I forgot to send the cluster summary sheet. Here is it.

# Input lh.stroke.fsgd.glmdir/contrast/sig.mgh

# Frame Number 0

# srcsubj fsaverage

# hemi lh

# surface white

# annot aparc

# SUBJECTS_DIR /Users/CT/Documents/stroke

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 149953

# Bonferroni 0

# Minimum Threshold 2

# Maximum Threshold infinity

# Threshold Sign abs

# AdjustThreshWhenOneTail 1

# Area Threshold 0 mm^2

# CSD thresh 2.000000

# CSD nreps 5000

# CSD simtype mc-z

# CSD contrast contrast

# CSD confint 90.000000

# Overall max 2.26504 at vertex 146861

# Overall min -2.73325 at vertex 144073

# NClusters 13

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 0

# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot

1 -2.733 144073 70.23 -31.5 -61.0 -15.8 0.99400 0.99260 0.99540 101 fusiform

2 -2.537 153213 28.08 -14.2 40.2 12.1 1.00000 -0.00020 1.00000 57 superiorfrontal

3 -2.348 57351 30.35 -63.3 -39.6 8.0 1.00000 -0.00020 1.00000 77 bankssts

4 2.265 146861 20.30 -38.8 -57.9 25.4 1.00000 -0.00020 1.00000 45 inferiorparietal

5 -2.261 116880 21.63 -33.3 -48.7 60.5 1.00000 -0.00020 1.00000 45 superiorparietal

6 2.248 83406 24.49 -5.2 28.6 18.6 1.00000 -0.00020 1.00000 47 caudalanteriorcingulate

7 -2.182 90669 20.62 -50.9 -56.2 -12.6 1.00000 -0.00020 1.00000 28 inferiortemporal

8 2.143 32579 5.79 -7.9 -10.3 40.1 1.00000 -0.00020 1.00000 14 posteriorcingulate

9 -2.052 159218 3.21 -5.0 -33.8 32.9 1.00000 -0.00020 1.00000 7 isthmuscingulate

10 -2.050 127337 7.16 -17.7 6.2 -15.5 1.00000 -0.00020 1.00000 16 lateralorbitofrontal

11 -2.013 93626 1.61 -37.4 -13.7 54.8 1.00000 -0.00020 1.00000 3 precentral

12 -2.006 9896 0.87 -27.3 -0.6 -35.9 1.00000 -0.00020 1.00000 2 entorhinal

13 -2.001 75892 0.47 -22.0 -33.4 -11.8 1.00000 -0.00020 1.00000 1 parahippocampal

On Fri, Sep 22, 2017 at 9:37 PM, miracle ozzoude <miracooloz@gmail.com> wrote:

Hello,

I ran cortical thickness analyses using the following contrast and fsgd. After that, I corrected for multiple comparison using monte carlo 5000 with cluster forming threshold of 2 and unsigned/2-tailed t-test (abs). I wanted to confirm my interpretation of the results.

1) Since my contrast is (-1 1 0 0 representing control>stroke), it should be red/yellow and if blue, it should be control<stroke. However, I see clusters with colors different from the aformentioned (see attached screenshot). How should I interpret them?

2) I want to view the uncorrected p-values, which of the columns in the summary text file should I concentrate, and should the p < or > 0.05?

3) Looking at the CWP column in the summary text file, can I conclude that the obtained regions/clusters are significant? This is because non of the cluster-wise p-values are below 0.05 (--cwp 0.05).

4) Which of the columns represent the sign of my contrast i.e. where Control>Stroke and Control<Stroke because i used abs? Max?

FSGD file
GroupDescriptorFile
Title StrokevsControl
Class1 Stroke
Class2 Control
Variable bmi
Input 6001 Stroke 20
Input 8001 Control 30

Contrast:
-1 1 0 0 (Control>Stroke removing the effects of bmi)

Thank you,
Paul