🐛 Skull stripping or brain extraction with fsl BET does not properly remove the neck regions in some subjects.

[tergeorge]

Describe the bug

When fsl BET is used for skull stripping or brain extraction, the neck regions from the anatomical image does not get removed for some subjects.
As you can see in this example, the final output of fsl BET(red) includes the brain and the neck regions.

In order correct for this issue, we need to use fsl robustfov(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/InitialProcessing) before using BET.
For example, using robustfov in the case above, we get the following output image without the neck regions.

To reproduce

Only happens for some subjects. To reproduce this issue use fsl BET for brain extraction. The brain mask generated will also contain the neck regions in addition to the brain.

Preconfig

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

Custom pipeline configuration

No response

Run command

No response

Expected behavior

The output of fsl BET should only include the brain without other regions of the head (neck, skull).

Acceptance criteria

fsl BET should extract only the brain and should be able to remove all the other additional regions of the head such as the skull and the neck for all subjects.

Screenshots

No response

C-PAC version

No response

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response

[sgiavasis]

Next item:

• Enabling this as an option in the pipe config.

[tergeorge]

fsl robustfov is enabled as an option in pipeline config.

Tested the output of fsl BET after fsl robustfov is applied to it on CPAC using a problematic data set that did not perform skull stripping with fsl BET alone.

The images below show the results of BET applied after fsl robustfov is applied to it.