Parcellating using dscalar

[Andraž Matkovič]

Dear HCP team,

Is there a way to use the wb_command to parcellate the dtseries.nii file using the dscalar.nii file, which contains functional maps based on soft parcellations, such as ICA or NMF? I managed to parcellate the files using Python (Nibabel + NumPy), but I was wondering if there is a direct way to do this using wb_command.

Best regards,

Andraž

[Glasser, Matthew]

We do not currently have a method of “weighted” parcellation beyond RSNRegression (which works for sICA, tICA, and PFMs using its various modes).

 

Matt.

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[Tim Coalson]

The cifti parcellated format effectively encodes a hard parcellation in its XML, so you'd need to generate that in addition to the computation of the soft parcellation values.  You can then combine them, either in python/matlab (or other language with a cifti library), or with -cifti-convert -from-text.  wb_command doesn't currently have the algorithms for ICA or NMF.

Hard parcellations don't overlap, so that is a simple computation of (usually) averaging the values (weighting by vertex area for correctness).  For generic soft parcellations, you may want to solve it as a multiple regression problem, such that reconstructing from the result gets close to the original timeseries data.  Of course, if the soft parcellation comes from a decomposition like ICA/NMF, the component timeseries are probably already available.

Tim

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