0000903: DICOM files not loading through Add Volume

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Category

Severity

Reproducibility

Date Submitted

Last Update

0000903

[Slicer3] Base Code

major

always

2010-07-07 11:03

2010-07-15 10:23

Reporter

Saurabh

View Status

public

Assigned To

lorensen

Priority

normal

Resolution

open

Status

assigned

Summary

0000903: DICOM files not loading through Add Volume

Description

When I try to load the DICOM files, I get the following error message :-
ERROR: In ..\..\..\Slicer3\Libs\MRML\vtkMRMLVolumeArchetypeStorageNode.cxx, line 330
vtkMRMLVolumeArchetypeStorageNode (18A38EE8): ReadData: Cannot read file, fullName = D:/DICOM/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 D:/DICOM/subj006reg001/001.DCM

I have checked that the dataset is right. It works on MicroDicom and lists tags as well. Other users also said it's working on ImageJ and ITK-SNAP as well. However, its giving this error message on Slicer 3.6. Also, it is also not showing any description of the file when selected in the Add Volume selection box that opens up.

Additional Information

Another user reported :-

These files will convert using the module Converters -> DICOM to NRRD Converter. Then open the resulting nrrd file.

Note that the conversion appears to work fine, but there is an informational error returned:

"""
ERROR: In
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
line 1622
vtkCommandLineModuleLogic (0xd49b9a8): Dicom to Nrrd Converter standard
error:

Unrecognized vendor.
"""

*************************************************************
Another user reported :-

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

Tags

No tags attached.

Attached Files

subj006reg001.rar [^] (3,878,063 bytes) 2010-07-07 11:03

Relationships

duplicate of

0000858

assigned

pieper

Dicom load failure when no meta-header

Notes
(0001833) fedorov (developer) 2010-07-07 14:41	see the discussion on slicer-users here: http://massmail.spl.harvard.edu/public-archives/slicer-users/2010/003087.html [^]

(0001835) lorensen (developer) 2010-07-08 13:24	These files do not have a DICOM preamble. The itkGDCMImageIO that reads these files currently rejects files without a preamble. We will change itkGDCMImageIO so that it will accept these bad DICOM files, but provide a warning. As a temporary workaround, the lines in itkGDCMImageIO.cxx that read: bool preamble; if( gdcm::Document::CanReadFile(file, preamble) ) { // By default only support DICOM with preamble (DICM magic number): return preamble; } can be changed to: bool preamble; if( gdcm::Document::CanReadFile(file, preamble) ) { itkWarningMacro(<< "The DICOM file: " << filename << " does not have a preamble."); return true; }

Issue History
Date Modified	Username	Field	Change
2010-07-07 11:03	Saurabh	New Issue
2010-07-07 11:03	Saurabh	File Added: subj006reg001.rar
2010-07-07 11:05	Saurabh	Tag Attached: DICOM
2010-07-07 11:05	Saurabh	Tag Attached: not loaded
2010-07-07 11:05	Saurabh	Tag Attached: Slicer 3.6
2010-07-07 11:05	Saurabh	Tag Attached: Volume
2010-07-07 14:41	fedorov	Note Added: 0001833
2010-07-08 13:24	lorensen	Note Added: 0001835
2010-07-12 14:23	pieper	Relationship added	duplicate of 0000858
2010-07-15 10:22	nicole	Tag Detached: DICOM
2010-07-15 10:22	nicole	Tag Detached: not loaded
2010-07-15 10:22	nicole	Tag Detached: Volume
2010-07-15 10:22	nicole	Tag Detached: Slicer 3.6
2010-07-15 10:23	nicole	Assigned To	=> lorensen
2010-07-15 10:23	nicole	Status	new => assigned

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