Nipype can't find FSL executable file

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1

Hello, I’m using FSL with nipype and it is unable to find the executable file ‘feat_model’ from fsl, even though it’s definitely in my fsl installation - any suggestions? I must be missing a simple command to help nipype find it…

Code:

import pandas as pd
import glob
from nipype.interfaces.base import Bunch
import nipype.interfaces.fsl as fsl  
import nipype.pipeline.engine as pe 
import nipype.algorithms.modelgen as model  
import os  

data_path = '/path/to/my/processed/data/'; 
os.chdir(data_path)

fsl.FSLCommand.set_default_output_type('NIFTI_GZ')

#Set up model fitting workflow
modelfit = pe.Workflow(name='modelfit')

# Use nipype.algorithms.modelgen.SpecifyModel to generate design information
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec",output_names="session_info")
modelspec.inputs.input_units = 'secs'
modelspec.inputs.functional_runs = ['/Users/mycomputer/anaconda3/pkgs/nibabel-3.0.0-py_0/site-packages/nibabel/tests/data/functional.nii']
modelspec.inputs.high_pass_filter_cutoff = 0
modelspec.inputs.time_repetition = 0
modelspec.inputs.subject_info = my_subject_info

#Use nipype.interfaces.fsl.Level1Design to generate a run specific fsf file for analysis
level1design = pe.Node(interface=fsl.Level1Design(),
    name="level1design",
    input_names=['session_info'])
level1design.inputs.interscan_interval = 0 
level1design.inputs.bases = {'dgamma':{'derivs': True}} 
level1design.inputs.model_serial_correlations=bool(False) 

# Use nipype.interfaces.fsl.FEATModel to generate a run specific mat file for use by FILMGLS
modelgen = pe.MapNode(
    interface=fsl.FEATModel(),
    name='modelgen',
    iterfield=['fsf_file', 'ev_files'])

# Use nipype.interfaces.fsl.FILMGLS to estimate a model specified by a mat file and a functional run
modelestimate = pe.MapNode(
    interface=fsl.FILMGLS(smooth_autocorr=True, mask_size=5, threshold=1000),
    name='modelestimate',
    iterfield=['design_file', 'in_file'])

### COMBINE NODES & RUN
modelfit.connect([
    (modelspec, level1design, [('session_info', 'session_info')]),
    (level1design, modelgen, [('fsf_files', 'fsf_file'), ('ev_files','ev_files')]),
    (modelgen, modelestimate, [('design_file', 'design_file')])
])

try:
    mdl = modelfit.run()
except(RuntimeError) as err:
    print("RuntimeError:", err)
else:
    raise
2

From the same shell you’re running your code, can you run feat_model?

3

Hi thank for your response! I can run feat_model from the command line, but when I try to access it via nipype by using the fsl.FEATModel() command in a node it can’t find the executable file.

4

How are you running nipype?

5

I’m running the python script in Spyder and importing the nipype packages as above

6

It is likely that your PATH inside Spyder doesn’t match your PATH in your shell.

7

I can’t seem to align them - I’ve tried adding all the fsl and nipype folders to the path in spyder, changing my working directory to where the fsl files are stored, etc. Any suggestions how I might make the feat_model command usable in nipype?

8

Try running it from the shell, not Spyder? I don’t know what’s required to make Spyder work. You could also try running Spyder from the shell, to ensure the environment variables propagate.

9

Thanks for your help @effigies - as an update, it was indeed an issue with my spyder path. To fix this I open spyder by navigating in terminal to the file where my fsl files are stored (for me, /usr/local/fsl) and open the IDE from there.