BUG: Fix incorrect reading of MINC2 files, convert RAS coordinates to LPS

[gdevenyi]

Replaces #147

PR Checklist

• No API changes were made (or the changes have been approved)
• No major design changes were made (or the changes have been approved)
• Added test (or behavior not changed)
• Updated API documentation (or API not changed)
• Added license to new files (if any)
• Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5
• Added ITK examples for all new major features (if any)

Refer to the ITK Software Guide for
further development details if necessary.

[gdevenyi]

TODO:

• port TransformMINC fixes
• add tests
  • read in MINC file, read in NIFTI file, confirm identical with internal representation
• wrap in some kind of ITK legacy warning

[seanm]

I'd be interested to try this in our app when you think it's in shape...

[vfonov]

I'll try to make changes....

[vfonov]

TODO:

• port TransformMINC fixes

• add tests

  • read in MINC file, read in NIFTI file, confirm identical with internal representation

• wrap in some kind of ITK legacy warning

https://github.com/vfonov/ITK/commits/MINC_IMAGE_RAS_LPS_VF/ - here is my work in progress, i am going to add tests for all the new cases...

[blowekamp]

Would any of the enums enums for the AnatomicalOrientaion PR be useful here?

I am seeing a lot of LPS and RAS terms in this PR which can be little ambiguous. At lease the public interface of "RAS_to_LPS" the setter getter could be clarified and be make unambiguous.

[vfonov]

At lease the public interface of "RAS_to_LPS" the setter getter could be clarified and be make unambiguous.

What would make it less ambiguous?

[vfonov]

OK, How do i push my changes here from https://github.com/vfonov/ITK/tree/MINC_IMAGE_RAS_LPS ?

[jhlegarreta]

Pushing to Gabriel's branch should work:

git push gdevenyi MINC_IMAGE_RAS_LPS

The above assumes that the you have created your MINC_IMAGE_RAS_LPS branch from gdevenyi's branch. If not, I believe

git remote add gdevenyi https://github.com/gdevenyi/ITK.git
git fetch gdevenyi
git checkout MINC_IMAGE_RAS_LPS
git branch -u gdevenyi/MINC_IMAGE_RAS_LPS
git push gdevenyi MINC_IMAGE_RAS_LPS

should have the desired effect. If you run into trouble, you can start a fresh branch (assuming you rename your local MINC_IMAGE_RAS_LPS to something else to avoid issues) and cherry-pick your commit:

git remote add gdevenyi https://github.com/gdevenyi/ITK.git
git fetch gdevenyi
git checkout -b gdevenyi MINC_IMAGE_RAS_LPS
git cherry-pick 7688f522b685eb4ace0b9753f0bbf145fd6389bb
git push gdevenyi MINC_IMAGE_RAS_LPS

[vfonov]

git push gdevenyi MINC_IMAGE_RAS_LPS

ERROR: Permission to gdevenyi/ITK.git denied to vfonov.

[jhlegarreta]

ERROR: Permission to gdevenyi/ITK.git denied to vfonov.

@gdevenyi should be able to grant permissions to push to his ITK fork on GitHub, which should fix the issue.

[gdevenyi]

I have invited @vfonov

[vfonov]

So itkSPSAOptimizerTest fails on Windows, do we need to do anything about that?

[blowekamp]

This newly merged class should provide some documentation to better describe the coordinate changes in an unambiguous fashion: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkAnatomicalOrientation.h

[vfonov]

so, where does this new class apply in the proposed change?

[blowekamp]

so, where does this new class apply in the proposed change?

Please document what you mean by RAS in the unambiguous terminology described in that class.

[vfonov]

so, where does this new class apply in the proposed change?

Please document what you mean by RAS in the unambiguous terminology described in that class.

So, it's a documentation question - i.e I should updated documentation of the MINC reader Module?

[vfonov]

@gdevenyi - can you make changes requested by @blowekamp ? I do not understand what's required here.