try
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.cluster.ocn.dat --excludeid 0
On 10/17/2018 12:57 AM, WON JONG CHWA wrote:
>
> External Email - Use Caution
>
> 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 1.30
> # CSD nreps 1
> # CSD simtype null-z
> # CSD contrast NA
> # CSD confint 90.00
> # 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
> 0.0 0.00020 3745 superiortemporal
> 2 -4.419 146292 2658.98 19.8 52.0 -5.7 0.00010
> 0.0 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
>
> sysnameDarwin
>
> hostname N-Volunteer-iMac.local
>
> machinex86_64
>
> useruser
>
> UseRobust0
>
> Loading mc-z.abs.th13.sig.cluster.mgh
>
> Loading y.mgh
>
> Voxel Volume is 1 mm^3
>
> Generating list of segmentation ids
>
> Found4 segmentations
>
> Computing statistics for each segmentation
>
> 0-468496849.000
>
> 1-254765476.000
>
> 2-116871687.000
>
> Reporting on3 segmentations
>
> Computing spatial average of each frame
>
> 012
>
> 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
