Hi Chester if you upload the dataset we will take a look
cheers Bruce On Fri, 4 Sep 2015, CHESTER DOLPH wrote:
Hello, I have one brain in a large dataset that is not skull stripping properly. I have tried the changing watershed parameters using the freesurfer tutorial, but brainmask.mgz does not seem to change and I am receiving this error: " The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas'" I tried gcut but it removed too much brain. I am aware that tkmedit enables manual editing but prefer to use the Brainsuite GUI. If I want to use primarily Freesurfer , may I augment brainmask.mgz using Brainsuite and then resume the recon pipeline? I am concerned that this would disrupt other files (e.g. brainmask.auto.mgz). Thanks, Chester the skull strip command that I explored (tried various wsthresh values): $ recon-all -subjid [removed] -skullstrip -wsthresh -20 -clean-bm -no-wsgcaatlas
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