Papermill Slurm Job Submission#
Author: Steffen Bollmann
Date: 22 June 2025
License:
Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.
Citation and Resources:#
Tools included in this workflow#
FSL
Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012). FSL. NeuroImage, 62(2), 782–790. https://doi.org/10.1016/j.neuroimage.2011.09.015
Dataset#
MP2RAGE T1-weighted average 7T model (human brain model)
Bollmann, Steffen, Andrew Janke, Lars Marstaller, David Reutens, Kieran O’Brien, and Markus Barth. “MP2RAGE T1-weighted average 7T model” January 1, 2017. doi:10.14264/uql.2017.266
Load software tools#
#load FSL 6.0.4
import module
await module.load('fsl/6.0.4')
await module.list()
['fsl/6.0.4']
Data preparation#
![ -f ./mp2rage-01.nii ] && echo "$FILE exist." || wget https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii -O ./mp2rage-01.nii
![ -f ./mp2rage-02.nii ] && echo "$FILE exist." || cp ./mp2rage-01.nii ./mp2rage-02.nii
--2026-02-28 05:29:19-- https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii
Resolving imaging.org.au (imaging.org.au)... 203.101.229.7
Connecting to imaging.org.au (imaging.org.au)|203.101.229.7|:443...
connected.
HTTP request sent, awaiting response... 200 OK
Length: 1536000352 (1.4G) [application/octet-stream]
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2026-02-28 05:29:39 (325 MB/s) - ‘./mp2rage-01.nii’ saved [1536000352/1536000352]
Analysis#
#This cell needs to be tagged as "parameters" and it will be replaced at runtime - this can be done by clicking the little cog-wheels in the top right and then tagging the cell
subject_id='01'
!bet mp2rage-{subject_id}.nii mask-sub-{subject_id}.nii -R
Running it on the HPC#
# Save Notebook and Run this on the terminal to test
# papermill papermill-slurm-submission-example.ipynb papermill_output.ipynb --parameters_raw subject_id 02
# create sbat file with the following content and make sure to replace account string and and execution times and modules loaded:
#then run the sbat file:
#sbatch papermill.sbat
Dependencies in Jupyter/Python#
Using the package watermark to document system environment and software versions used in this notebook
%load_ext watermark
%watermark
%watermark --iversions
Last updated: 2026-02-28T05:32:05.128210+00:00
Python implementation: CPython
Python version : 3.13.11
IPython version : 9.9.0
Compiler : GCC 14.3.0
OS : Linux
Release : 5.15.0-170-generic
Machine : x86_64
Processor : x86_64
CPU cores : 32
Architecture: 64bit