Hi Gwenaëlle,
Thanks even though i reduced the resolution i am not able to attach it is there is website where i can upload my tstat and corrrp_p map so that you can have a better look at them.
I will try using cope in cluster command as you suggested.
Thanks
venkat
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From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Tue 4/27/2010 2:46 PM
To: [log in to unmask]
Subject: [FSL] Re : [FSL] FSL results
Hi Venkat,
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I ran VBM on GM structures and when i superimposed my ..tfce_corrp_p_stats map on the MNI_2 mm image i found the activation p-map showing activation in WM regions like for instance in cerebral peduncle ( i have attached screen shot of images with and without superimposing p-map).Why is this?
- Could you please reattach the image but with a lower resolution so that it would not be deleted?
Also when i run cluster command to find out the regions which are active to report, i could see only 5 clusters (as below)
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)
5 55007 1 -54 -10 -46 0.29 7.17 5.66
4 163 0.964 -50 -46 -42 -48.4 -50.5 -44.1
3 96 0.973 -24 -64 66 -23.8 -61.2 64.2
2 80 0.966 32 -64 -6 32 -59.9 -8.1
1 25 0.952 22 -76 -6 22.8 -75.4 -4.88
I would like to know for instance in the above cluster table cluster 3 has 96 voxels with 1-p value of 0.973 and the coordinates corresponding to max t-value is -24 -64 66 so does all the 96 voxels in this cluster have 1-p value of 0.973 if so then i am not able to understand why only the coordinate -24 -64 66 is reported. Is there a documentation page to understand how this cluster command works and how clusters are formed etc.
- Indeed, all the voxels in a cluster surviving the correction for multiple comparisons using the cluster options in randomise (-c or -C) will have the same p-value. I am not sure how the 'cluster' command is working, but your "max" coordinate might simply be the centre of gravity of your cluster.
If you want to "trick" the cluster command into outputting the maximum (and other local maxima) values and coordinates in your clusters, you can simply feed your raw tstat map into 'cluster': --cope=your_raw_tstat1
Corresponding to this when i looked at the atlas (Harvard-Oxford Cortical Structural Atlas)
The above clusters are very limited in the sense that i see activations in other regions like motor areas which are not reported here in the cluster results. Is it possible to get complete activation report in all the regions whichever is active instead of using the FSLview to look at the regions which are active.
- This simply means that these motor regions are connected to one of the cluster described above. Again, you simply need to look for local maxima when using the 'cluster' command with your raw tstat map as "cope".
Cheers,
Gwenaëlle
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