Hello,
I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole.
Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible.
Can you please help me reconcile the 2 types of output? Thanks!
*** terminal output:
# Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # 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 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral
Simulation complete.