Anterior-Posterior and Right-Left axis flip

[10c7ccc7a4f0aff03c915c485565b9da]

When running the code cloned and compiled from ukftractography/master and the ukftractography binaries available on the PNL network, on LPS data, we notice an AP and LR axis flip.

On identified cause might be the following:

Teem, on January 19th, 2015, changed in src/nrrd/nrrdEnums.h line 458 the enumeration defining the space coordinate system (RAS, LPS, etc...) ( http://github.com/BRAINSia/teem/commit/f4862b566a55bfb17ec8e28b0137f84de8963b01#diff-48b4f9223977d5f67c5eccdd630c7114 ).

As a result, this enumeration is not consistent anymore with the one in ITK ( http://github.com/hinerm/ITK/blob/master/Modules/ThirdParty/NrrdIO/src/NrrdIO/NrrdIO.h.in#L1309 ).

Therefore, the data normalization in dwi_normalize is not performed for LPS scans, since I think ukftractography uses ITK to read the DWI file, and uses the enumeration from the Teem library in dwi_normalize.

Thank you.

[jcfr]

I think recent tests demonstrate the problem described here. See #114 (comment)