Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
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 
I created the file "textforvolumelabelimport.txt" with the following text:
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
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 

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 

Thank you very much,

From: Timothy Coalson []
Sent: Tuesday, August 08, 2017 4:39 PM
To: Xavier Guell Paradis
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 

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:

Though that script actually only outputs a volume file, and therefore it 
doesn't bother with having surface data in those temporary cifti files.


On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis 
<<>> 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 

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,

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