Registration

Use --action=reg for linear/nonlinear registration, saving reusable mapping fields, and applying those mappings to images or tractography.

Examples

Register a subject to a template

Use two modalities for registration and save the mapping field:

dsi_studio --action=reg \
  --source=subject_qa.nii.gz,subject_iso.nii.gz \
  --to=template_qa.nii.gz,template_iso.nii.gz \
  --output_mapping=mapping_field.mz

Apply a saved mapping

Warp a subject-space image to template space:

dsi_studio --action=reg \
  --source=subject_qa.nii.gz \
  --mapping=mapping_field.mz

Unwarp a template-space image to subject space:

dsi_studio --action=reg \
  --to=template_qa.nii.gz \
  --mapping=mapping_field.mz

Apply a saved mapping to multiple subject-space files:

dsi_studio --action=reg \
  --source=*.nii.gz \
  --mapping=mapping_field.mz

Register and transform additional files

Transform additional files from subject to template space:

dsi_studio --action=reg \
  --source=subject_qa.nii.gz \
  --to=template_qa.nii.gz \
  --s2t=additional_image1.nii.gz,additional_image2.nii.gz

Transform additional files from template to subject space:

dsi_studio --action=reg \
  --source=subject_qa.nii.gz \
  --to=template_qa.nii.gz \
  --t2s=additional_image1.nii.gz,additional_image2.nii.gz

Registration Parameters

Parameter	Description
--source	Subject/source image or images. Multiple modalities can be comma-separated. With --mapping, source files are transformed source-to-target.
--to	Template/target image or images. Multiple modalities can be comma-separated. With --mapping, target files are transformed target-to-source.
--output_mapping	Save the computed mapping field. Mapping files use .mz unless a supported mapping-image output is explicitly requested.
--mapping	Reuse a previously computed mapping field.
--s2t	Additional comma-separated files to transform from subject to template space while computing the registration.
--t2s	Additional comma-separated files to transform from template to subject space while computing the registration.
--output	Optional output directory for transformed files.

Current registration mapping can be applied to NIFTI images, TT tractography, and compatible DSI Studio SRC/FIB files (.sz, .src.gz, .fz, .fib.gz) when their source space matches the mapping.

Advanced Parameters

Parameter	Default	Description
--reg_type	1	Linear registration: 0 = rigid body; 1 = affine. The affine workflow proceeds to nonlinear registration unless --skip_nonlinear=1 is used.
--cost_function	depends on reg_type	Linear-registration cost. Mutual information is used for the rigid-body default and correlation for the affine default.
--match_vs	1	Match source and target resolution before registration.
--resolution	registration default	Relative resolution/downsampling used for nonlinear registration.
--speed	registration default	Nonlinear deformation speed.
--smoothing	registration default	Mapping-field smoothing.
--min_dimension	registration default	Minimum dimension used by nonlinear registration.
--large_deform	0	Use larger linear-registration search bounds when set to 1.
--skip_linear	0	Skip linear registration.
--skip_nonlinear	0	Skip nonlinear registration.
--overwrite	0	Overwrite existing outputs when set to 1.

Label images are resampled using label-preserving interpolation, while scalar images use continuous interpolation. Always confirm that the files being transformed belong to the source or target space expected by the mapping.