"ITK only supports orthonormal direction cosines" when using ANTs

Discussions
1

Hi all,

Although from the title it reads as an ANTs-related issue, it appears to be potentially related to the way Brainstorm exports MRI files.

I am trying to perform a transformation from the ICBM152 provided in Brainstorm to a subject's T1. I exported the MRI from the @default_subject, but I get this error related to the ICBM152 MRI file:

NiftiImageIO (0x55eddc235bc0): /mnt/d/T1.nii has unexpected scales in sform

Exception caught during reference file reading

itk::ExceptionObject (0x55eddc2105b0)
Location: "unknown"
File: /usr/local/ANTs/build/ITKv5/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx
Line: 2016
Description: ITK ERROR: ITK only supports orthonormal direction cosines.  No orthonormal definition found!

Any clue on what this could mean?

Thank you,
Ramtin

2

As per this GitHub issue, the issue in on the ITK side:

1 Like
3

They indeed suggested to me to neglect the sform-check if I trust the data, but do you think the sform of the template provided in Brainstorm could be double-checked for potential imprecision? Since this is the first time I encounter this issue while using ANTs.

Thank you,
Ramtin

4

Yes, we will check that.
Could you share a simple script with ANTs that prompts the error?

5

Hi Raymundo,

This should generate the error:

antsRegistrationSyN.sh -t "s" -d 3 -f <someT1file> -m <defaultBrainstormICBM> -o <output> -x <someMask> -n 4 -j 1

ITK people suggested to run export ITK_NIFTI_SFORM_PERMISSIVE=1 to make this work, by letting ITK adjust the sform. However this should be done if I am confident that the sform is pretty much correct.