Dear Freesurfer Team,

I am attempting to complete a surface reconstruction on a dataset with traumatic lesions both to the grey and white matter.

I am hoping to get some opinions on what would be considered as the 'Best practice' pipeline for dealing with such a dataset. We have access to T1 and T2-FLAIR images for a moderately large dataset and thus require a pipeline as fully-automated as is possible whilst still relatively accurate. I have seaerched the mailing list archives but many just relate to white matter lesions in MS for example.

My current thoughts were to use the T1 and Fair images with the -FLAIRpial flag in recon-all to improve pial segmentation, but also using an automated lesion segmentation tool to conduct lesion filling. However, I know this is more effective for white than Gray matter lesions due to the greater intensity variability in the Gray matter compared to the white matter.

Any reccomendations would be greatly appreciated.

Cheers Dan