If your "mycluster.nii" is in a different volume space than 222 MNI RPI space, then it may not let you use it that way. Compare the nifti header against this file in the HCP pipelines, using fslhd or wb_command -nifti-information -print-header:
global/templates/MNI152_T1_2mm.nii.gz If it is different, then you will need to resample your label volume. Tim On Wed, Aug 9, 2017 at 4:38 PM, Xavier Guell Paradis <xavie...@mit.edu> wrote: > Dear Tim, > Thank you for your reply > I have made sure that I have the group .dconn file opened, and I can see > that it is correctly opened because I can see connectivity when I click on > any structure. > However, I still have the same problem: I do not see the option of "Show > Cifti Connectivity" when I right-click the cluster of the dlabel file I > have created (however, I can see the dlabel file in the "Labels" list of > the "Features Toolbox"). > > These are the steps I followed to create the dlabel file; I imagine I did > something wrong in these steps but I cannot figure out what: > 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 > The resulting dlabel file is "mycluster_labelStep2.dlabel.nii" > > Thank you very much, > Xavier. > > ------------------------------ > *From:* Timothy Coalson [tsc...@mst.edu] > *Sent:* Wednesday, August 09, 2017 4:57 PM > *To:* Xavier Guell Paradis > *Cc:* Glasser, Matthew; hcp-users@humanconnectome.org > > *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to > dlabel files? > > 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/mast >> er/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
