Lab Tutorials

Neurocommand

3 min read

Neurocommand is a command-line interface to Neurodesk, which is designed to run on virtual machine or HPC.

To get NeuroCommand to work, you need to tell the bash shell system where to find the singularity folder and modules. For those set up users, the following codes are already in your .bashrc.

export PATH=~/bin:/usr/local/go/bin:${PATH}
source /etc/profile.d/lmod.sh
 
export SINGULARITY_BINDPATH='/cvmfs,/mnt,/home,/dss'
export SINGULARITYENV_TEMPLATEFLOW_HOME=/dss/.templateflow
module use /cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*

1 Command line and bash file usage

module load module_name
module list

For example, if you want to load module, you can use

module load fsl
module list

it shows

Currently Loaded Modules:
  1) fsl/6.0.7.16

module avail can show all modules available from the Neurocommand.

Scenario 1: Interactive Analysis

If you tunnel to the server with option -Y (i.e., ssh -Y account@lora), you should be able to send back fsl interface back to your local computer.

module load fsl
Feat &

It will show the ‘Feat’ interface locally.

Note

Tunnelling via SSH for the interface may be slow, particularly when you want to open the design matrix with multiple inputs. A better way to do this is via VNC interface, remotely running Feat or related software.

Scenario 2: Batch analysis using bash files

The following is an example of using the bet function from the fsl package in a bash file.

#!/bin/bash
module load fsl
# Set the main BIDS directory (modify if needed)
BIDS_DIR="/dss/open/ds000102"
# Loop through subject folders
for subj in ${BIDS_DIR}/sub-*; do
	subj_id=$(basename ${subj}) # Extract subject ID (e.g., sub-01)
	# Define input and output paths
	anat_dir="${subj}/anat"
	input_image="${anat_dir}/${subj_id}_T1w.nii.gz"
	output_image="${anat_dir}/${subj_id}_T1w_brain.nii.gz"
	# Check if input file exists
	if [ -f "${input_image}" ]; then
		echo "Running BET on ${input_image}..."
		bet "${input_image}" "${output_image}" -R -f 0.25 -g 0 # Adjust parameters as needed
	else
		echo "T1w image not found for ${subj_id}, skipping..."
	fi
done
 
echo "Brain extraction completed for all subjects."

2 Use in Python

Unfortunately, the Python environment cannot directly read the bash environment. So you need to set up the environment first in your Python. If you are using Jupyter Notebook, copy the following code to the beginning of your notebook:

import os
os.environ["SINGULARITY_BINDPATH"] = "/cvmfs,/mnt,/home,/home/lu32pog/dss"
os.environ["LMOD_CMD"] = "/usr/share/lmod/lmod/libexec/lmod"
os.environ["SINGULARITYENV_TEMPLATEFLOW_HOME"] = "/home/lu32pog/dss/.templateflow"
os.environ["MODULEPATH"] = "/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/*"

Then you can load modules via lmod

# need to load base (Python) from miniconda (all packages installed)
import lmod
#await lmod.purge(force=True)
await lmod.load('fsl')
await lmod.list()

3. Use with Google Colab

The official guidance is here

At the beginning of your notebook, you need to add:

import os
os.environ["LD_PRELOAD"] = "";
os.environ["APPTAINER_BINDPATH"] = "/content"
os.environ["MPLCONFIGDIR"] = "/content/matplotlib-mpldir"
os.environ["LMOD_CMD"] = "/usr/share/lmod/lmod/libexec/lmod"
 
!curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh
!chmod +x googlecolab_setup.sh
!./googlecolab_setup.sh
 
os.environ["MODULEPATH"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))

Then, you can use it:

import lmod
await lmod.avail()
 
await lmod.load('fsl/6.0.4')
!bet

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