NEW: Add support for FSL version 6.0.6 onwards #527
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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 |
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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.DockerfileAfter a very long installation process, this is the log you should be getting: $ 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) |
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I was able to run the defacing pipeline in pydra-deface using Pydra tasks calling FSL via this container image. |
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this looks great to me, thanks @ghisvail ! |
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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