Re: [Freesurfer] QDEC cluster output

[Greve, Douglas N.,Ph.D.]

Hi Lara, sorry, we don't really support qdec anymore for the very reason that 
we can't get into the code easily and answer these questions. Can you use the 
command-line stream?
doug


On 10/17/19 6:17 PM, Lara Foland-Ross wrote:

External Email - Use Caution
Hi Freesurfer experts,

I’m running a simple qdec analysis to examine group differences in surface 
measures between a patient and control group, controlling for age and TBV.

I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I 
get the following output in my terminal window:



# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
CWPHi   NVtxs   Annot

   17.365  125481   2114.03-34.44.11.6  0.01660  0.01500  
0.01820  4933  insula

   23.851   73048   1830.45 -8.4   30.1   29.4  0.03440  0.03210  
0.03670  3210  superiorfrontal

   3   -3.248  128137   4923.73 -8.1  -64.05.8  0.00010  0.0  
0.00020  7680  lingual



Simulation complete.



However, when I click on “Find clusters and go to max”, the output in my 
terminal window changes to be as follows:



Generating cluster stats using min threshold of 1.3...

Found 3 clusters

Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35

ClusterNo  Max   VtxMax  Size(mm2)   TalX   TalY   TalZ NVtxs Annotation

-  ---   --  -          - --

1   -4.  334923.73   -12.0  -67.1   34.7 7680  precuneus

21.7799   92114.03   -26.3   23.8   -6.0 4933  
lateralorbitofrontal

31.4634  211830.45-6.6   33.8   49.8 3210  superiorfrontal


Lastly, I see that the x/y/z coordinates of the peak coordinates listed above 
are on the very edge of the corrected cluster. Yet, visual inspection of the 
peaks from uncorrected significance maps suggest that the peaks it is quite far 
from the “hottest” parts of the uncorrected significance maps.

My questions are:


  1.  Why are these values different, and what values should I report?
  2.  Are the peaks listed above the center of gravity? Or highest p value of 
the cluster? Curious as to why the heatmap values are so different from the 
values above.

Many thanks,
Lara



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] QDEC cluster output

[Lara Foland-Ross]

External Email - Use Caution

Hi Freesurfer experts,

I’m running a simple qdec analysis to examine group differences in surface 
measures between a patient and control group, controlling for age and TBV.

I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I 
get the following output in my terminal window:



# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
CWPHi   NVtxs   Annot

   17.365  125481   2114.03-34.44.11.6  0.01660  0.01500  
0.01820  4933  insula

   23.851   73048   1830.45 -8.4   30.1   29.4  0.03440  0.03210  
0.03670  3210  superiorfrontal

   3   -3.248  128137   4923.73 -8.1  -64.05.8  0.00010  0.0  
0.00020  7680  lingual



Simulation complete.



However, when I click on “Find clusters and go to max”, the output in my 
terminal window changes to be as follows:



Generating cluster stats using min threshold of 1.3...

Found 3 clusters

Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35

ClusterNo  Max   VtxMax  Size(mm2)   TalX   TalY   TalZ NVtxs Annotation

-  ---   --  -          - --

1   -4.  334923.73   -12.0  -67.1   34.7 7680  precuneus

21.7799   92114.03   -26.3   23.8   -6.0 4933  
lateralorbitofrontal

31.4634  211830.45-6.6   33.8   49.8 3210  superiorfrontal


Lastly, I see that the x/y/z coordinates of the peak coordinates listed above 
are on the very edge of the corrected cluster. Yet, visual inspection of the 
peaks from uncorrected significance maps suggest that the peaks it is quite far 
from the “hottest” parts of the uncorrected significance maps.

My questions are:


  1.  Why are these values different, and what values should I report?
  2.  Are the peaks listed above the center of gravity? Or highest p value of 
the cluster? Curious as to why the heatmap values are so different from the 
values above.

Many thanks,
Lara
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer