"ITK ERROR: ITK only supports orthonormal direction cosines" when using antsRegistrationSyN.sh

[ramBrain]

Hi everyone,

I am trying to generate a transformation using antsRegistrationSyN.sh, but there seems to be an issue with one of the MRIs. Specifically, I get this error:

WARNING: In /usr/local/ANTs/build/ITKv5/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934
NiftiImageIO (0x560b169efbb0): ../defT1_bs.nii has unexpected scales in sform

Exception caught during reference file reading 

itk::ExceptionObject (0x560b169c95b0)
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!

 file ../defT1_bs.nii
Exception Object caught: 

itk::ExceptionObject (0x560b169c95b0)
Location: "unknown" 
File: /usr/local/ANTs/build/staging/include/ITK-5.4/itkCenteredTransformInitializer.hxx
Line: 35
Description: ITK ERROR: CenteredTransformInitializer(0x560b169ebcd0): Moving Image has not been set

By checking the header, the sform looks like this:

sto_xyz:1       0.995191 -0.009849 0.097461 -95.062607                            sto_xyz:2       0.047470 0.918793 -0.391875 -52.154037                            sto_xyz:3       -0.085687 0.394617 0.914842 -189.548813                           sto_xyz:4       0.000000 0.000000 0.000000 1.000000 

Any clue?

Thank you,
Ramtin

[cookpa]

Please post the full output of

PrintHeader ../defT1_bs.nii

as well as your OS and ANTs version.

[ramBrain]

The output of that line of code is as follows:

WARNING: In /usr/local/ANTs/build/ITKv5/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934
NiftiImageIO (0x55875b149920): ../defT1_bs.nii has unexpected scales in sform
cant read ../defT1_bs.nii

OS is WSL under Windows 10 (Ubuntu 22.04.2 LTS)

ANTs version: 2.4.3.post23-g2d10611 (as reported in ANTsVersionConfig.h)

Many thanks,
Ramtin

[cookpa]

Thanks. There were some ITK updates to try to avoid this problem. ITK requires an orthonormal cosine matrix, there can't be a shear or scaling (other than the voxel spacing). But sometimes it's too sensitive in detecting this.

Can you try the most recent ANTs? You can try binaries from the release page if you don't want to build from source again

[ramBrain]

Unfortunately the issue is still persistent. The difference with the previous prompt is that now it looks for ITKv5 in another folder, namely: /home/runner/work/_temp instead of /usr/local/ANTs

I cannot navigate to that directory though for some reason

[cookpa]

OK, I'll have to look more into this and possibly involve the ITK folks. Can you share the problematic image? If not, can you share the header? You can do this with

head -c 352 image.nii > header.nii

Note you need to unzip first (it doesn't work with .nii.gz)

[ramBrain]

The problematic image is actually the default ICBM152 included in the Brainstorm toolbox, hence I can share it (attached).

I was wondering if I should install ITK separately? Or shall the binary files suffice to make ANTs work?

Many thanks
defT1_bs.zip

[cookpa]

Perfect, you don't need to install ITK separately. The libraries are built into the executables. If you build from source, ITK will be downloaded and compiled first.

[gdevenyi]

The problematic image is actually the default ICBM152 included in the Brainstorm toolbox, hence I can share it (attached).

I was wondering if I should install ITK separately? Or shall the binary files suffice to make ANTs work?

Many thanks defT1_bs.zip

The official MNI atlases are available in NIFTI form from the original authors, https://nist.mni.mcgill.ca/atlases/

[cookpa]

It looks like this problem is caused by the header transform being almost orthonormal, but not quite enough for ITK. If you're OK with using the latest ANTs release, and dealing with some slight deviations in the image coordinates, you can set

export ITK_NIFTI_SFORM_PERMISSIVE=1

ITK will then "correct" the sform transform to be exactly orthonormal when reading the image. In this case:

 % fslhd defT1_bs.nii  | grep sto       
sto_xyz:1	0.969521 0.001320 -0.000507 -92.588768 
sto_xyz:2	-0.002264 0.970083 0.011989 -129.316452 
sto_xyz:3	0.003088 0.007503 0.991950 -78.728951 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 
descrip		Written with Brainstorm

% PrintHeader defT1_bs.nii 2> /dev/null | grep srow         
    srow_x = 0.969521 0.00131987 -0.000507485 -92.5888
    srow_y = -0.00226438 0.970083 0.0119889 -129.316
    srow_z = 0.00308824 0.00750341 0.99195 -78.729

[cookpa]

Updated the wiki

https://github.com/ANTsX/ANTs/wiki/How-does-ANTs-handle-qform-and-sform-in-NIFTI-1-images%3F

[ramBrain]

Many thanks for your help, I will try and see how it works.

Ramtin

[ethanharvey98]

Any idea how to set

export ITK_NIFTI_SFORM_PERMISSIVE=1

in ANTsPy?

[cookpa]

os.environ['ITK_NIFTI_SFORM_PERMISSIVE'] = '1'
import ants