Hi! I’ve recently started up a Neurodebian virtual machine and the goal is to set up pipeline for post processeing of neuro data with help of nipype. My goal for the moment is just to get started with some example pipeline and learn the basic in how to use Nodes etc.
This example is what I’m doing right now: https://miykael.github.io/nipype_tutorial/notebooks/basic_nodes.html#Example-of-a-simple-node
When I’m running:
from nipype import Node
from nipype.interfaces.fsl import IsotropicSmooth
smooth_node = Node(IsotropicSmooth(), name=“smoothing”)
smooth_node.inputs.in_file = ‘/home/brain/Documents/BIDS_format/sub-01/anat/sub-01_T1w.nii.gz’
smooth_node.inputs.fwhm = 4
smooth_node.inputs.out_file = ‘/home/brain/Documents/out_test/node_T1w_smooth.nii.gz’
smooth_res = smooth_node.run()
I get following error: No command “fslmaths” found on host neurodebian. Please check that the corresponding package is installed.
I’ve google a lot and so far I’ve run “gedit ~/.bashrc” in the terminal and added:
export FSLDIR PATH
If I start a new terminal window and type “fsl”, fsl i starting so it’s at least working. Any suggestions?