Re: [HCP-Users] Projecting Label into White Matter

[Glasser, Matthew]

We recommend you run tractography directly from the surfaces using probtrackx2.  You can use these surfaces if you want your other volume (i.e. non-cortical) ROIs in native subject space: ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii Or these if you want them in MNI space: ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii We recommend you stop tracking at the pial surface to avoid crossing sulci and that you use waystop masks in the subcortical greymatter to avoid connections going to sub cortex and then looping back around to cortex (which creates false positives). Peace, Matt. From: John Plass <johncpl...@gmail.com> Date: Friday, February 13, 2015 at 2:10 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Projecting Label into White Matter Hello, I have a few questions about using HCP structural data to create waypoints/masks for tractography. In the past, we've created masks of the white matter adjacent to a label of interest with Freesurfer's mri_label2vol, using the "proj" argument to project from the label into the adjacent white matter. I'd like do this with the HCP data, but its a bit unclear to me what would be the proper files to use: 1. I believe this command uses the ?h.white surface by default. The extended preprocessed structural data contains multiple white matter surfaces (?h.white, ?h.white.hires, lh.white.deformed lh.white.prehires). I am not sure which to use. Which surface were the labels defined on? 2. What is the best .mgz file to use as a template volume? T1.hires.norm.mgz appears to be a good match for the T1 nii.gz file, but I'd like to be sure I'm using the best file. Any help would be greatly appreciated! John Plass _______________________________________________ HCP-Users mailing list 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