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

[Johnson, Hans J]

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




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| 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  |
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