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Hello,
	The p-numbers are listed in order of descending cluster size for the  
clusters found. The coordinates are the location of the max-z value in  
the cluster and the cluster center respectively. I'm surprised you get  
a difference in the reported % - using the atlas tool from within  
Fslview I obtain the same probability ( 45% ) - you may want to use  
one of the other atlases in fslview as well ( maybe the harvard-oxford  
subcortical atlas? ).

Hope this helps

Matthew
>
> I would like to report VBM changes obtained from our structural T1-W  
> data. So i looked at the FSL archives and learned how to use  
> "cluster"and "atlasquery" commands. I am wondering is there a  
> documentation page for these two commands as it is hard to figure  
> out things from few questions.
>
> I would like to clarify the following, my cluster command  "cluster  
> --in=fslvbm_tfce_corrp_tstat1 --thresh=0.95 -- 
> oindex=fslvbm_tfce_corrp_tstat1_coord --mm" gives the following output
>
>
> Cluster Index   Voxels  Z-MAX   Z-MAX X (mm)    Z-MAX Y (mm)    Z- 
> MAX Z (mm)   Z-COG X (mm)     Z-COG Y (mm)    Z-COG Z (mm)
> 6       41818   1       -34     16      -30     1.06    8.26    3.49
> 5       222     0.974   34      -64     -8      28.9    -63.9   -7.53
> 4       91      0.963   16      -86     8       16      -86.2   5.41
> 3       22      0.952   -24     16      48      -24.7   14      47.3
> 2       20      0.969   -26     -62     66      -23.7   -62.2   65.7
> 1       1       0.95    40      -42     60      40      -42     60
>
> I am wondering whether there is an option in cluster command which i  
> can make use of to give result for every 0.005 increase in 1-p  
> values for instance like 0.95, 0.955, 0.96......instead of this  
> default numbers. My next question is when i use atlasquery command  
> as follows on one of these coordinates
>
>  atlasquery -a "MNI Structural Atlas" -c -34,16,-30
>
> 45% Temporal Lobe
>
> My first question here is for instance cluster 6 with coordinates  
> -34,16,-30 has ~ 41000 voxels so what does this single coordinate  
> (-34,16,-30) mean/represent.
>
> My second question is if i position my crosshair on the coordinate  
> -34,16,-30 in fslview with the MNI template and my  
> "fslvbm_tfce_corrp_tstat1" image superimposed, i could see that this  
> coordinate is in 100% temporal lobe location whereas atlasquery says  
> it is "45% Temporal Lobe" so i am not able to understand the results  
> of atlasquery. My last question is, is it possible to identify /get  
> the names of different regions which are activated within the  
> temporal lobe instead collectively saying it as 45% temporal lobe.
>
> Thanks
>
> venkateswaran
>
>
>
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