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<p class="MsoNormal"><span style="font-size:11.0pt">ITK Developers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The following patch provides 100% backwards compatibility and an end-user modifiable interface for setting the intents of the qform & sform.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://review.source.kitware.com/#/c/21795/">http://review.source.kitware.com/#/c/21795/</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx#L1717">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx#L1717</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform_brief_usage">https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform_brief_usage</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The qform_code should be set to either NIFTI_XFORM_UNKNOWN or NIFTI_XFORM_SCANNER_ANAT.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The sform code should be set to either NIFTI_XFORM_UNKNOWN, NIFTI_XFORM_ALIGNED_ANAT, NIFTI_XFORM_TALAIRACH or NIFTI_XFORM_MNI_152.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">=================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">This is a long-standing bug that should be fixed with a new patch set:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The sform & qform defaults were EXACTLY BACKWARDS from the recommended uses.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">================= QUESTION ==========<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Please help me determine the balance between backwards compatibility conformance and improved interpretation of these nifi files.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Hans<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">========================================================================<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| Hans J. Johnson, Ph.D., Associate Professor |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| Appointments: |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Electrical and Computer Engineering (Primary) |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Biomedical Engineering |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Psychiatry ,NMMM~ |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Health Informatics MMMMMMMMMMMMMMN |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Iowa Institute for Biomedical Imaging MMMMMMMMMMMMMMMMMMM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| - Iowa Informatics Institute MMMMMMMMMMM MMMM MMM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| MMMMMMMMMM I ?MMM MM M |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| hans-johnson@uiowa.edu MMMMMMM ,$M, MMMM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| (319) 621 7185 (cell) MMMM~ MMMM MMMMMM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| (319) 384 3538 ECE Phone (Primary) MM 8MMMMMM MM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| M MMMMMMM, ,M~ M |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| 4316 Seamans Center MMMMMM MM |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">| Iowa City, IA 52242 ,? |<o:p></o:p></span></p>
<p class="MsoNormal" style="background:#FEF49C"><span style="font-size:8.5pt;font-family:Menlo;color:black">========================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">http://emailcharter.org</span><o:p></o:p></p>
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