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