You need to have a dtseries (or dconn) file open before you can see any kind of connectivity. If you only have the labels/rois open, how do you expect it to figure out connectivity information?
Note that we only have options for averaging things inside a label, the ROI file will not be useful in the GUI for this purpose. Tim On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis <xavie...@mit.edu> wrote: > Dear Matt, > Thank you for your reply. I have realized that a very curious thing > happens: > - If I open the dlabel file and right-click the cluster in wb_view, I do > not see any option > - If I open the dscalar file and right-click the cluster in wb_view, I do > not see any option > - If I open the dlabel file *AND* the dscalar file and right-click the > cluster in wb_view (note that the cluster is now present twice: in the > dlabel file and in the dscalar file), I see the "Show Data/Time Series > Graph" but not the "Show Cifti Connectivity" option. > > I opened wb_view multiple times to make sure that this is true: I only see > the "Show Data/Time Series Graph" once I have opened both files; but I > still do not see the "Show Cifti Connectivity" option. > > This is a strange pattern, but perhaps it is a clue to find out what I am > doing wrong. > > An extra piece of information that might be useful: when I open the dlabel > file, I can see it listed in the "Labels" list of the "Features ToolBox". > > Thank you very much, > Xavier. > ------------------------------ > *From:* Glasser, Matthew [glass...@wustl.edu] > *Sent:* Wednesday, August 09, 2017 2:13 PM > *To:* Xavier Guell Paradis; NEUROSCIENCE tim > > *Cc:* hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to > dlabel files? > > It should work if you skip the last step and use the dlabel file. > > Peace, > > Matt. > > From: Xavier Guell Paradis <xavie...@mit.edu> > Date: Wednesday, August 9, 2017 at 9:43 AM > To: Timothy Coalson <tsc...@mst.edu>, Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: RE: [HCP-Users] How can I convert subcortical nifti files to > dlabel files? > > Dear Tim and Matt, > Thank you very much for your reply. > > I tried -volume-label-import, followed by -cifti-create-label, followed by > -cifti-all-labels-to-rois. > After this, when I right-click the cluster in wb_view, I see the option > "Show Data/Time Series Graph For Parcel [my cluster]" *but I do not see > the option "Show Cifti Connectivity* For Parcel [my cluster]" (even > though I can see this option for other parcels, such as the Yeo map). > I have been trying different things but cannot figure it out. > > Some extra information in case it is useful: > > My clusters are a group average registered to the HCP > "S900_Average_T1w_restore.nii", so at this point I am not concerned about > comparison across subjects. I would like to calculate functional > connectivity from each of my subcortical clusters using your S900 .dconn > file. > My original nifti file with the right cerebellum cluster is called > "mycluster.nii". > > I created the file "textforvolumelabelimport.txt" with the following text: > > CEREBELLUM_RIGHT > > 1 1 1 1 > > Then I did the following: > > wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt > mycluster_label.nii > > wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume > mycluster_label.nii mycluster_label.nii > > wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 > mycluster_labelStep3.dscalar.nii > > When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can > see the option of "Show Data/Time Series Graph" *but not the option of > "Show Cifti Connectivity*". > > Thank you very much, > Xavier. > > ------------------------------ > *From:* Timothy Coalson [tsc...@mst.edu] > *Sent:* Tuesday, August 08, 2017 4:39 PM > *To:* Xavier Guell Paradis > *Cc:* hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to > dlabel files? > > I'm assuming you want them to match a standard grayordinate space, so that > they can be compared across subjects. > > The simple way that doesn't account for residual subject differences in > subcortical locations is to first resample the data to the appropriate > resolution/orientation MNI space (222 for the 91k grayordinates), then use > -cifti-create-dense-from-template with the -volume-all option. > > The better but more involved way is to take the subject's subcortical > structure labels from freesurfer, import them to workbench format with the > names that -cifti-create-label specifies, use -cifti-create-label to make a > subject-specific cifti file (you will also need to provide some dummy > surface data for the next step to work), and then use -cifti-resample to > use only the same-structure-overlap information, and dilate to fill in any > holes if desired. > > We use this second method for fMRI data in the pipelines, see here: > > https://github.com/Washington-University/Pipelines/blob/ > master/fMRISurface/scripts/SubcorticalProcessing.sh#L40 > > Though that script actually only outputs a volume file, and therefore it > doesn't bother with having surface data in those temporary cifti files. > > Tim > > > On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis <xavie...@mit.edu> > wrote: > >> Dear HCP experts, >> I have several subcortical nifti files, each containing one cluster. I >> would like to convert them to dlabel files, so that then I can use wb_view >> to see the functional connectivity from each of these clusters (using your >> group .dconn file). >> >> How can I convert subcortical nifti files to dlabel files? >> I have been exploring several wb_commands but I cannot figure it out. >> >> Thank you very much, >> Xavier. >> >> _______________________________________________ >> 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
