Thanks Tim! For running with the option -gifti-all-labels-to-rois, we need to provide a <map> as per the documentation in the first link you shared. What do we provide as <map>? We tried passing the number 1 and got a .func.gii file representing the ROI having Key=1 in the input XML. We then thought passing 2, 3, …, 180 would give us the ROIs having those values as the keys in the input XML but we got an error as follows:
ERROR: Invalid map number or name specified Could you share what we should provide as <map>? We printed the input XML and saw that the map name was #1 and then tried passing that, but that gave us some error as well. Our understanding of what you’ve said is that we need to create a single metric .func.gii file representing all the 180 ROIs by running using the -gifti-all-labels-to-rois option exactly once (which we couldn’t do as explained above), followed by running -metric-merge 180 times, each time passing -column as the values in the integer set [1, 180]. Is this right? Thanks! Karthik From: Timothy Coalson [mailto:tsc...@mst.edu] Sent: Monday, October 24, 2016 4:49 PM To: Gopalakrishnan, Karthik <gkart...@gatech.edu> Cc: Glasser, Matthew <glass...@wustl.edu>; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii http://www.humanconnectome.org/software/workbench-command.php?function=-gifti-all-labels-to-rois http://www.humanconnectome.org/software/workbench-command.php?function=-metric-merge You'll need to run -metric-merge once for each roi to get them all as separate files, wb_command doesn't generate hundreds of files from a simple command. Tim On Mon, Oct 24, 2016 at 3:33 PM, Gopalakrishnan, Karthik <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> wrote: Thanks Matt! So after using wb_command -cifti-separate on the .dlabel.nii file containing the MMP-1.0 parcellation for the hemisphere, we have a .label.gii file representing the 180 ROIs in the corresponding hemisphere. Can someone point out how we could go from this .label.gii file to 180 separate .gii files representing each ROI so that we can run probtrackx with these ROIs for a given subject? We want to be able to run probtrackx using each of the 180 ROIs as seeds to all 180 possible targets. Thanks, Karthik From: Glasser, Matthew [mailto:glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Friday, October 21, 2016 4:14 PM To: Gopalakrishnan, Karthik <gkart...@gatech.edu<mailto:gkart...@gatech.edu>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii You can convert the CIFTI file to a GIFTI label file using wb_command -cifti-separate. As for going from GIFTI label to surf+label (probtrackx’s interpretation of GIFTI), you’ll need to use the label2surf. Hopefully either one of the oxford folks can explain how to use that here or on the FSL list. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, October 21, 2016 at 2:12 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Converting MMP-1.0 180 ROIs dlabel.nii file to surf.gii Hi all, How do we convert a dlabel.nii file containing 180 ROIs (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) to a surf.gii file? We want to do that such that the output ROIs can be used in probtracx. Thanks! Regards, Karthik _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
