Hi Claudia, it is better to post these things to the freesurfer list as martinos-tech is no longer active. The total cortical surface area (65416.6mm2) is incorrect. The total should be 82219.960938. The reported value is the actual surface area of the fsaverage white surface. However, the average white surface has a much lower surface area than areas of any of the input subjects because the surface coordinate averaging causes minor folding to be smoothed out. To get around this, we keep track of the average surface area of the input subjects (rather than the surface area of the average surface, if that is not too confusing). The size of the cluster reported (76467.08mm2) is accurate.
doug
On 09/12/2016 07:52 AM, Claudia Dacquino claudia.dacquino@gmail.com [martinos-tech] wrote:
Hi all,
I've run GLM surface analysis and I've got a summary table like this:
# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
# $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
# CreationTime 2016/09/12-08:47:18-GMT
# cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th40/mc-z.csd --mask lh.Compr.glmdir/mask.mgh --cwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat --cwpvalthresh 0.05 --o lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white
# cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts
# sysname Linux
# hostname Piras-TC2
# machine x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh
# Frame Number 0
# srcsubj fsaverage
# hemi lh
# surface white
# annot aparc
# SUBJECTS_DIR /media/TREKSTOR/SUBJ
# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149953
# Bonferroni 2
# Minimum Threshold 4
# Maximum Threshold infinity
# Threshold Sign pos
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold 0 mm^2
# CSD thresh 4.000000
# CSD nreps 10000
# CSD simtype null-z
# CSD contrast NA
# CSD confint 90.000000
# Overall max 1e+10 at vertex 3
# Overall min 0 at vertex 8
# NClusters 1
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 0
#
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 0.00000 0.00040 149953 rostralmiddlefrontal
Is it possible to have a Cluster Size (76467.08 mm2) greater than the Total Cortical Surface (65416.6 mm2).
Are there some errors in this?
Thanks a lot to all of you.
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di Neuropsichiatria
Dipartimento di Neurologia Clinica e Comportamentale
IRCCS Fondazione Santa Lucia
via Ardeatina 306 - 00179 Roma
Tel. +39 (0)6 51501358
Fax +39 (0)6 51501575
web: http://www.neuropsichiatrialab.com http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli
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Posted by: Claudia Dacquino claudia.dacquino@gmail.com
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