Fod2fixel script -crop option not a valid flag

Dear Experts,

I am running the last part of step 7 for the fixel analysis and I am running into an error with the -crop flag. It does not appear to be a valid flag, however, the directions on the utilize it to threshold the .msf file. Is there a new option to threshold the file at 0.2? Any help would be greatly appreciated. Is the -fmls_peak_value flag the same thing?



Hi James,
The -crop option is part of the fixelthreshold command. I’m guessing there must be an issue inside your script?

Thanks Dave. I definitely just misread the script. I appreciate the help.