combining bbregister, fsl and ants to warp functional images

warpinfo.rst

ANTS : http://picsl.upenn.edu/ANTS/ c3d : http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D

export PATH=/software/ANTS-dev:$PATH

c3d_affine_tool -ref [A] -src [B] bbreg.mat -fsl2ras -oitk fsl2antsAffine.txt

WarpImageMultiTransform 3 [B] [C] -R [D] [A_Warp].nii.gz [A_Affine].txt fsl2antsAffine.txt

• A = your structural brain/orig.mgz, but converted to nii. you should already have this in your ANTS output
• B = con/t/z image that you want to warp
• bbreg.mat = when your bbregister node has out_fsl_file = True
• C = warped con/t/z image
• D = ANTS template or other template to which you computed the ANTS warp (unless you have another affine transform see note below)
• A_Warp = should equal the Warp fields from running ANTS, they should be called sth_Warp[xyz]vec.nii.gz. you simply need to provide sth_Warp.nii.gz
• A_Affine = there should also be an affine transform in the place where ANTS was run.

Note

if you also have an affine transform using flirt for your own template to MNI space and you did not use the MNI spaced template as your target

c3d_affine_tool -ref [E] -src [D] flirt.mat -fsl2ras -oitk fsl2antsTemplateAffine.txt

WarpImageMultiTransform 3 [B] [C] -R [E] fsl2antsTemplateAffine.txt [A_Warp].nii.gz [A_Affine].txt fsl2antsAffine.txt

• E = template in MNI space after flirting

Hi Satra,

I am also wondering about this question.
I like the results from ANTs in registering lesioned images to reference. I would like to use these ANTs' warp field outputs in fsl's probtrackx2 for a tractography analysis. However, testing the warp field on the moving image to the fixed image using fsl's applywarp does not yield a good registration alignment. I read in the fsl email discussion in jiscmail that the discrepancy is in the different ways warp fields are created and defined in different software, and that the discrepancy is not resolved (2015). I read in Sitek et al (2016) that they used the ANTs-obtained registration in fsl's probtrackx2 algorithm. I am wondering if the there is now a way to use ANTs registration in fsl.

Thank you very much!

Miguel

@satra @9999sotelom

Hi,

I have a similar use case:

I applied a rigid+deformable transformation for my b0 image to map it on my T1 image.

Now I want to transfer the warp image in ANTS format into FSL format???

I know I can do the inverse using c3d to transfer FSL format into ANTS, but it works only for affine registration, not for non-linear registration.

Do you have any ideas?