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