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April 29, 2021 11:08AM
Hi everyone,
I've just been comparing commands with 3dClusterize and 3dclust and I'm wondering why the mean, SEM and max intensity differ?

3dclust -nosum -no_1Dformat -1dindex 5 -1tindex 6 -2thresh -2.8 2.8 -NN2 33 file+tlrc
Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS
------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
45 -40.0 -40.1 -14.6 -43.5 -37.5 -47.5 -29.5 -16.5 -10.5 0.0852 0.0025 -0.1195 -39.5 -43.5 -14.5

3dClusterize -nosum -no_1Dformat -idat 5 -ithr 6 -bisided -2.8 2.8 -NN 2 -clust_nvox 33 -inset file+tlrc
Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS
------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- -----
45 -40.0 -40.1 -14.6 -43.5 -37.5 -47.5 -29.5 -16.5 -10.5 8323.4 242.99 -11670 -39.5 -43.5 -14.5

It's the same when I use a different threshold. From 3dClusterize are always round about, but not exactly 100.000 times higher.
Does anyone know why this might be?
Also, is seems to me that both tools are missing a minus (-) in front of the mean... When I click on the voxels of that cluster within AFNI, all the values appear to be negative. This is also logical, as the cluster has negative z values (sub-brick 6), therefore I would assume the beta-values of sub-brick 5 to be negative.

And last but not least, does anyone know to export clusters found by 3dclust/3dCclusterize to separate masks?
-pref_map from 3dClusterize puts them all into one'mask with separate integers. I guess I could use 3dcalc in a loop to only keep voxels with values of 1,2,3... Is there an more efficient method?
Subject Author Posted

3dClusterize vs 3dclust

AFNIuser007 April 29, 2021 11:08AM

Re: 3dClusterize vs 3dclust

ptaylor April 29, 2021 11:49AM

Re: 3dClusterize vs 3dclust

AFNIuser007 April 29, 2021 01:21PM

Re: 3dClusterize vs 3dclust

ptaylor May 05, 2021 10:12PM

Re: 3dClusterize vs 3dclust

AFNIuser007 May 10, 2021 04:28AM



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