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Hello,

I am doing skull stripping with free surfer v6.0, and have tried various watershed cut-offs to do skull stripping on T2 scans. But, it removes a lot of brain portion.

Here are my commands:

mri_convert /Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz /Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz

recon-all -s patient_20_t2 -autorecon1 

## to be used only when increasing or decreasing threshold of skull stripping.
recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2

Is there any way that I can improve upon this and get better results if I am missing something?

Thanks,

Rohan

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