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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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