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.
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.