Conversion between warps ANTs <-> FSL

[mblesac]

Dear experts,

I know that this question comes from time to time but I was wondering if there are any guides about how to convert the warps from fsl to ants and vice-versa.

I've been using c3d_affine_tool for the affine matrices and workbench for the warps. It worked for my data, but I'm not sure if it's the recommended approach. Any comments on the best way to achieve this? Thanks in advance.

Best regards,

Manuel

[ntustison]

I wasn't aware of the workbench solution so thanks for bringing that to our attention. We don't have an alternative solution within the toolkit so I would recommend continuing with the tools you are currently using.

[mblesac]

Hi,

Thanks for your reply! I post here the commands I use, just in case anybody finds it useful (I'm working with neonatal data).

template:

subject:

Registration:
antsRegistrationSyN.sh -d 3 -f template.nii.gz -m subject.nii.gz -f template_GM.nii.gz -m subject_GM.nii.gz -f template_WM.nii.gz -m subject_WM.nii.gz -o ants_OUT_ -t 'b' -r 8 -j 1
This is based in the dHCP pipeline

The warped image:

Now the conversion of the affine matrix:
c3d_affine_tool -ref template.nii.gz -src subject.nii.gz -itk ants_OUT_0GenericAffine.mat -ras2fsl -o flirt_OUT.mat

The warp:
wb_command -convert-warpfield -from-itk ants_OUT_1Warp.nii.gz -to-fnirt OUT_fnirt.nii.gz template.nii.gz

convertwarp --ref=template.nii.gz --premat=OUT_flirt.mat --warp1=OUT_fnirt.nii.gz --out=OUT_fsl_warp.nii.gz

applywarp -i subject.nii.gz -r template.nii.gz -w OUT_fsl_warp.nii.gz -o RESULT.nii.gz

The resulting image after applying the warp converted to FSL:

Best regards,

Manuel

[cookpa]

Thanks for this contribution. I think the system you've worked out yourself and validated for your data is best. I'd advise anyone translating between software to validate carefully on their own data. Ambiguities or disagreements in the interpretation of physical coordinates or transforms can cause unexpected results in some data but not others.

[cookpa]

This might also be helpful

https://nitransforms.readthedocs.io/en/latest/index.html

[hbraunDSP]

This approach isn't working for me with HCP data. I'm doing the following:

wb_command -convert-warpfield -from-fnirt acpc_dc2standard.nii.gz MNI152_T1_1mm_brain.nii.gz -to-itk acpc_dc2standard_itk.nii.gz
antsApplyTransforms -d 3 -i T1w_acpc.nii.gz -o T1w_mni.nii.gz -t acpc_dc2standard_itk.nii.gz -v -r MNI152_T1_1mm_brain.nii.gz
applywarp -i T1w_acpc.nii.gz -o T1w_mni_fsl.nii.gz -r MNI152_T1_1mm_brain.nii.gz -w acpc_dc2standard.nii.gz

After executing this code, the T1w_mni_fsl file from applywarp is correctly registered but the T1w_mni file output by antsApplyTransforms is not. I've also tried the following variations:

• using the "absolute" mode of wb_command
• using different files in the reference geometry part of wb_command: ACPC T1, diffusion space T1, and the supplied DK atlas segmentation, which is also in ACPC space.

Do you know what the problem could be?

[ntustison]

Have you considered this difference between ANTs and FSL?

[hbraunDSP]

Good idea, but I just checked using nibabel and no relevant file has a discrepancy between its sform and qform.

[ntustison]

The issue is not discrepancy between files but the discrepancy with the way individual packages treat the sform and qform.

[hbraunDSP]

My reading of your link is that ITK/ANTS will use the qform in some circumstances where many other packages will use the sform. If the sform and qform match, isn't that a non-issue?

[ntustison]

If the sform and qform match, isn't that a non-issue?

I don't see how that's inferred from the link that I posted. But from what I understand, it's more complicated than that. However, perhaps @cookpa can weigh in as he actually wrote that explanation.

[cookpa]

One thing I can add is that when dealing with warps, you not only have to consider the coordinate system of the image, but also that of the vectors stored at each voxel. They can diverge in some contexts, for example diffusion gradient vectors. I don't know if the same issue is at play with fnirt warp fields.