[ITK-dev] NIFTI -- Proposed change to be more compliant

Johnson, Hans J hans-johnson at uiowa.edu
Mon Nov 21 10:08:39 EST 2016


ITK Developers,

The following patch provides 100% backwards compatibility and an end-user modifiable interface for setting the intents of the qform & sform.
http://review.source.kitware.com/#/c/21795/


The previous configuration for NIFTI files is OK if we only live in an ITK echo-system.  In the ITK echo-system we ignore both the sform & qform the intent codes because we only use the values in the qform.  These two lines have intent codes that are EXACTLY BACKWARDS from the recommendations

https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx#L1717

https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform_brief_usage
The qform_code should be set to either NIFTI_XFORM_UNKNOWN or NIFTI_XFORM_SCANNER_ANAT.
The sform code should be set to either NIFTI_XFORM_UNKNOWN, NIFTI_XFORM_ALIGNED_ANAT, NIFTI_XFORM_TALAIRACH or NIFTI_XFORM_MNI_152.


=================
This is a long-standing bug that should be fixed with a new patch set:

The sform & qform defaults were EXACTLY BACKWARDS from the recommended uses.

================= QUESTION  ==========

Please help me determine the balance between backwards compatibility conformance and improved interpretation of these nifi files.

Thanks,
Hans




========================================================================
| Hans J. Johnson, Ph.D.,  Associate Professor                         |
| Appointments:                                                        |
|   - Electrical and Computer Engineering (Primary)                    |
|   - Biomedical Engineering                                           |
|   - Psychiatry                                     ,NMMM~            |
|   - Health Informatics                         MMMMMMMMMMMMMMN       |
|   - Iowa Institute for Biomedical Imaging    MMMMMMMMMMMMMMMMMMM     |
|   - Iowa Informatics Institute             MMMMMMMMMMM MMMM MMM      |
|                                            MMMMMMMMMM I ?MMM  MM M   |
| hans-johnson at uiowa.edu                     MMMMMMM ,$M,        MMMM  |
| (319) 621 7185 (cell)                        MMMM~     MMMM   MMMMMM |
| (319) 384 3538  ECE Phone (Primary)           MM    8MMMMMM       MM |
|                                               M    MMMMMMM, ,M~    M |
| 4316 Seamans Center                                MMMMMM     MM     |
| Iowa City, IA 52242                                 ,?               |
========================================================================
http://emailcharter.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-developers/attachments/20161121/ca4edfbf/attachment.html>


More information about the Insight-developers mailing list