Fsl interface not working in conda environment

Software Support
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1

I have to run a python script involving nipype workflow for ICA. But FSL interfaces are not working in conda environments even when fsl is installed on host . Can anyone help me out with this? I have attached the output of running some dummy script using FSL SUSAN for reference.

Screenshot (84)
Screenshot (84)977×615 68.2 KB

2

Hi @Satwick and welcome to neurostars!

Try setting the FSLDIR environment variable in your script.

import os
os.environ['FSLDIR'] = '/path/to/fsldir' # replace with your own installation

Best,
Steven

3

Thanks for the help ,Steven. All I needed to do was explicitly add the PATH using os.environ after adding the FSLDIR , and it worked fine after that.
Regards,
Satwick

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