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IDProjectCategoryView StatusDate SubmittedLast Update
0002945Slicer4Core: CLI infrastructurepublic2013-02-12 11:312017-06-07 23:27
Reporterpieper Assigned Tojcfr  
PriorityhighSeveritymajorReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.2.2-1 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0002945: dicom files get wrong origin and directions from CreateADICOMSeries
Description

DICOM header is wrong.

Steps To Reproduce

1) Download MRhead (or any file)
2) Pick Create A DICOM Series
3) Run the export
4) Re-load the dicom file using the Add Data dialog (or the DICOM module)
5) compare the images and get the attached images.

TagsITKv4

Relationships

has duplicate 0003254 closedjcfr Tilted volumes lose correct orientation on DICOM export 
child of 0002289 closedmillerjv CreateADICOMSeries using ITKv4 does not properly write out Z-spacing 

Activities

2013-02-12 11:33

 

Screen Shot 2013-02-12 at 4.32.50 PM.png (372,148 bytes)

2013-02-12 11:33

 

Screen Shot 2013-02-12 at 4.33.03 PM.png (332,737 bytes)
pieper

pieper

2013-07-04 10:54

administrator   ~0008834

I'd really like to see this fixed for the 4.3 release. It must be something simple to fix!
millerjv

millerjv

2013-07-09 07:36

developer   ~0008942

I suspect that this was fixed in ITK in

https://github.com/Kitware/ITK/commit/df6614403b19139c3831762d443c3390a29ad5e3

commit df6614403b19139c3831762d443c3390a29ad5e3
Author: Hans Johnson <hans-johnson@uiowa.edu>
Date: Fri Jun 7 21:32:49 2013 -0500

BUG: ImageSeriesWriter + GDCMImageIO loses info

When directional cosines are copied from 3D volume to 2D slices by
ImageSeriesWriter, only the upper-left 2x2 matrix can be copied, due to the
dimension of m_Direction matrix.

Then GDCMImageIO sets zeros in the missing values of the first 2 lines of th
matrix.

This is not a problem if the directional cosines matrix is the identity matr
otherwise DICOM tag (0020,0037) Image Orientation (Patient) of the output
DICOM files is not valid.

ITK-281

Change-Id: I44bac496fb1132abb85a5f9d66bd7ad469c774b2
millerjv

millerjv

2013-07-09 07:45

developer   ~0008943

So we will need to manage the ITK version we use or create our own patched version.

I am surprised that this was checked in in June. I thought it had been addressed earlier this year.
pieper

pieper

2013-07-09 08:16

administrator   ~0008948

I added this to the agenda for the developers meeting today:

http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/20130709#To_discuss
hjmjohnson

hjmjohnson

2013-07-09 12:23

developer   ~0008971

ITK has this, Discussed at T-Con about how to move forward to using this version.

commit df6614403b19139c3831762d443c3390a29ad5e3
Author: Hans Johnson <hans-johnson@uiowa.edu>
Date: Fri Jun 7 21:32:49 2013 -0500

BUG: ImageSeriesWriter + GDCMImageIO loses info

When directional cosines are copied from 3D volume to 2D slices by
ImageSeriesWriter, only the upper-left 2x2 matrix can be copied, due to the
dimension of m_Direction matrix.

Then GDCMImageIO sets zeros in the missing values of the first 2 lines of the
matrix.

This is not a problem if the directional cosines matrix is the identity matrix,
otherwise DICOM tag (0020,0037) Image Orientation (Patient) of the output
DICOM files is not valid.

ITK-281

Change-Id: I44bac496fb1132abb85a5f9d66bd7ad469c774b2
jcfr

jcfr

2013-07-10 09:54

administrator   ~0008987

Fixed in r22163
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=22163
fedorov

fedorov

2013-07-31 06:14

developer   ~0009294

The issue does not appear to be resolved. Please see related issue 0003254 that provides screenshots demonstrating the issue and the datasets that allow to reproduce it.
jcfr

jcfr

2013-08-28 20:38

administrator   ~0009692

Fixed in r22355
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=22355
jcfr

jcfr

2014-03-06 05:22

administrator   ~0011176

Closing resolved issues that have not been updated in more than 3 months
jcfr

jcfr

2017-06-07 23:27

administrator   ~0014639

Fix committed to 2145-support-for-installing-extension-from-file branch.

Related Changesets

Slicer: 2145-support-for-installing-extension-from-file 552f2cbe

2013-07-10 13:53:17

jcfr

Details Diff 		BUG: Fix origin&directions in CreateADICOMSeries - Update ITKv4 project

This problem is captured by issue 0002945 and the associated fix has been
pushed to ITK master.

During developer hangout of July 9th 2013, we discussed [1] what could
be the approach to build against a version of ITK including
commit df661440 without risking to break Slicer including new ITKv4 feature.

We concluded that working with ITK maintainers so that a patch release
ITK v4.4.1 including a list of carefully selected [2] commits is created was
the most reasonable approach.
Doing so ensures that only bug fixes are considered in the updated
version of ITK build by Slicer.

This commit update the ITKv4 external project so that the release
branch that will soon become ITKv4.4.1 is considered.

More particularly it include commit 9fa55c [3] fixing Slicer issue 0002945

Fixes 0002945

Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>

[1] http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/20130709#Conclusion
[2] http://www.itk.org/pipermail/insight-developers/2013-July/022922.html
[3] http://itk.org/gitweb?p=ITK.git;a=commit;h=9fa55c414d9000e467a57415329436e76356bebb

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22163 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

Issue History

Date Modified Username Field Change
2013-02-12 11:31 pieper New Issue
2013-02-12 11:31 pieper Status new => assigned
2013-02-12 11:31 pieper Assigned To => millerjv
2013-02-12 11:33 pieper File Added: Screen Shot 2013-02-12 at 4.32.50 PM.png
2013-02-12 11:33 pieper File Added: Screen Shot 2013-02-12 at 4.33.03 PM.png
2013-02-12 11:33 pieper Relationship added child of 0002289
2013-02-12 11:34 pieper Tag Attached: ITKv4
2013-07-04 10:53 pieper Priority normal => high
2013-07-04 10:53 pieper Target Version => Slicer 4.3.0
2013-07-04 10:54 pieper Note Added: 0008834
2013-07-09 07:36 millerjv Note Added: 0008942
2013-07-09 07:45 millerjv Note Added: 0008943
2013-07-09 08:16 pieper Note Added: 0008948
2013-07-09 12:23 hjmjohnson Note Added: 0008971
2013-07-10 09:54 jcfr Note Added: 0008987
2013-07-10 09:54 jcfr Status assigned => resolved
2013-07-10 09:54 jcfr Fixed in Version => Slicer 4.3.0
2013-07-10 09:54 jcfr Resolution open => fixed
2013-07-29 12:26 pieper Relationship added has duplicate 0003254
2013-07-31 06:14 fedorov Note Added: 0009294
2013-07-31 06:14 fedorov Status resolved => feedback
2013-07-31 06:14 fedorov Resolution fixed => reopened
2013-08-28 20:38 jcfr Note Added: 0009692
2013-08-28 20:38 jcfr Status feedback => resolved
2013-08-28 20:38 jcfr Resolution reopened => fixed
2014-03-06 05:22 jcfr Note Added: 0011176
2014-03-06 05:23 jcfr Status resolved => closed
2017-06-07 23:27 jcfr Changeset attached => Slicer 2145-support-for-installing-extension-from-file 552f2cbe
2017-06-07 23:27 jcfr Note Added: 0014639
2017-06-07 23:27 jcfr Assigned To millerjv => jcfr