I am running my first FBA in 69 human subjects. So far I could create a template and have segmented FOD images to extract fixels (using the new directory format, not the old .msf). However, I couldn’t find the fixelthreshold script in the installation directory. Has this function been transfered to other scripts in the new MRtrix version?
Sorry we’ve not been able to get round to answering you in the last couple of weeks…
Yes, that command is no longer there. Since the new fixel format now relies on storing fixel-wise data using regular images, you can now invoke any command on them as you would for regular images – and that includes
mrcalc. So can now threshold your fixel data using a simple
mrthreshold -abs invocation.