NEW: Add support for FSL version 6.0.6 onwards

[ghisvail]

My initial attempts at building a container image for FSL (which lead to #523) failed, as the FSL installer gets stuck to 0% during stage 2 according to the logs. I gave up and decided to spend my efforts contributing a working image for 6.0.6+ instead.

Closes #524

[djarecka]

I will wait for @kaczmarj review of this, but can I ask you to also update the user_guide to provide an updated list of available versions (search --fsl).

[codecov[bot]]

Codecov Report

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[ghisvail]

To test:

cd neurdocker
pipx install --force .
neurodocker generate docker -p apt -b ubuntu:latest --fsl version=6.0.6.4 > fsl-6.0.6.4.Dockerfile
podman build --tag fsl:6.0.6.4 --file fsl-6.0.6.4.Dockerfile

After a very long installation process, this is the log you should be getting:

Installing FSL ...
FSL installer version: 3.5.0
Press CTRL+C at any time to cancel installation
Running the installer script as root user is discouraged! You should run this script as a regular user - you will be asked for your administrator password if required.
Installation log file: /tmp/fslinstaller_suvwhm5s.log

FSL 6.0.6.4 selected for installation
Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.6.4_linux-64.yml...

Installing FSL in /opt/fsl-6.0.6.4

Downloading miniconda from https://github.com/conda-forge/miniforge/releases/download/22.11.1-4/Mambaforge-22.11.1-4-Linux-x86_64.sh...
[#############################################################] 85.0 / 85.0 MB |
Installing miniconda at /opt/fsl-6.0.6.4...
[################################################################] 100 / 100 % |
Installing FSL into /opt/fsl-6.0.6.4...
[################################################################] 100 / 100 % |

FSL successfully installed

$ podman run -it --rm fsl:6.0.6.4 bet -h

Usage:    bet <input> <output> [options]

Main bet2 options:
  -o          generate brain surface outline overlaid onto original image
  -m          generate binary brain mask
  -s          generate approximate skull image
  -n          don't generate segmented brain image output
  -f <f>      fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
  -g <g>      vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
  -r <r>      head radius (mm not voxels); initial surface sphere is set to half of this
  -c <x y z>  centre-of-gravity (voxels not mm) of initial mesh surface.
  -t          apply thresholding to segmented brain image and mask
  -e          generates brain surface as mesh in .vtk format

Variations on default bet2 functionality (mutually exclusive options):
  (default)   just run bet2
  -R          robust brain centre estimation (iterates BET several times)
  -S          eye & optic nerve cleanup (can be useful in SIENA - disables -o option)
  -B          bias field & neck cleanup (can be useful in SIENA)
  -Z          improve BET if FOV is very small in Z (by temporarily padding end slices)
  -F          apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly)
  -A          run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)
  -A2 <T2>    as with -A, when also feeding in non-brain-extracted T2 (includes registrations)

Miscellaneous options:
  -v          verbose (switch on diagnostic messages)
  -h          display this help, then exits
  -d          debug (don't delete temporary intermediate images)

[ghisvail]

I was able to run the defacing pipeline in pydra-deface using Pydra tasks calling FSL via this container image.

[kaczmarj]

this looks great to me, thanks @ghisvail !