It looks like you are running a T2 through recon-all, which won't work. recon-all only takes T1-weighted. You can run it through samseg, eg, samseg --i T2_age_reg_bias.nii.gz --o samseg You can then binarize the seg.mgz to get everything inside the skull
On 4/7/2021 2:17 PM, Rohan Bareja wrote:
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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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