Doing some experiments for a <a href="https://github.com/spinal-cord-7t/coil-qc-code/i

Does `-param deformation` have an impact when used with `algo=rigid`? about spinalcordtoolbox HOT 2 CLOSED

jcohenadad commented on September 26, 2024

Does `-param deformation` have an impact when used with `algo=rigid`?

from spinalcordtoolbox.

Comments (2)

jcohenadad commented on September 26, 2024

Hum, one possible cause is that there are two APIs depending on the slicewise parameter:

spinalcordtoolbox/spinalcordtoolbox/registration/core.py

Lines 361 to 384 in a7e538c

 # ANTS 3d 

 elif step.algo.lower() in ants_registration_params and step.slicewise == '0': # FIXME [AJ] 

 warp_forward_out, warp_inverse_out = algorithms.register_step_ants_registration( 

 src=src, 

 dest=dest, 

 step=step, 

 masking=masking, 

 ants_registration_params=ants_registration_params, 

 padding=param.padding, 

 metricSize=metricSize, 

 verbose=param.verbose, 

 ) 

 # ANTS 2d 

 elif step.algo.lower() in ants_registration_params and step.slicewise == '1': # FIXME [AJ] 

 warp_forward_out, warp_inverse_out = algorithms.register_step_slicewise_ants( 

 src=src, 

 dest=dest, 

 step=step, 

 ants_registration_params=ants_registration_params, 

 fname_mask=fname_mask, 

 remove_temp_files=param.remove_temp_files, 

 verbose=param.verbose, 

 )

BUT: The default slicewise is 0. So it shouldn't matter...

from spinalcordtoolbox.

jcohenadad commented on September 26, 2024

When tweaking params, eg; adding multi-step shrink factors (4, 2, 1), I do see a difference in the src/src_reg, so maybe the original issue is simply data-related (ie: no convergence, and hence registration matrix is identity).

from spinalcordtoolbox.

Does `-param deformation` have an impact when used with `algo=rigid`? about spinalcordtoolbox HOT 2 CLOSED

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	# ANTS 3d
	elif step.algo.lower() in ants_registration_params and step.slicewise == '0': # FIXME [AJ]
	warp_forward_out, warp_inverse_out = algorithms.register_step_ants_registration(
	src=src,
	dest=dest,
	step=step,
	masking=masking,
	ants_registration_params=ants_registration_params,
	padding=param.padding,
	metricSize=metricSize,
	verbose=param.verbose,
	)

	# ANTS 2d
	elif step.algo.lower() in ants_registration_params and step.slicewise == '1': # FIXME [AJ]
	warp_forward_out, warp_inverse_out = algorithms.register_step_slicewise_ants(
	src=src,
	dest=dest,
	step=step,
	ants_registration_params=ants_registration_params,
	fname_mask=fname_mask,
	remove_temp_files=param.remove_temp_files,
	verbose=param.verbose,
	)