Hello Saad, I just tryed doing what you told Jose. I executed first the following command for adding all the seed masks:
fslmaths -dt double "mask1_path" -add "mask2_path" "resultImage_path"
that's fine.
I put the type of the images as double because when I open them in MATLAB it says that they are double type.
that is not necessary
Then, I executed the probtrackx command with the following options:
probtrackx --mode=seedmask -x "resultImage_path" -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s "bedpostDirectory+/merged" -m "nodif_brain_mask_path" --dir="output directory" --omatrix1
looks fine.
Well, it did created the files it should have created: the coords_for_fdt_matrix1, fdt_matrix1, fdt_paths and waytotal. But there is something strange, although it does find tracks because in the waytotal file it appears the number 1.5015e+07 when I open the fdt_paths there is nothing! The other images dimensions are correct. And when I open the images I can visualize something.
make sure you get the registration right between seed and diffusion space, and pass it on to probtrackx using --xfm option.
Other quesiton I have is, in your code when you write seeds = {'seed1','seed2',...}; 'seed1' and 'seed2' are the paths of the seed images or what?
these are just file names for sub-masks within your big seed. I.e. the mas1_path etc. in your case.
Cheers,
Saad.
Thanks,
--
Monica Giraldo
Master student in Biomedical Engineering
Universidad de Barcelona - Universidad Politécnica de Cataluña
