fsl: Command not found.
works and brings up a FSLviewer GUI, though it's the version of 4.0.1 (not 5.0).
I tried typing "fsl" then hit the TAB key, and it seems that there're a lot of available commands that need to be run as
It shows the help for the bet2 function (because I didn't run it with the correct arguments, I suppose):
Part of FSL (build 506)
BET (Brain Extraction Tool) v2.1 - FMRIB Analysis Group, Oxford
Usage:
bet2 <input_fileroot> <output_fileroot> [options]
Optional arguments (You may optionally specify one or more of):
-o,--outline generate brain surface outline overlaid onto original image
-m,--mask generate binary brain mask
-s,--skull generate approximate skull image
-n,--nooutput don't generate segmented brain image output
-f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
-g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
-r,--radius=<r> head radius (mm not voxels); initial surface sphere is set to half of this
-w,--smooth=<r> smoothness factor; default=1; values smaller than 1 produce more detailed brain surface, values larger than one produce smoother, less detailed surface
-c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
-t,--threshold -apply thresholding to segmented brain image and mask
-e,--mesh generates brain surface as mesh in vtk format
-v,--verbose switch on diagnostic messages
-h,--help displays this help, then exits
All these make me think that there's something wrong with my FSL installation. Should I uninstall it and reinstall it again? Any advice on this?