Dear HCP experts, I have some questions about the HCP structural processing pipeline.
1. The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w folder has excessive voxels removed in the cortical surface, which resulted in erroneous pial surface estimation. Is there a way that I could adjust any parameters of brain extraction in the PreFreeSurfer.sh file to have a larger brain mask? 2. There is another file "brainmask_fs.nii.gz". Is this the same mask derived from "T1w_acpc_dc_restore_brain.nii.gz" and "T2w_acpc_dc_restore_brain.nii.gz"? 3. In the structural processing QC scene, is there a way that I could also display the boundary of the extracted brain alongside with pial and white surfaces in the coronal brain? Thank you. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
