On Thu, Jun 4, 2009 at 11:51 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load the FSGD and look at the scatter plot, the y-axis will be the thickness value (assuming you're doing a thickness study:).

doug

Judith Segall wrote:

Doug and freesufer list.

When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that "The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold." But then what units is it in?

When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team.

- Judith

On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

It is the maximum vertex-wise -log10(p) found in the cluster. Why
do you think otherwise? You should be able to load the sig map
into tksurfer and go to that vertex to find out.

doug

Judith Segall wrote:

Thanks, for you responses Doug and Pratap. But, both of your
responses need more clarification, because I believe that we
are not all referring to the same 'max'.

Doug:

I understand that when I display the sig.cluster.mgh that the
a CWP value of 0.0001 would be displayed as a 4 by the color
bar in tksurfer, since it is the -log10(p). However, in this
case, which is about the cluster growing summary, the
-log10(p) of the CWP does not equal the Max. Max is -3.312 and
the CWP is 0.08250. Or an additional example form another
sig.cluster.summary, where the Max is -4.310 and the CWP is
0.0192.
ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot
1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual

In Pratap's email his answer to my question of what is the max
in the CWP is, "Yes thickness. The MAX indicates the maximum
-log10(pvalue) in that cluster." Which, is stating that it is
both the thickness and the pvalue. I really think that it is
thickness measure, but need some clarification from mgh.

So, is the Max in column 2 of the cluster growing summary
report, from monte carlo simulations, thickness?

Thanks,

Judith S.

On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

It will be whatever you used as input. In this case, it is the
-log10(p) value of the maximum in the cluster (not the
thickness
value).

doug

Pratap Kunwar wrote:

Hi Judith,

Yes thickness. The MAX indicates the maximum
-log10(pvalue) in
that cluster.

Hi all. After looking over our monte-carlo results, I a
simple question
about the sig.cluster.summary output.

Is the " Max" in column 2 below a measurement of
thickness?
thickness, is the correct interpretation the following:
the most
significant
cluster is in the laterorbitofrontal region.
yes at lateral orbital frontal.
The max vertex in that
cluster
has an average thickness of 3.312 mm and the negative
directionality
indicates that it is thinner in that region than in the
fsaverage (from
freesufer) used in the group analysis/simulations?
yes you are correct.
If it does not refer to thickness, is it a
statistic, etc?

# Minimum Threshold 2
# Maximum Threshold infinity
# Threshold Sign abs
# AdjustThreshWhenOneTail 1
# Area Threshold 0 mm^2
# CSD thresh 2.000000
# CSD nreps 10000
# CSD simtype mc-z
# CSD contrast lh-Avg-thickness-CAQ-CCI
# CSD confint 90.000000
# Overall max 2.05497 at vertex 92846
# Overall min -3.3122 at vertex 60632
# NClusters 11
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 1
#
# ClusterNo Max VtxMax Size(mm^2) TalX TalY
TalZ
CWP
CWPLow CWPHi NVtxs Annot
1 -3.312 60632 278.00 -15.2 47.7
-15.4
0.08250
0.07900 0.08600 341 lateralorbitofrontal
2 -3.231 51202 118.54 -39.5 24.9
16.9
0.53620
0.52980 0.54260 212 rostralmiddlefrontal
3 -3.229 67407 163.06 -19.2 12.0
46.9
0.36360
0.35740 0.36980 337 superiorfrontal
4 -2.463 117667 37.51 -47.8 -50.8
8.0
0.63240
0.62620 0.63860 79 bankssts
5 -2.379 151243 12.92 -30.9 -42.8
36.6
0.63240
0.62620 0.63860 38 superiorparietal

I am trying to finish writing up my results and
just need
answer to this
question to continue.

Thanks,

Judith S.
Mind Research Network
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MGH-NMR Center
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