If you make a patch that you’d like to see incorporated into the HCP pipelines (i.e. FreeSurfer.sh for generation and in the PostFreeSurfer pipeline’s FreeSurfer2CaretConvertAndRegisterNonlinear.sh module for conversion to the HCP’s spaces and NIFTI/GIFTI/CIFTI), send us a pull request in GitHub. These would be at the parcel/label level, rather than becoming new CIFTI subcortical structures (e.g. the left thalamus is a CIFTI structure, but it can be parcellated in a CIFTI label file into thalamic nuclei).
Matt. From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Friday, February 8, 2019 at 11:51 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] FreeSurfer6 subcortical segmentation We are implementing the segmentHA_T1.sh and the segmentThalamicNuclei.sh scripts that are int he bin directory of FreeSurfer 6 (dev) We are currently working on generating these from the Freesurfer output of the HCP Pipelines and then transforming them into the subject MNI Surface Space. J ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, February 6, 2019 6:29:21 PM To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] FreeSurfer6 subcortical segmentation ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. I don’t see these being generated in our current test FreeSurfer 6.0 runs. How are they generated? Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, February 6, 2019 at 12:56 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] FreeSurfer6 subcortical segmentation Hey HCP community When Freesurfer 6.0 is implemented into the HCP Pipeline, are there plans to use the subcortical segmentation script outputs (amygdala and thalamus mgz files) into cifti space (column 3)? If so will they be an addition to the current ROI atlas or will they be separate? Thanks so much Juan _______________________________________________ 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
