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 <miracoo...@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 > >
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