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Hello Freesurfers, I recently analyzed about 600 subjects from HCP database using the Freesurfer recon-all algorithm. However, I noticed that in almost one third of the subjects, the software did not perform the skull stripping correctly when I checked the results in Freeview. To address this issue, I repeated the skull stripping step for each subject using the code "recon-all -skullstrip -wsthresh 35 -clean-bm -s <subject name>". The skull stripping went well, and then I repeated the analysis using the code "recon-all -autorecon-pial -subjid <subject name>". When I compared the pre and post-correction stats folder, I noticed that some volumetric values had changed, especially in the specific areas related to the initial skull stripping error. However, my concern is that when I loaded the .pial and .aseg files into Freeview, there was no change compared to before the correction visually. Is this okay, or should I take additional steps? I would appreciate your help. Thank you,YunusBellow is an example. NumberS 1 and 2 are brain masks before and after correction. Numbers 2 and 3 are superimposed .aseg files before and after correction.
