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Hi, freesurfer experts,
As I mentioned in my last email, I see no answer. I think it is possible that my description is not clear enough.
I used qdec to compare the cortical thickness of two groups and tried to correct for multiple comparisons using the button in qdec of monte carlo simulation.
I saw only one big cluster in the display window of qdec, whereas I saw three clusters in the terminal (printed text in the terminal) and in the .summary file. What is the problem here? Why is there the difference between the two?
Below are some contents of the mc-z.abs.th20.sig.cluster.summary file:
# Input /fsdata/example/qdec/test2/lh-Diff-male-female-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /fsdata/example # SearchSpace_mm2 73217.3 # SearchSpace_vtx 141808 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.35442 at vertex 136194 # Overall min -8.31037 at vertex 29648 # NClusters 3 # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -8.310 29648 1472.33 -47.4 -7.6 44.8 0.00010 0.00000 0.00020 3372 -9795.07 precentral 2 -7.098 121377 277.37 -17.8 -15.5 63.6 0.02400 0.02200 0.02600 656 -1605.27 precentral 3 -4.500 83861 241.90 -36.3 51.7 -6.3 0.04790 0.04520 0.05060 326 -790.83 rostralmiddlefrontal
In the qdec display window, I only saw the cluster 1, the other two clusters were not displayed.
I also tried to visualize the result using freeview and loaded the mc-z.abs.th20.sig.vertex.mgh. I saw one cluster. but when I loaded the mc-z.abs.th20.sig.ocn.annot file, I saw three different clusters.
Thanks a lot!
Best,
Yuanchao
qdec should not be used for correction of multiple comparisons. Use mri_glmfit-sim directly instead.
On 5/11/18 10:32 PM, yuanchao.zhang8@gmail.com wrote:
Hi, freesurfer experts,
As I mentioned in my last email, I see no answer. I think it is possible that my description is not clear enough.
I used qdec to compare the cortical thickness of two groups and tried to correct for multiple comparisons using the button in qdec of monte carlo simulation.
I saw only one big cluster in the display window of qdec, whereas I saw three clusters in the terminal (printed text in the terminal) and in the .summary file. What is the problem here? Why is there the difference between the two?
Below are some contents of the mc-z.abs.th20.sig.cluster.summary file:
# Input /fsdata/example/qdec/test2/lh-Diff-male-female-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /fsdata/example # SearchSpace_mm2 73217.3 # SearchSpace_vtx 141808 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.35442 at vertex 136194 # Overall min -8.31037 at vertex 29648 # NClusters 3 # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -8.310 29648 1472.33 -47.4 -7.6 44.8 0.00010 0.00000 0.00020 3372 -9795.07 precentral 2 -7.098 121377 277.37 -17.8 -15.5 63.6 0.02400 0.02200 0.02600 656 -1605.27 precentral 3 -4.500 83861 241.90 -36.3 51.7 -6.3 0.04790 0.04520 0.05060 326 -790.83 rostralmiddlefrontal
In the qdec display window, I only saw the cluster 1, the other two clusters were not displayed.
I also tried to visualize the result using freeview and loaded the mc-z.abs.th20.sig.vertex.mgh. I saw one cluster. but when I loaded the mc-z.abs.th20.sig.ocn.annot file, I saw three different clusters.
Thanks a lot!
Best,
Yuanchao
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