1 is correct for <map>, take another look at the output file, and note that it has 180 columns in it.
Yes, that is what I meant about -metric-merge. Tim On Mon, Oct 24, 2016 at 4:56 PM, Gopalakrishnan, Karthik < gkart...@gatech.edu> wrote: > 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> 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] > *Sent:* Friday, October 21, 2016 4:14 PM > *To:* Gopalakrishnan, Karthik <gkart...@gatech.edu>; > 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> on behalf of > "Gopalakrishnan, Karthik" <gkart...@gatech.edu> > *Date: *Friday, October 21, 2016 at 2:12 PM > *To: *"hcp-users@humanconnectome.org" <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 > 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 > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
