Re: [HCP-Users] Area 25 grayordinates

[Harms, Michael]

Hi, We just recently discovered that the OFP03 parcellation was missing from the distributed dlabel file. See this in the HCP-User list archives for a fixed version: http://www.mail-archive.com/hcp-users%40humanconnectome.org/msg02609.html cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Zimmerman, Jared Perry" <jpzimmer...@partners.org> Date: Tuesday, June 14, 2016 at 10:12 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Area 25 grayordinates Hi HCP Users, I'm interested in vmPFC structures including the subgenual ACC and in particular area 25, which I'm noticing doesn't seem to be fully represented in standard grayordinate space.  When I look at any dense connectome file, either ones I've generated or the population averages, it seems the most caudal parts of the vmPFC, particularly area 25 are missing.  Here I'm defining area 25 simply based on the OFP03 parcellation borders registered to the fs_LR atlas.  In particular I notice that the left hemisphere area 25 seems to be completely absent from the standard grayordinate space, and the right hemisphere appears to be partially included. This seems odd for a number of reasons.  In particular, when I look at the goodvoxels.nii.gz for my subjects the voxels in the most caudal vmPFC regions are included, so the signal from these voxels is getting sampled into standard grayordinate space somewhere.  Also, when I look at the medial wall masks, none of them seem to exclude the area 25 parcellation region, so I don't think it's getting masked out. I guess I'm confused about how and/or why these regions are getting excluded from the grayordinate system.  My thoughts are twofold.  1) Maybe this is just a problem with visualization or registration of the OFP03 parcellation to the fs_LR surfaces. The Van Essen '11 paper in Cerebral Cortex says those drawn onto a flat surface, registered to the PALS atlas and then registered to the fs_LR atlas.  Could it just be that the registration didn't work well in this region?  2) Could it be an actual issue with the anatomy in this region getting left out of the grayordinate space based on how that space is defined?  I'm thinking about the cortical gray matter that is ventral and medial to the most anterior end of the striatum, which maybe is getting excluded from the cortical surface, but also not included in the subcortex because it is not a part of any of the subcortical structures within the grayordinate space. Any ideas on what's happening here?  I'm confident the signal is there after looking at the RibbonToSurfaceMapping, I just don't know where that signal is, or if it's been mixed with signal from more rostral areas of the vmPFC.  Any help would be much appreciated. Thanks, Jared   The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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