Miscellaneous tips

CUDA for FSL

Refer to this page for how to install and test CUDA 11 with FSL 6.0.6.X on Ubuntu 20.04/22.04. There are instructions on how to install other versions of cuda with other versions of FSL and Ubuntu here.

Katana on-demand

Katana on demand allows for requesting resources from webpage, and access the desktop graphic interface of your requested resource. It can be useful if there’s any issue with graphics via ssh login.

optiBET.sh error - [[: not found

[[ is a bash-builtin. Add #!/bin/bash at the top of optiBET.sh file, or call bash optiBET.sh.

Building singularity with image on Docker Hub

Reference 1 Reference 2

export SINGULARITY_CACHEDIR=/srv/scratch/cheba/Imaging/my_tmp
export APPTAINER_CACHEDIR=/srv/scratch/cheba/Imaging/my_tmp
TEMP=/srv/scratch/cheba/Imaging/my_tmp
TMPDIR=$TEMP
TMP=$TEMP
export TEMP TMP TMPDIR

singularity pull mriqc.sif docker://nipreps/mriqc

singularity run mriqc.sif --version    # check image version
singularity run --cleanenv -B $HOME:/home/aslprep --home /home/aslprep aslprep.simg --version  # for aslprep

# If building singularity image on Katana failed,
# try build on GRID and copy to Katana.