Dear Saad,
Thanks a lot for the help. I will now normalize my data first, using the following one-liner:
fslmaths 001/001.probtrackX_accumbens/fdt_paths -div `cat 001/001.probtrackX_accumbens/waytotal` 001/001.probtrackX_accumbens/fdt_paths_norm
However, I do not know yet how to run the tracking in standard space. I am currently using the parameters indicated below and this produces an fdt_paths image in standard space, but if I understand it correctly, the analysis itself was run in diffusion space.
probtrackx --mode=seedmask -x /ROIs/L+R_Caudate.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --xfm=/TODO.bedpostX/xfms/standard2diff.mat --forcedir --opd -s /TODO.bedpostX/merged -m /TODO.bedpostX/nodif_brain_mask --dir=/TODO/TODO.probtrackX_std_caudate
Any idea what parameters to use to run the probtrackx in standard space?
Thanks in advance.
Best, Henk
|