Thanks for answering my question. I realized I am getting different results when I run the same data on different spaces. Because I do not have enough space on my laptop I have to use the external hard drive. For example, When I follow the initial steps to make the whole brain tractography image (image stored on my hard drive), in the 3rd step which is performing “Constrained Spherical Deconvolution (CSD)”, I get the wrong result, but when I transfer those images on my laptop and run the same commands, I get correct results.
The same problem sometimes happens with the “response function estimation” file as well.
The other problem is when I make the mask and check it, it is alright. But when I run the dwi2fod command, it says the mask is empty, then I check the mask and it is empty. It seems like it disappeared after running the second command. It is strange.
These are the commands I run:
dwi2mask dti.mif mask.mif
mrview dti.mif -roi.load mask.mif
dwi2response tournier dti.mif -mask mask.mif response.txt
dwi2fod csd dti.mif response.txt fod.mif -mask mask.mif
I would appreciate it if you solve this mystery.