Dear mrtrix3 experts,
Hello, I have a question about dwiextract before doing dwipreproc. I have about 80 subjects, so I want to use foreach bash for time saving, but I dont know how to apply it for dwiextract.
I used bash for dwidenoise and degibbs, and ready to proceed to further steps : motion and distortion correction.
I am currently following the BATMAN tutorial using my own data.
I got some error note, and tried bunch of different things, but I cannot find the solution.
$ foreach gibbs/.mif : dwiextract IN gibbs/PRE.mif - -bzero | mrmath - mean mean_b0_AP.mif -axis 3
dwiextract: [ERROR] Expected exactly 2 arguments (3 supplied)
dwiextract: [ERROR] Usage: dwiextract input output
dwiextract: [ERROR] Yours: dwiextract gibbs/.mif gibbs/*.mif -
mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
mrmath: [ERROR] error opening image “-”