How did YOU call the FreeSurfer Pipeline in your subject with an issue? Matt.
From: Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Tuesday, April 9, 2019 at 8:42 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Some questions about the HCP structural processing pipeline Hi Matt, I called the FreeSurfer pipeline using the script "FreeSurferPipelineBatch.sh" in the "Examples" folder. Do you mean that these brain extracted T1w and T2w images "T1w_acpc_dc_restore_brain.nii.gz" and "T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the FreeSurfer pipeline? Thank you. Aaron ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Monday, April 8, 2019 10:50 PM To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Some questions about the HCP structural processing pipeline The brain masked file should not be used for surface estimation. How are you calling the FreeSurfer pipeline? Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Monday, April 8, 2019 at 9:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Some questions about the HCP structural processing pipeline 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
