use –action=reg to apply linear and/or nonlinear registration.


*Apply linear and nonlinear registration to register subject’s QA/ISO to template QA/ISO

dsi_studio --action=reg --from=subject_qa.nii.gz --from2=subject_iso.nii.gz --to=template_qa.nii.gz --to2=template_iso.nii.gz --output=subject_qa_in_template_space.nii.gz

*Warp the subject image to the template space

dsi_studio --action=reg --apply_warp=subject_qa.nii.gz --warp=warp_field.nii.gz

*Warp all nifti image and all tract files from the template space to the subject space

dsi_studio --action=reg --apply_warp=*.nii.gz,*.tt.gz --inv_warp=warp_field.nii.gz

Registration Functions

The function registers the subject/source image with the template/target image

Parameters Description
from specify the nifti file of the subject/source image.
the image can be smoothed by specifying –from=t1w.nii.gz+gaussian or –from=t1w.nii.gz+mean
from2 (optional) specify the nifti file of the second image modality of the subject/source image.
to specify the nifti file of the template/target image.
to2 (optional) specify the nifti file of the second image modality of the template/target image.
output (optional) specify the nifti file of the warped subject/source image.
output_warp (optional) specify the file to store the warping field (e.g., –
apply_warp specify the image (.nii.gz) or tracts (.tt.gz) to be warped or unwarped from the subject space to the template space. Use comma to specify multiple files.
Parameters Default Description
cost_function mi specify the cost function to linear registration.
mi: mutual information
cc: correlation coefficient
reg_type 1 specify whether nonlinear registration is needed. set it to 0 if only linear registration is needed
normalize_signal 1 specify whether pre-registration signal normalization is needed. The normalization scales the image value between 0 and 1
resolution 2 Specify the final resolution. The value can be 1,2,4,8. 2 means the nonlinear registration will be conducted at x2 down sampling.
speed 1 specify the convergence speed for nonlinear registration
smoothing 0.2 specify the mapping field smoothing for nonlinear registration. The value can be 0 (no smoothing) or 0.95 (more smoothing applied)
iterations 200 specify number of iterations applied to compute nonlinear registration
min_dimension 8 specify the minimum dimension to start the nonlinear registration.

Warping Functions

The function applies warping to the subject/source image, or applies inversed warping to the template/target image.

Parameters Description
warp or inv_warp specify the mapping data (.map.gz) to warp (use –warp=) or unwarp (–inv_warp=) the image
apply_warp specify the image (.nii.gz) or tracts (.tt.gz) to be warped or unwarped.