That would only be needed if we had surface-based cerebellar data. This is unfortunately not currently obtainable.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Xavier Guell Paradis <[email protected]<mailto:[email protected]>> Date: Thursday, February 2, 2017 at 11:53 AM To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters Dear Tim, Thank you very much for your message. In the last step (-cifti-weighted-stats), I am not sure which file to use for the -cerebellum-area-metric. I would like to obtain cerebellar cluster sizes in mm^3. Would it be possible to use a cerebellar volumetric atlas such as Cerebellum-MNIfnirt-maxprob-thr25.nii (this is an atlas available here http://www.diedrichsenlab.org/imaging/propatlas.htm), so that the output of -cifti-weighted-stats says in which cerebellar lobule(s) each cluster is found? Thank you very much, Xavier. ________________________________ From: Timothy Coalson [[email protected]<mailto:[email protected]>] Sent: Monday, January 30, 2017 6:18 PM To: Xavier Guell Paradis Cc: [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters The -cifti-find-clusters command assigns a separate integer within each cluster. You can use -cifti-label-import and then -cifti-all-labels-to-rois to get each cluster in a separate map. Then, -cifti-weighted-stats with -spatial-weights and -sum will give you mm^2 for surface clusters and mm^3 for volume clusters. Unfortunately, it is not easy to tell from the command line whether each cluster is on the surface or in the volume. However, you could make a cifti file using the output of -surface-wedge-volume and a volume file containing the voxel volume, and use that in -cifti-weighted-stats with -cifti-weights and -sum to get both surface and volume clusters in mm^3 (which assumes that surface clusters are the full width of the ribbon). Tim On Mon, Jan 30, 2017 at 4:26 PM, Xavier Guell Paradis <[email protected]<mailto:[email protected]>> wrote: Dear HCP experts, After using -cifti-find-clusters, is there a way to know the size of the clusters that the command has found? We know that the clusters will be larger than the specified volume-value-threshold, but is there a way to know the mm^3 or number of voxels of the clusters identified? Thank you very much, Xavier. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
