No it will be based on the HCP data, though it is worth keeping in mind that this is a tough region for in vivo functional neuroimaging because it is right near the gradient echo signal dropout region.
As for the medial wall masks, they indeed have some imperfections, (though I am not convinced that we are missing most of area 25 vs the registration of the OFP03 parcellation in this region is not perfect, I do think we miss some of area 33 in this region however). David would be the best person to comment on both the definition of the mask and the registration as he did both of these things. To some extent, it comes down to where do you think the neocortex ends and the basal forebrain begins. At some point in the future there will be an update to the CIFTI grayordinates space to define the medial wall a bit better and more subcortical nuclei. In the mean time, if you really need some vertices that are currently excluded, you can use the native mesh timeseries (which are masked a bit more liberally) we provide, make your own medial wall mask that includes these vertices, and bring the data onto the 32k mesh for analysis. Peace, Matt. From: "Zimmerman, Jared Perry" <[email protected]<mailto:[email protected]>> Date: Wednesday, June 15, 2016 at 11:53 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] Area 25 grayordinates Thanks Matt, Can you clarify what you mean by having a new definition available shortly? Will it simply be from the parcellation in the included paper? The OFP03 parcellation really has some advantages to that in being a more fine grained delineation of regions with more detailed cyto and chemo-architectonic criteria, so it would be nice to be confident that it’s registered well. I also still have some remaining questions about the grayordinate system in this region and the medial wall masks used in dtseries generation (which appear to be the problem in this case). See the attached figures that Michael asked for and which might be helpful in explaining my questions. I’ve also zipped them and made them available at this link in case the attachments get scrubbed by the list-serv http://gate.nmr.mgh.harvard.edu/filedrop2/?p=8q9k7ehu6wg Fig1 is the s900 average dconn file with no medial wall mask demonstrating the lack of data in area 25 and some area 32 and 24 vertices. Fig2 is the same with the VGD11b parcellation underlayed and the medial wall mask from that parcellation included. Notice the blue area 25 label and green area 24 label coming through under the dconn data where vertices are excluded. Fig3 is the same with the Conte69 medial wall mask underlayed. It seems like this was the medial wall mask that was sued in the generation of dtseries and dconn files which masks out these regions of area 25. Fig4 is the dconn file for a vertex/voxel within area 25 demonstrating that there is no data there but that in the volume this vertex/voxel is cortical grey matter in the volume. The dconn is empty here in either the surface or volume. Fig5 is the same at a point slightly more ventral and posterior that has data in the volume. So here it does appear that some of the more ventral portions of area25 start to get into the VS. This is why I’m wondering a little bit about how well the parcellations are registered in this region. Fig6 is the same at a point more anterior that is on the 25/32 border that is included in the surface data. Basically, I’m wondering why the points in Fig4 are not included in the grayordinate system when they appear to be clearly part of the cortical grey matter. It seems like this is a result of using the Conte69 medial wall mask to make the dconn and dtseries files which masks out these areas. Can you lend any insight into how the Conte69 medial wall mask was generated and why that was used as opposed to the other mask that’s part of the parcellation file. Do you anticipate there being any fix to this problem, or will these continue to be masked out in future releases? This region is very important for many psychiatric disorders including MDD and anxiety, so it might be nice to have it in the normative data releases given the future directions of the project. Any input would be much appreciated. Thanks, Jared From: Glasser, Matthew [mailto:[email protected]] Sent: Tuesday, June 14, 2016 3:27 PM To: Harms, Michael; Zimmerman, Jared Perry; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Area 25 grayordinates The registration may not be ideal here. I would point you to this paper: http://www.sciencedirect.com/science/article/pii/S1053811915003535 We have a new definition of area 25 on the surface that will be available shortly… Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>> Date: Tuesday, June 14, 2016 at 10:39 AM To: "Zimmerman, Jared Perry" <[email protected]<mailto:[email protected]>>, "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Area 25 grayordinates Yes, some small figures would probably be helpful. Not sure what the list allows though. If they don’t come through, you’ll have to upload them to a sharing site. -- 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: [email protected]<mailto:[email protected]> From: "Zimmerman, Jared Perry" <[email protected]<mailto:[email protected]>> Date: Tuesday, June 14, 2016 at 10:36 AM To: "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] Area 25 grayordinates Thanks Michael, That was actually me who asked that original question and I have the updated version. To my knowledge and according to the scripts that were included with that most recent distribution, the only thing that's different about the new and old parcellations is that the 13b label was missing in the left hemisphere and is now replaced. This only changed the label file and did not affect the borders at all (the 13b label was added from the borders with border-to-roi), so this should not affect the registration of the borders for area 25. I don't have access to the data right now, but I can include some figures showing clearly what I mean if that would be helpful. If there are other outstanding issues with those border and label files though it would be helpful to know especially as the next phase of the project begins about the connectomics of psychiatric disease given that these regions are critical for many psychiatric conditions. Thanks, Jared ________________________________ From: Harms, Michael [[email protected]<mailto:[email protected]>] Sent: Tuesday, June 14, 2016 11:23 AM To: Zimmerman, Jared Perry; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Area 25 grayordinates 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: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of "Zimmerman, Jared Perry" <[email protected]<mailto:[email protected]>> Date: Tuesday, June 14, 2016 at 10:12 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 . 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