Instructions for streamlines registration/transformation

scil_tractogram_register.py MOVING_FILE STATIC_FILE

The file outputted by this script is a 4x4 matrix (see the help for the option)

Linear transformation

If you want to apply a transformation coming from the previous script

scil_tractogram_apply_transform.py MOVING_FILE REFERENCE_FILE TRANSFORMATION OUTPUT_NAME

Due to a difference in convention between image and tractogram the following script must be called using the –inverse flag if the transformation was obtained using AntsRegistration

scil_tractogram_apply_transform.py MOVING_FILE REFERENCE_FILE  0GenericAffine.mat OUTPUT_NAME --inverse

Non-linear deformation

To apply a non-linear transformation from ANTS

scil_tractogram_apply_transform.py MOVING_FILE REFERENCE_FILE  0GenericAffine.mat OUTPUT_NAME --inverse --in_deformation DEFORMATION_FILE

• The DEFORMATION_FILE needs to be the InverseWarp.nii.gz (very important)

• The OUTPUT_NAME is the output tractogram

Complete example

antsRegistrationSyNQuick.sh -d 3 -f mni_masked.nii.gz -m 100307__fa.nii.gz -t s -o to_mni
scil_tractogram_apply_transform.py 100307__tracking.trk mni_masked.nii.gz to_mni0GenericAffine.mat 100307__tracking_linear.trk --inverse
scil_tractogram_apply_transform.py 100307__tracking.trk mni_masked.nii.gz to_mni0GenericAffine.mat 100307__tracking_nonlinear.trk --inverse --in_deformation to_mni1InverseWarp.nii.gz

Apply back and forth tractogram transformation with the ANTS transformation

# The ANTS commands is MOVING->REFERENCE
antsRegistrationSyNQuick.sh -d 3 -f ${REFERENCE_NII.GZ_REF-SPACE} -m ${MOVING_NII.GZ_MOV-SPACE} -t s -o to_reference_

# This will bring a tractogram from MOVING->REFERENCE
scil_tractogram_apply_transform.py ${MOVING_FILE_MOV-SPACE} ${REFERENCE_FILE_REF-SPACE}
                                   to_reference_0GenericAffine.mat ${OUTPUT_NAME}
                                   --inverse
                                   --in_deformation to_reference_1InverseWarp.nii.gz

# This will bring a tractogram from REFERENCE->MOVING
scil_tractogram_apply_transform.py ${MOVING_FILE_REF-SPACE} ${REFERENCE_FILE_MOV-SPACE}
                                   to_reference_0GenericAffine.mat ${OUTPUT_NAME}
                                   --in_deformation to_reference_1Warp.nii.gz
                                   --reverse_operation