Trouble running ICA_AROMA; KeyError: 'FSLDIR'

1

Hello all,

I’m a bit perplexed trying to run ICA_AROMA. I’ve installed the python and fsl dependencies, but when I run my command:

sudo python2.7 ICA_AROMA.py -feat /mnt/c/Users/Ben/Desktop/test_asl_pipeline/003/analysis.feat/ -out /mnt/c/Users/Ben/Desktop/test_asl_pipeline/003/analysis.feat/ICA_AROMA/ -overwrite

I am getting an error:

Traceback (most recent call last):
File “ICA_AROMA.py”, line 145, in
fslDir = os.path.join(os.environ[“FSLDIR”], ‘bin’, ‘’)
File “/usr/lib/python2.7/UserDict.py”, line 40, in getitem
raise KeyError(key)
KeyError: ‘FSLDIR’

I assumed that my environment was set up incorrectly, but $FSLDIR gives me /usr/share/fsl/5.0/bin.

If I go into python2.7 and try:

import os
fslDir = os.path.join(os.environ[“FSLDIR”], ‘bin’, ‘’)
print(fslDir)

I get

/usr/share/fsl/5.0/bin/

Do you have any ideas about what is causing the error?

2

I’d say your user and root have different environments (i.e. FSLDIR is not defined for root).

Please remove that sudo from the python call.

1 Like
3

Yes, exactly. Thank you so much.