Since ITK 5.3 NIFTI IO is more strict when loading data. Which can lead to problems with data where the axis are not totaly orthonormal (e.g. also due to rounding errors).
With ITK 5.4 the offer a switch in ther NIFTI IO to set the reader into permissive mode.
See:
https://github.com/InsightSoftwareConsortium/ITK/pull/4009
https://github.com/InsightSoftwareConsortium/ITK/issues/3994
Proposed solution:
- We introduce a preference with which you can set permissve mode ON.
- TBD: does that also work for mini apps?)
- Overwrite FixedNiftiImageIO::ReadImageInformation: check the preferene and set this->SetPermissiveMode accordingly; then call Superclass::ReadImageInformation
This task can be addressed as soon as ITK 5.4 is out and we have it integrated.