Dear FSL experts,
I'm trying to start using probtrackx2 with surfaces in order to have a more precise tractography but I'm failing to use FIRST surfaces to compute the registration.
I have read and compare the difference help websites but I cannot manage to get any result (but I can do it using freesurfer surfaces).
I will be glad if someone could give me some advice to do it.
Here are my steps:
1) DTI preprocessing to compute bedpostx folder in dti native space
2) apply FIRST on native t1w image
run_first_all -i t1w -o first
3) Rigid transformation between t1 and dti
first -in fa -ref t1w -omat dti2t1.mat
convert_xfm -omat t12dti.mat -inverse dti2t1.mat
4) Probtrackx2
probtrackx2 -s bedpostX/merged --seed=Subject-L_Puta_first.vtk --meshspace=first --seedref=t1 --xfm t12dti.mat -m dtimask [other opts] -V 1
The output is similar to this
Load bedpostx samples
1_1
1_2
1_3
2_1
2_2
2_3
nfibres : 2
nsamples : 50
Done loading samples.
Surface seeds
surface 0
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
run
2.122e-314 3.7168e-316 3.71704e-316
It seeems it always uses the same point and the fdt_paths is empty. The registration matrix is correct.
Someone could help me please?
Thank you very much
Daniel
|