There is no
fod2peak command that I’m aware of… Do you mean
sh2peaks, you can simply use the
-num 1 option to request the single largest peak. If you’ve already computed your peaks using
sh2peaks and want to extract the largest one, then:
$ mrconvert peaks.mif -coord 3 0,1,2 first_peak.mif`
will do the trick (just extract the first 3 volumes).
Other than that:
fod2peaks actually refers to
fod2fixel, then the output of that command is in fixel format, which is quite a different beast. You can convert back to a ‘regular’ image using the
fixel2voxel command. If you want the single largest direction, then I think the correct call would be something like
$ fixel2voxel fixel_folder/peaks.mik split_data first_peak.mif -number 1
No doubt @rsmith will correct me if I’ve got this wrong.
Yes, this is normal:
sh2peaks returns the actual peak of the FOD, while
fod2fixel will provide the mean orientation of the peak, integrated over its solid angle. The idea is that this might be more robust to subtle asymmetries and other potential oddities in the FOD.
Unfortunately not, sorry…