BET failed to run


When I’m trying to run the code down here.

import nipype.interfaces.fsl as fsl
myb.inputs.in_file = ‘/home/sunny/nipype_tutorial/data/sub001/struct.nii.gz’
myb.inputs.out_file = ‘/home/sunny/nipype_tutorial/output/sub001/struct_bet.nii.gz’

It cames an error like this:

Traceback (most recent call last):
File “/home/cynthia/PycharmProjects/FSL_installation/”, line 4, in
from nipype.interfaces.fsl import MCFLIRT, FLIRT
File “/home/cynthia/anaconda3/lib/python3.6/site-packages/nipype/interfaces/fsl/”, line 13, in
from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
File “/home/cynthia/anaconda3/lib/python3.6/site-packages/nipype/interfaces/fsl/”, line 661, in
class FILMGLS(FSLCommand):
File “/home/cynthia/anaconda3/lib/python3.6/site-packages/nipype/interfaces/fsl/”, line 694, in FILMGLS
if Info.version() and LooseVersion(Info.version()) > LooseVersion(‘5.0.6’):
File “/home/cynthia/anaconda3/lib/python3.6/site-packages/nipype/interfaces/fsl/”, line 77, in version
out = open(’%s/etc/fslversion’ % (basedir)).read()
FileNotFoundError: [Errno 2] No such file or directory: ‘/usr/share/fsl/etc/fslversion’

By the way, when I type fsl in the terminal, I can see the FSLGUI and I can do bet with the GUI successfully. And when I type bet in the terminal It cames like this:

sunny@cynthia-PC:~$ bet

Usage: bet [options]

Main bet2 options:
-o generate brain surface outline overlaid onto original image
-m generate binary brain mask
-s generate approximate skull image
-n don’t generate segmented brain image output
-f fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
-g vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
-r head radius (mm not voxels); initial surface sphere is set to half of this
-c centre-of-gravity (voxels not mm) of initial mesh surface.
-t apply thresholding to segmented brain image and mask
-e generates brain surface as mesh in .vtk format

Variations on default bet2 functionality (mutually exclusive options):
(default) just run bet2
-R robust brain centre estimation (iterates BET several times)
-S eye & optic nerve cleanup (can be useful in SIENA)
-B bias field & neck cleanup (can be useful in SIENA)
-Z improve BET if FOV is very small in Z (by temporarily padding end slices)
-F apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly)
-A run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)
-A2 as with -A, when also feeding in non-brain-extracted T2 (includes registrations)

Miscellaneous options:
-v verbose (switch on diagnostic messages)
-h display this help, then exits
-d debug (don’t delete temporary intermediate images)

Is there anyone who can tell me what I can do to fix this? I’m really confused with it.


Sorry, Don’t have anything to add, just connecting the conversation here with the one on github, so people know what’s already been tried.


I just tried installing nipype and fsl and it did gave me issues from pycharm.
Then I tried running the python code from terminal with the python with which I installed nipype, and it worked perfectly.
try running your code from a python script from terminal


Thank you very much! Actually it just was a Pycharm issue.And It runs well in spyder.