Dear Dr. Greve: Hooray! All has run successfully for the Paired Analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis).

I used the [1 0] contrast to examine whether there are different within-group changes in brain structure for an Intervention (PA) and Control (C) group..

After running —

(Full terminal output below)

Will you help me read the output of mri_glmfit? I am not sure what to check for results. Are the results corrected for multiple comparisons? THANKS.

gdfRead(): reading paired-diff.fsgd
INFO: ignoring tag subs 
INFO: gd2mtx_method is dods
Reading source surface /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65416.984375
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt
cmdline mri_glmfit.bin --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh 
sysname  Darwin
hostname laurachaddock.vp.illinois.edu
machine  x86_64
user     laurachaddock
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD paired-diff.fsgd
labelmask  /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired-diff
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired-diff
Loading y from /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
  ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to lh.paired-diff/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.29787
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149946 voxels in mask
Saving mask to lh.paired-diff/mask.mgh
Reshaping mriglm->mask...
search space = 74607.309418
DOF = 106
Starting fit and test
Fit completed in 0.0936 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.984663, ar1std=0.005741, gstd=3.255205, fwhm=7.665423
Writing results
 mean
   maxvox sig=3.95093  F=16.1054  at  index 115412 0 0    seed=1563757270
mri_glmfit done
bash-3.2$