Hi all,
what is the best way to register the segmentation of a tract from the JHU White-Matter Tractography Atlas (e.g. CST) to a new subject (e.g. a HCP subject)? It has to work on the command line so it can be used in a script. This would be my guess, but not sure if it is the best/right way to do it:
flirt -ref ${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz -in my_FA -omat my_affine_transf.mat
fnirt -ref ${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz --in=my_FA --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=myconfig.cnf
applywarp --ref=${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz --in=${FSLDIR}/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz --warp=my_nonlinear_transf --out=warped_tracts
------- Myconfig.cnf -------
--subsamp=8,4,2,2 # sub-sampling scheme, default 4,2,1,1
--infwhm=12,6,2,2 # FWHM (in mm) of gaussian smoothing kernel for input volume, default 6,4,2,2
--reffwhm=12,6,2,2 # FWHM (in mm) of gaussian smoothing kernel for ref volume, default 4,2,0,0
--lambda=300,75,30,30 # Weigth of membrane energy regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
--estint=1,1,1,0 # Estimate intensity-mapping if set, deafult 1 (true)
--intmod=global_linear # Model for intensity-mapping [none global_linear global_non_linear local_linear global_non_linear_with_bias local_non_linear]
Thanks
Jakob
