Open tergeorge opened 1 year ago
Next item:
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.
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.![image](https://user-images.githubusercontent.com/88160056/232609288-adb17015-f4d1-404f-898a-2f0640298aa2.png)
In order correct for this issue, we need to use fsl![image](https://user-images.githubusercontent.com/88160056/232611657-a0cb5cbb-cbba-4967-a098-c7fb2d41038a.png)
robustfov
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/InitialProcessing) before usingBET
. For example, usingrobustfov
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
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
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C-PAC version
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Container platform
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Docker and/or Singularity version(s)
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Additional context
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