Hi,
I’m trying to generate a track file unsing the command
tckgen FOD_2.nii CSD_${track_string}.tck -seed_image ${outputin[0]} -mask mask.nii -angle 40 -number 500000 -maxlength 100 -unidirectional -force
but it generates 0 fibers written
I suppose that the problem is in an problem on the registration.
I register the dti subject’s file.nii on a template.nii,
using the command
antsIntroduction.sh -d 3 -r $mni_file -i $b0_file -o ${OUTPUTNAME}
but I noted that the subject’s file.nii results not aligned with the the template file.
So I insert the transformation option in the command:
antsIntroduction.sh -d 3 -r $mni_file -i $b0_file -o ${OUTPUTNAME} -t DD
I tried differents options (DD, GR, SY, S2, EL) but the problem persist.
Do you have some ideas?
Thank you