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<mailto:xavie...@mit.edu>> Date: Wednesday, August 9, 2017 at 9:43 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:tsc...@mst.edu>] Sent: Tuesday, August 08, 2017 4:39 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org<mailto: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<mailto: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<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
