ENH: Allow running SyN SDC without using prior

[mgxd]

This PR makes the use of a prior during SyN SDC optional, since distortions may differ depending on population. Eventually, it would be nice to add a range of priors, either within SDCFlows directly or easily plugged in from other tools.

Relevant to nipreps/nibabies#393

[codecov]

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Project coverage is 83.87%. Comparing base (5a55a81) to head (d2de7ba).
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[effigies]

Could you show a command.txt from a syn_sdc_wf.syn node?

[mgxd]

Sure, here's from a current dev run in nibabies

antsRegistration --collapse-output-transforms 1 \
--dimensionality 3 --initialize-transforms-per-stage 0 \
--interpolation Linear --output fmap_syn \
--transform SyN[ 0.8, 6.0, 3.0 ] \
--metric Mattes[ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/syn_preprocessing_auto_00001/anat2epi/clipped_noise_corrected_trans.nii.gz, /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/clip_epi/clipped.nii.gz, 0.5, 48, Random, 0.8 ] \
--metric Mattes[ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/lap_anat_norm/clipped_noise_corrected_trans_maths_norm.nii.gz, /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/lap_epi_norm/clipped_maths_norm.nii.gz, 0.5, 48, Random, 0.8 ] \
--convergence [ 200x100, 1e-06, 5 ] --smoothing-sigmas 2.0x0.0vox --shrink-factors 1x1 \
--use-histogram-matching 1 --restrict-deformation 0.1x1.0x0.1 \
--masks [ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/syn_preprocessing_auto_00001/mask2epi/sub-X_ses-V02_space-T2w_desc-brain_mask_trans_uint8.nii.gz, /scratch/nibabies_25_0_wf/single_subject_X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/epi_umask/clipped_mask_union.nii.gz ] \
--transform SyN[ 0.8, 2.0, 1.0 ] \
--metric Mattes[ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/syn_preprocessing_auto_00001/anat2epi/clipped_noise_corrected_trans.nii.gz, /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/clip_epi/clipped.nii.gz, 0.5, 48 ] \
--metric Mattes[ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/lap_anat_norm/clipped_noise_corrected_trans_maths_norm.nii.gz, /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/lap_epi_norm/clipped_maths_norm.nii.gz, 0.5, 48 ] \
--convergence [ 10, 1e-08, 2 ] \
--smoothing-sigmas 0.0vox --shrink-factors 1 --use-histogram-matching 1 --restrict-deformation 0.1x1.0x0.1 \
--masks [ /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/syn_preprocessing_auto_00001/mask2epi/sub-X_ses-V02_space-T2w_desc-brain_mask_trans_uint8.nii.gz, /scratch/nibabies_25_0_wf/single_subject_sub-X_ses-V02_wf/fmap_preproc_wf/wf_auto_00001/epi_umask/clipped_mask_union.nii.gz ] \
--winsorize-image-intensities [ 0.001, 0.998 ]  --write-composite-transform 0

[effigies]

Okay. Cross-referencing #291, it looks like the third mask is never used in any case because we only have two registration stages.

From antsRegistraion --help:

 -x, --masks [fixedImageMask,movingImageMask]
      Image masks to limit voxels considered by the metric. Two options are allowed 
      for mask specification: 1) Either the user specifies a single mask to be used 
      for all stages or 2) the user specifies a mask for each stage. With the latter 
      one can select to which stages masks are applied by supplying valid file names. 
      If the file does not exist, a mask will not be used for that stage. Note that we 
      handle the fixed and moving masks separately to enforce this constraint. 

Given that we're not using the prior at all, does it make sense to remove it altogether and then we can consider re-adding it in a concerted PR?

I think we can leave the inputspec the same, for backwards compatibility, just don't ever hook up sd_prior.

[mgxd]

@effigies is d2de7ba what you meant?

[effigies]

Yeah, I think this looks good. syn-sdc is a mess and I really am not looking forward to figuring out how to get the prior working again.