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Washington-University / HCPpipelines

Processing pipelines for the HCP
https://www.humanconnectome.org/
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smoothing for grayordinates #49

Closed shu-hai closed 7 years ago

shu-hai commented 7 years ago

Hello, I notice that grayordinates includes both the surface and subcortical voxels. Now I got some results on grayordinates, and I want to _spatially smooth_ the values using Gaussian kernels. Do you have any code and example to do such smoothing on surface vertices? Thanks.

glasserm commented 7 years ago

Connectome Workbench wb_command -cifti-smoothing

shu-hai commented 7 years ago

Hi, glasserm, I am not so familiar with Connectome Workbench. If I want to do 4mm FWHM for both surface and subcortical voxels, how to operate it in Connectome Workbench? Any example code?

glasserm commented 7 years ago

I guess you'll just have to become familiar then. The usage available when you type the above command. You can download Connectome Workbench from here:

https://www.humanconnectome.org/software/connectome-workbench

Really this forum is only for issues with the pipeline code. For more general questions like the one you asked, it is better to ask on the hcp-users mailing list:

https://www.humanconnectome.org/contact-us

coalsont commented 7 years ago

If you can read bash scripts, here is a line that uses the command:

https://github.com/Washington-University/Pipelines/blob/master/TaskfMRIAnalysis/scripts/TaskfMRILevel1.v2.0.sh#L179

The help info is also available online, see these two pages in particular:

https://www.humanconnectome.org/software/workbench-command/-cifti-smoothing https://www.humanconnectome.org/software/workbench-command/-arguments-help

As Matt said, though, this issue tracker is intended for reporting problems with the HCP Pipelines scripts themselves, and is not a general help forum.