FSL & Nipype IOError

[CL]

Hello,

I recently installed nipype in a neurodebian virtual box. I believe I have correctly altered the necessary environmental variables in .bashrc for FSL to include-

FSLDIR=/usr/share/fsl/5.0
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

I am able to run BET, SUSAN ect through terminal, however when I try to run the same commands through nipype in ipython or spyder, I receive the error-

/usr/lib/pymodules/python2.7/nipype/interfaces/fsl/base.py:116: UserWarning: FSL environment variables not set. setting output type to NIFTI
  warnings.warn(('FSL environment variables not set. setting output '
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 540, in runfile
    execfile(filename, namespace)
  File "/home/brain/.spyder2/.temp.py", line 10, in <module>
    myBet.run()
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 946, in run
    runtime = self._run_interface(runtime)
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/fsl/preprocess.py", line 142, in _run_interface
    runtime = super(BET, self)._run_interface(runtime)
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 1376, in _run_interface
    (self.cmd.split()[0], runtime.hostname))
IOError: bet could not be found on host neurodebian
Interface BET failed to run.

The code that produced this error was

import nipype.interfaces.fsl as fsl



inPath = '/home/brain/Desktop/T1.nii.gz'
outPath='/home/brain/Desktop/T1bet.nii.gz'


myBet = fsl.BET()
myBet.inputs.in_file = inPath
myBet.inputs.out_file = outPath


myBet.run()

What could cause this? Could it be something specific to neurodebian? Any help would be greatly appreciated.

Thank you!

[Satrajit Ghosh]

hi,

if outside of python you type 'bet' in the command line it should display it's help. 

perhaps you didn't source the bashrc after modification?

cheers,

satra

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[CL]

bashrc has been sourced, I can cd into $FSLDIR. I don't believe the issue is specifically with bet, any FSL tool (I've also tried SUSAN) will give the same error.

[Satrajit Ghosh]

hi,

if you type bet into the command line, does it actually return help. so here is the sequence you should try in the same terminal (script.py is the code you have):

$ which bet #should return the path to bet

$ python script.py 

cheers,

satra

[CL]

Thank you for the assistance, I determined yesterday that iPython and Spyder were using a different shell profile than terminal, and as such did not have access to the environmental variables.