slow_surface_clustsim.py choosing blur value

AFNI Message Board
1

Hello everyone,

I am trying to run a clustersim on surface data but I’m not sure if I am correctly selecting blur values. I know that with 3dclustsim I need to obtain estimates for the noise smoothness. I’m not sure if thats what I am supposed to be doing slow_surface_clustsim.py or if the blur value should be the same as my smoothing kernel. Here is the command I used to test things out:

slow_surf_clustsim.py -save_script 118.surf.sim_1000 -on_surface yes -uvar blur 6.0 -uvar spec_file 118_lh.spec -uvar surf_vol 118_SurfVol+orig.BRIK -uvar pthr_list 0.05 0.01 0.002 0.001 -uvar niter 10000 -uvar results_dir clust.results.10000

Any clarification/help would be appreciated.

Naail

2

Hi Naail,

For surface based analysis, blur is applied to a certain level. So use whatever level is in any SurfSmooth command that was run on the data.

If SurfSmooth was not applied, maybe SurfFWHM would be appropriate to use.

  • rick
3

Thank you Rick!