.func.gii files are simply arrays of values, where one dimension is the number of vertices in the surface, and the other is the number of maps in the file. Every vertex of the relevant surface gets a value. The special case of "ROIs" is just that the values are all either 0 or 1. So, while in the second ROI map, different vertices have values of 1 than the first ROI map, both maps span all vertices.
Surface coordinates are stored in .surf.gii files - neither .func.gii nor cifti files contain vertex coordinates. Cifti does not support using a different set of brainordinates in different maps of the file - every map in a single cifti file uses the same set of brainordinates. Internally cifti files are just another rectangular matrix, but used in a different way (and with different, more elaborate metadata). Tim On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu <[email protected]> wrote: > Dear experts, > > Could I ask an additional question following my previous emails about the > CIFTI data display? > > If two surface ROIs of one *.func.gii* file are displayed in separate > maps of Connectome Workbench instead of simultaneously shown on one brain > surface, does it mean the two ROIs are saved separately with two sets of > global grayordinate coordinates? Thanks. > > Best regards, > Xinyang > > > At 2018-08-27 11:16:42, "Glasser, Matthew" <[email protected]> wrote: > > Would have to ask that on the FSL list. > > Matt. > > From: Xinyang Liu <[email protected]> > Date: Sunday, August 26, 2018 at 10:14 PM > To: Matt Glasser <[email protected]> > Cc: Timothy Coalson <[email protected]>, HCP 讨论组 < > [email protected]> > Subject: Re: [HCP-Users] two maximum points using -metric-extrema > > Hi, Matt. > I saw the second ROI on WB as you said then. Thank you so much！ > > Then another left question is, when I use $FSL/*surf2surf* to change the * > .func.gii *file (with two ROIs included) to *.asc* format, I only saw the > coordinates information of one ROI (vertices with 1 values). The > .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking > the transformed .asc file, I only found the ROI coordinates of the first > ROI (127 vertices), not the second. > > Does it mean the two produced ROIs are saved separately in .func.gii, but > the "surf2surf "command can only transform one of them to .asc? > > Best regards, > Xinyang > > > At 2018-08-27 01:12:54, "Glasser, Matthew" <[email protected]> wrote: > > The other should be in the next map of the ROI file. > > Matt. > > From: Xinyang Liu <[email protected]> > Date: Sunday, August 26, 2018 at 2:41 AM > To: Matt Glasser <[email protected]> > Cc: Timothy Coalson <[email protected]>, HCP 讨论组 < > [email protected]> > Subject: Re: [HCP-Users] two maximum points using -metric-extrema > > Hi, Matt. > Sure. I attached two pictures and two produced GIFTI files here. > > In data processing, I first used *-metric-extrema* to find the maximum > point within a certain fMRI region. The "maximum_IPS.JPG" attached was > among the condition that two maximum points were found (please see the two > yellow points in the first attached picture). The corresponding GIFTI file > is "L.maxima.func.gii". > > Then I continued using the "L.maxima.func.gii" and > *-metric-rois-from-extrema* to draw ROIs, the result only showed one > created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) > attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. > > I also used the *-metric-stats* to calculate the vertex number of the > created ROI, but the result provided two values: 127, 48. > > So I am quite confusing about what happened here. > > Best regards, > Xinyang > > > > At 2018-08-26 13:03:42, "Glasser, Matthew" <[email protected]> wrote: > > How about posting some screen captures so we know what is happening? > > Matt. > > From: Xinyang Liu <[email protected]> > Date: Saturday, August 25, 2018 at 11:51 PM > To: Timothy Coalson <[email protected]> > Cc: Matt Glasser <[email protected]>, HCP 讨论组 < > [email protected]> > Subject: Re: [HCP-Users] two maximum points using -metric-extrema > > Dear Tim, dear Matt, > > Thank you very much for your helpful answers. > > Sorry that I may not described very clearly before. As Tim mentioned, we > used the -metric-extrema to find the maximum point within a certain region > (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema > to draw ROIs (produced "ROI.func.gii" file). > > Then there is a contradictory thing emerged. When we used "wb_command > -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a > few results showed two values, which might indicate two ROIs based on the > two maximum points. We checked the maxima.func.gii files, and found there > do existed two maximum points in such condition. However, when we looked > at the created ROI images on Connectome Workbench, we only saw one target > ROI drawn on the brain surface. This confused us a lot. We don't know > whether there were one or two ROIs produced. Do you have any suggestions > about that? Thanks. > > Best regards, > Xinyang > > > > At 2018-08-25 04:16:48, "Timothy Coalson" <[email protected]> wrote: > > The -metric-extrema command doesn't draw ROIs, it sets single vertices to > 1 or -1 based on if they are a local maximum or minimum. By default, if > there are two equal values that are closer than the search range, then > *neither* of them will be identified as an extrema. If they are further > then the search range, then both may be extrema. > > The -consolidate-mode acts somewhat differently - if two equal values are > touching, neither is treated as an initial extrema, but as long as there is > at least one vertex separating them, they may both be treated as initial > extrema. After the initial extrema are found, all extrema that are close > to other extrema are "consolidated" together. The details are somewhat > complicated, and it was implemented by request of others, it is not > something that we use. > > Tim > > > On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu <[email protected]> > wrote: > >> Hi, Matt. Thank you very much for your reply. >> >> The extreme point was searched in a certain surface area. Do you mean >> that even there are two maximum points with the same value, they were >> controlled in a limited distance and therefore, the final drawn ROI is a >> combined region of two drawings instead of two separate ones? >> >> Because the problem is that, when I count the total vertex number for >> each created ROI using -metric-stats, a few results showed two values for >> one ROI. I am wondering why this happen and how to deal with that. >> >> Best regards, >> Xinyang >> >> >> At 2018-08-24 19:14:56, "Glasser, Matthew" <[email protected]> wrote: >> >> I believe there is a configurable setting that sets the minimum distance >> between extrema. It is a local min/max that is found. >> >> Matt. >> >> From: <[email protected]> on behalf of Xinyang Liu < >> [email protected]> >> Date: Friday, August 24, 2018 at 4:21 AM >> To: HCP 讨论组 <[email protected]> >> Subject: [HCP-Users] two maximum points using -metric-extrema >> >> Dear HCP experts, >> >> Hi. When using workbench command "-metric-extrema" to draw ROI around the >> maximum point of the fMRI surface region, what would happen if there are >> two maximum points? Will the software keep both of them or only keep one? >> Thanks a lot. >> >> Best regards, >> Xinyang >> >> >> >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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. 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