0003457: Loading DICOM SPECT data causes incrrect z spacing and orientation - MantisBT

ID	Project	Category	View Status	Date Submitted	Last Update

0003457	Slicer4	Module DICOM	public	2013-10-24 17:18	2017-06-14 13:07

Reporter	pearsomark	Assigned To	pieper
Priority	normal	Severity	major	Reproducibility	always
Status	resolved	Resolution	unable to reproduce
Product Version	Slicer 4.3.0
Target Version		Fixed in Version

Summary	0003457: Loading DICOM SPECT data causes incrrect z spacing and orientation
Description	DICOM SPECT reconstructions which load correctly in version 4.2.2 have the wrong z spacing and orientation in version 4.3.1.
Additional Information	The issue has been reproduced on Linux 64 bit and MAC OS X, not tested on windows. Attached is files.zip with screenshots showing the same file loaded into each version and a compressed SPECT file.
Tags	No tags attached.

2013-10-24 17:18	files.zip (864,338 bytes)

2013-10-24 17:35	Slicer4.2.2-1.jpg (107,218 bytes) Slicer4.2.2-1.jpg (107,218 bytes)

2013-10-24 17:36	Slicer4.3.1.jpg (75,861 bytes) Slicer4.3.1.jpg (75,861 bytes)

pieper 2013-11-11 06:45 administrator ~0010302	Interesting - this is probably a side effect slicer's change to ITKv4. Looking at the header it seems like the SliceThickness has the same value as the z spacing - in general this is not a reliable place to get the slice spacing but maybe for spect it is the right place. Running a pure ITK program that just tries to read the file can replicate the issue, as shown below, and the messages even point to where the issue is. 0000009 spect $ ~/slicer4/latest/Slicer-superbuild/Slicer-build/lib/Slicer-4.3/cli-modules/GaussianBlurImageFilter -s 1 file0001 /tmp/file.nrrd Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 775, function <unknow> FIXME Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 974, function <unknow> Dont know how to handle spacing for: (0028,0009) ?? 4 Loaded:4 Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 775, function <unknow> FIXME Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 974, function <unknow> Dont know how to handle spacing for: (0028,0009) ?? 4 Loaded:4 Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 775, function <unknow> FIXME Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 974, function <unknow> Dont know how to handle spacing for: (0028,0009) ?? 4 Loaded:4 Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 775, function <unknow> FIXME Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 974, function <unknow> Dont know how to handle spacing for: (0028,0009) ?? 4 Loaded:4 Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 775, function <unknow> FIXME Warning: In /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 974, function <unknow> Dont know how to handle spacing for: (0028,0009) ?? 4 Loaded:4 Here's the header of the resulting file.nrrd (with spacing of 1). NRRD0004 Complete NRRD file format specification at: http://teem.sourceforge.net/nrrd/format.html type: short dimension: 3 space: left-posterior-superior sizes: 128 128 128 space directions: (4.4180599999999997,0,0) (0,4.4180599999999997,0) (0,0,1) kinds: domain domain domain endian: little encoding: gzip space origin: (0,0,0)

pieper 2013-11-11 06:59 administrator ~0010304	Issue filed on ITK bug tracker: https://issues.itk.org/jira/browse/ITK-3221

lassoan 2017-06-14 13:07 developer ~0014837	It works correctly in Slicer 4.7.0-2017-05-27

Date Modified	Username	Field	Change
2013-10-24 17:18	pearsomark	New Issue
2013-10-24 17:18	pearsomark	Status	new => assigned
2013-10-24 17:18	pearsomark	Assigned To	=> pieper
2013-10-24 17:18	pearsomark	File Added: files.zip
2013-10-24 17:35	pearsomark	File Added: Slicer4.2.2-1.jpg
2013-10-24 17:36	pearsomark	File Added: Slicer4.3.1.jpg
2013-11-11 06:45	pieper	Note Added: 0010302
2013-11-11 06:59	pieper	Note Added: 0010304
2017-06-14 13:07	lassoan	Status	assigned => resolved
2017-06-14 13:07	lassoan	Resolution	open => unable to reproduce
2017-06-14 13:07	lassoan	Note Added: 0014837