5ttgen [ERROR] Could not find FSL program "bet";

seveni · February 29, 2024, 12:07pm

Hi everybody, when I use 5ttgen fsl input output method, during its processing it prints this error:

5ttgen:[ERROR] Could not find FSL program "bet"; please verify FSL install

I wonder what’s the reason, since I’ve used bet in the previous process, which was working fine at that time, so so I think my bet don’t have a problem. And I’ve reinstalled fsl, yet it still has this error. Moreover, I’ve also checked my environment setting, which is well set as well. So I really don’t know what happened.
My linux version is ubuntu 22 and my fsl version is 6.0.7.8
please help me, I really don’t know what to do

smeisler · March 2, 2024, 12:01am

Hi @seveni,

Is it possible you are running mrtrix in an environment where your $PATH might not include FSL?

You can see how mrtrix is looking for FSL using these codes:

github.com

MRtrix3/mrtrix3/blob/325dcc1244fc5de796ad52f29f78a834cd7d7736/lib/mrtrix3/fsl.py#L96


      
                return candidate
            app.debug('No CPU version of eddy found')
            return ''
          
          
          
          # In some FSL installations, all binaries get prepended with "fsl5.0-". This function
          #   makes it more convenient to locate these commands.
          # Note that if FSL 4 and 5 are installed side-by-side, the approach taken in this
          #   function will select the version 5 executable.
          def exe_name(name): #pylint: disable=unused-variable
            from mrtrix3 import app #pylint: disable=import-outside-toplevel
            if find_executable(name):
              output = name
            elif find_executable('fsl5.0-' + name):
              output = 'fsl5.0-' + name
              app.warn('Using FSL binary \"' + output + '\" rather than \"' + name + '\"; suggest checking FSL installation')
            else:
              raise MRtrixError('Could not find FSL program \"' + name + '\"; please verify FSL install')
            app.debug(output)
            return output

github.com

pypa/distutils/blob/main/distutils/spawn.py#L75


      
                  ) from exc
          
              if exitcode:
                  if not DEBUG:
                      cmd = cmd[0]
                  raise DistutilsExecError(
                      "command {!r} failed with exit code {}".format(cmd, exitcode)
                  )
          
          
          def find_executable(executable, path=None):
              """Tries to find 'executable' in the directories listed in 'path'.
          
              A string listing directories separated by 'os.pathsep'; defaults to
              os.environ['PATH'].  Returns the complete filename or None if not found.
              """
              _, ext = os.path.splitext(executable)
              if (sys.platform == 'win32') and (ext != '.exe'):
                  executable = executable + '.exe'
          
              if os.path.isfile(executable):

Best,
Steven