antspy is much slower than ANTs.

[hz1z]

For the same functionality, I can get results in one minute using the ANTs command line, but it’s very slow and doesn’t produce results when using Python.

python

import ants

fix_img_pt = '/home/hyh/code/coregister/tmax.nii.gz'
move_img_pt = '/home/hyh/code/coregister/dwi_dcm.nii.gz'
save_path = './reg_img.nii.gz'

fix_img = ants.image_read(fix_img_pt)
move_img = ants.image_read(move_img_pt)

outs = ants.registration(fix_img, move_img, type_of_transforme='Affine')

reg_img = outs['warpedmovout']
ants.image_write(reg_img, save_path)

ANTs

antsRegistrationSyN.sh -d 3 -f tmax,nii.gz -m dwi_dcm.nii.gz -o aff -t a

[ntustison]

Even though they're both affine registrations, the parameters between the two are different.

[cookpa]

There were some speed differences fixed in #703, but as @ntustison says, parameters differ. To compare like to like, you need to use type_of_transform='antsRegistrationSyN[a]'

[hz1z]

outs = ants.registration(fix_img, move_img,
                             type_of_transforme='Affine', verbose=True)

try to use verbose to debug, i find ...

I think it didn’t perform the registration; it just got stuck at…

[hz1z]

It’s possible that I want to register DWI to the three-component Tmax, and I tried with one component T1 and DWI, and there was no issue; it worked.

[ntustison]

Note that there is overlap when you use the family of transforms, e.g., type_of_transforme="antsRegistrationSyN[a]". Consult the help menu for further guidance.

[cookpa]

It’s possible that I want to register DWI to the three-component Tmax, and I tried with one component T1 and DWI, and there was no issue; it worked.

That's probably the problem then, antspy sees the 4D image and tries to do a 4D registration (much slower).

In your command line example you had -d 3. You must extract a 3D image to use here (eg, b0 from dwi) or the output will be incorrect

[cookpa]

https://github.com/ANTsX/ANTs/wiki/Dimensionality-or-ImageDimension-option-in-ANTs

[cookpa]

Faster ANTsPy now available in 0.5.4