mail address may be stored on the
>> Infosys e-mail system.
>> ***INFOSYS******** End of Disclaimer ********INFOSYS***
>> _______________________________________________
>> slicer-users mailing list
>> slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to
>> slicer-users-request at massmail.spl.harvard.edu
>> <mailto:slicer-users-request at massmail.spl.harvard.edu>  with
>> unsubscribe as the subject
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> slicer-users mailing list
>> slicer-users at bwh.harvard.edu
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to slicer-users-request at massmail.spl.harvard.edu with unsubscribe as the subject
>>      
> _______________________________________________
> slicer-users mailing list
> slicer-users at bwh.harvard.edu
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to slicer-users-request at massmail.spl.harvard.edu with unsubscribe as the subject
>    



More information about the slicer-users mailing list