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Dear FreeSurfer Experts,
I am running Qdec 1.4 and I want to extract raw data (in this case, volume) from the significant clusters after Monte-Carlo simulation. In this particular case, the summary file shows 5 significant clusters after correction:
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2018/10/16-23:28:21-GMT # cmdline mri_surfcluster --in /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh --csd /Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd --mask /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh --cwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh --vwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh --sum /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary --ocn /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh --oannot /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot --csdpdf /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat --annot aparc --cwpvalthresh 0.05 --o /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh --surf white # cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # sysname Darwin # hostname N-Volunteer-iMac.local # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # SearchSpace_mm2 64328 # SearchSpace_vtx 149926 # Bonferroni 0 # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 2.06685 at vertex 34785 # Overall min -4.82491 at vertex 356 # NClusters 5 # Total Cortical Surface Area 64328 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.825 356 2272.51 60.8 -9.4 -1.7 0.00010 0.00000 0.00020 3745 superiortemporal 2 -4.419 146292 2658.98 19.8 52.0 -5.7 0.00010 0.00000 0.00020 3104 rostralmiddlefrontal 3 -4.267 138330 1525.99 35.6 35.2 7.0 0.00460 0.00370 0.00550 1936 rostralmiddlefrontal 4 -3.304 140353 1712.65 34.9 -30.2 56.6 0.00220 0.00160 0.00280 3540 postcentral 5 -3.050 28351 1096.87 19.6 -34.8 -8.7 0.04530 0.04260 0.04800 1687 parahippocampal
------ However, when I run the command to extract the raw data from these clusters using this line: mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0
The terminal window outputs this:
rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0
sysname Darwin
hostname N-Volunteer-iMac.local
machine x86_64
user user
UseRobust 0
Loading mc-z.abs.th13.sig.cluster.mgh
Loading y.mgh
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 4 segmentations
Computing statistics for each segmentation
0 -4 6849 6849.000
1 -2 5476 5476.000
2 -1 1687 1687.000
Reporting on 3 segmentations
Computing spatial average of each frame
0 1 2
Writing to mc-z.abs.th13.cluster.ocn.dat
mri_segstats done -----
So I get a .dat file that only has 3 columns, which does not match up to the 5 that I originally observed after the correction. If you could let me know what the problem is that would be greatly appreciated.
Thank you.
William