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" <glass...@wustl.edu> wrote: Would have to ask that on the FSL list. Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Sunday, August 26, 2018 at 10:14 PM To: Matt Glasser <glass...@wustl.edu> Cc: Timothy Coalson <tsc...@mst.edu>, HCP 讨论组 <hcp-users@humanconnectome.org> 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" <glass...@wustl.edu> wrote: The other should be in the next map of the ROI file. Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Sunday, August 26, 2018 at 2:41 AM To: Matt Glasser <glass...@wustl.edu> Cc: Timothy Coalson <tsc...@mst.edu>, HCP 讨论组 <hcp-users@humanconnectome.org> 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" <glass...@wustl.edu> wrote: How about posting some screen captures so we know what is happening? Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Saturday, August 25, 2018 at 11:51 PM To: Timothy Coalson <tsc...@mst.edu> Cc: Matt Glasser <glass...@wustl.edu>, HCP 讨论组 <hcp-users@humanconnectome.org> 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" <tsc...@mst.edu> 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 <xinyang_ie...@163.com> 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" <glass...@wustl.edu> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <xinyang_ie...@163.com> Date: Friday, August 24, 2018 at 4:21 AM To: HCP 讨论组 <hcp-users@humanconnectome.org> 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 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 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. 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
