1. FreeSurfer does not fully segment the hippocampus on the surface. 2. I probably wouldn’t look at this in this way. In general, one wants the brain to be roughly aligned well without major obvious deformations. If you want an example of too much distortion, try ANTs. 3. The parcellation is available here https://balsa.wustl.edu/file/show/3VLx and you can use wb_command -cifti-parcellate across rows and columns of a dense connectome that has been tracked to the surface. As far as generating such a dense connectome with FSL, I think there might be some scripts floating around in the GitHub. I would have a look at the diffusion lectures and see what they suggest.
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: Wednesday, February 13, 2019 at 12:27 AM 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 data quality check Dear HCP experts, I have some questions about data quality check when using the HCP pipeline. 1. In the panel on the lower left corner on page 23 of the data quality slides (https://wustl.app.box.com/s/krekn5svmg4rgig2ossqqhuhcbrgg8c6), is the brain segmentation there missing some parts of the temporal lobe? 2. On page 25 of the slides, what's the criteria of determine "good" or "bad" volume distortion? Fewer number of above-threshold blobs the better? I also have a question about structural connectome of the HCP diffusion data. Is there any shared script to generate parcel to parcel structural connectivity using Dr. Glasser's multi-modal parcellation scheme? 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
