[ITK] [ITK-users] dicom viewer/nifti discrepancy

Nicholas Tustison ntustison at gmail.com
Fri Apr 24 15:02:51 EDT 2015


Thanks Hans.  I’ll stew over that and see if it gets me anywhere.


> On Apr 24, 2015, at 11:47 AM, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:
> 
> I don’t have a definitive answer, but NIFTI internal representation is an RAS system, DICOM & ITK internal representations are LPS.
> 
> Perhaps there is a coordinate space incompatibility.
> 
> Hans
> 
> ========================================================================
> Hans J. Johnson, Ph.D.,  Associate Professor 
> Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry  
> hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>   
> (319) 621 7185 (cell)
> (319) 384 3538  ECE Phone (Primary)
> (319) 353 8587 Psychiatry Phone (Secondary)
> 
> 4316 Seamans Center
> Iowa City, IA 52242
> 
>> On Apr 24, 2015, at 1:37 PM, Nicholas Tustison <ntustison at gmail.com <mailto:ntustison at gmail.com>> wrote:
>> 
>> Hi all,
>> 
>> I have a set of dicom data that were annotated by clinical
>> folk.  Specifically, I have slice numbers for each image 
>> volume which indicate a particular feature of interest.  The 
>> problem is that the slice number can either be counted from
>> the most inferior slice or the most superior slice.  When I
>> view these dicom image volumes in Osirix or Fiji, the slice
>> number provided by the viewer corresponds to my clinical 
>> numbers.  However, when I convert to nifti (using dcm2nii or 
>> mriconvert), the index, in ITK terminology, always starts from the 
>> most inferior slice.  At first, I thought it was some dicom tag that 
>> was being read by the viewer to orient the index but, after following 
>> a couple of possibilities, I haven’t found anything.  Has anyone
>> come across anything like this?
>> 
>> Thanks,
>> Nick
>> _____________________________________
>> Powered by www.kitware.com <http://www.kitware.com/>
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20150424/a600ffc6/attachment.html>
-------------- next part --------------
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users


More information about the Community mailing list