generate and warp subject streamlines to template space

subject_tck_in_template_space.sh

#/bin/env bash

do_nonlinear_registration=false

tmp_dir=$(mktemp -d -t tcktransform-XXXXXXXXXX)
cd $tmp_dir

# ____ 0. get DWI data and create two ODFs ____
for sub in sub-02 sub-03; do
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_dwi.bval
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_dwi.bvec
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_brainmask.nii.gz
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_dwi.nii.gz

wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_tissue-WM_response.txt
done

for sub in sub-02 sub-03; do
tail -1 "${sub}"_tissue-WM_response.txt > rf.tmp
dwi2fod csd "${sub}"_dwi.nii.gz rf.tmp -fslgrad "${sub}"_dwi.bvec "${sub}"_dwi.bval -mask "${sub}"_brainmask.nii.gz "${sub}".mif -lmax 4
done

# ____ 1. create subject and template files ____
# in this example, sub-02.mif transformed by a rigid transformation is used as subject (source) image
# sub-03.mif smoothed is used as template (target) image

echo "0.8 0.1 0 -100
-0.1 1 0 20
0 0 1.2 4" > A.txt
transformcalc A.txt rigid R.txt

mrtransform sub-02.mif -linear R.txt -reorient no subject.mif -force
mrfilter sub-03.mif smooth -std 3 template.mif -force


# _____ 2. create template to subject warp ____

if ${do_nonlinear_registration}; then # _____ nonlinear registration version
	# co-register subject and template ____
	mrregister subject.mif template.mif -nl_warp_full warp_full.mif
	# create template to subject warp ____
	warpconvert warp_full.mif warpfull2deformation w_t2s.mif -from 2 -template subject.mif

else # _____ linear registration version
	# subject-to-template trafo
	mrregister subject.mif template.mif -type rigid -rigid rigid_s2t.txt
	# template-to-subject trafo
	transformcalc rigid_s2t.txt invert rigid_t2s.txt
	# make warp in subject-space
	warpinit template.mif w_i.mif
	transformcompose w_i.mif rigid_t2s.txt w_t2s.mif -template subject.mif
fi

# ____ 3. create subject tck and warp to template space ____
tckgen subject.mif subject.tck -seed_dynamic subject.mif -select 5k -cutoff 0.4
tcktransform subject.tck w_t2s.mif subject_at_template.tck

# ____ 4. create subject tck in template space ____
mrview template.mif -tractography.load subject_at_template.tck

echo "please delete content of $tmp_dir"