Hi Emily,

I suspect the error you're getting is because you have the first line of 0 0 0 in your bvec file. 3dDWItoDT assumes that this line exists and you can just remove it (or use row selectors) and run the program again.

You can use 3dTcat to create a new dataset without the b0 volumes or to append that averaged b0 volume to the front or both at the same time using something like:

3dTcat -prefix subj01_dwi new_b0+orig.HEAD old_dwi+orig.HEAD[1..10,12..16,18..32]

I seem to recall that you can give 3dDWItoDT a DWI file with multiple b0's in it (i.e. not average them), though there are certainly arguments for why you may want to average the b0 volumes. Also if you use TORTOISE (new version 2.5 out), it will take care of the preprocessing and tensor fitting... at great cost of computer power!



Edited 1 time(s). Last edit at 12/16/2014 02:41PM by Peter Molfese.