Hi.  I have a question about cluster size determination within Freesurfer.

 

We are running linear mixed model on our Freesurfer generated volume data over the left and right cortex parcellations, and would like to look at cluster size at the p < 0.01 cluster-forming threshold level.

 

1)      After running the models, we have created a .mgh image of the F-stats results, separately for the negative and positive results, saving them with fs_write_Y.

2)      We then run these data through mri_surfcluster, which reports the maximum cluster size of 216 voxels.  This was run with the command:

 

a.       mri_surfcluster --hemi lh --in F_lhstats.mgh --o F_lhstats _negCluster.mgh --subject fsaverage --thmin 6.8 --sign pos

b.       The “sign” is set to positive because this is running on F-numbers.

 

3)      Next, we run mri_segstats on the output of the last command to get the location and sizes of the individual clusters, as follows:

a.       mri_segstats --seg F_lhstats _negCluster.mgh --annot lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt

 

The problem is that this is the output of that file (F_lhstats_negCluster.txt):

 

# Title Segmentation Statistics

#

# generating_program mri_segstats

# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $

# cmdline mri_segstats --seg F_lhstats_negCluster.mgh --annot lh.aparc.annot lh parc --slabel fsaverage lh --seg --sum F_lhstats_negCluster.txt

# sysname  Linux

# hostname loginnode2

# machine  x86_64

# user     mwagshul

# anatomy_type volume

#

# SUBJECTS_DIR /home/mrrc-all/MRE_LAB/Holtzer/QdecAnalysis

# subjectname fsaverage

# SegVolFile F_lhstats_negCluster.mgh

# SegVolFileTimeStamp  2019/07/18 11:21:52

# Annot fsaverage lh parc

# Label fsaverage lh --seg

# ExcludeSegId

# Only reporting non-empty segmentations

# VoxelVolume_mm3 1

# TableCol  1 ColHeader Index

# TableCol  1 FieldName Index

# TableCol  1 Units     NA

# TableCol  2 ColHeader SegId

# TableCol  2 FieldName Segmentation Id

# TableCol  2 Units     NA

# TableCol  3 ColHeader NVoxels

# TableCol  3 FieldName Number of Voxels

# TableCol  3 Units     unitless

# TableCol  4 ColHeader Volume_mm3

# TableCol  4 FieldName Volume

# TableCol  4 Units     mm^3

# TableCol  5 ColHeader StructName

# TableCol  5 FieldName Structure Name

# TableCol  5 Units     NA

# NRows 8

# NTableCols 5

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName

  1   0    161454   161454.0  Seg0000

  2   6       524      524.0  Seg0006

  3   7       897      897.0  Seg0007

  4   8       413      413.0  Seg0008

  5   9       311      311.0  Seg0009

  6  10       165      165.0  Seg0010

  7  11        61       61.0  Seg0011

  8  12        17       17.0  Seg0012

 

This clearly is reporting clusters larger than the 216 voxels reported by mri_surfcluster.  Hope someone can help us figure out the discrepancy here, thanks!

 

(As an aside, what are we doing wrong with the mri_segstats command which is not printing out the actual anatomical locations for each cluster?).

 

Mark

 

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: mark.wagshul@einstein.yu.edu

 

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