On 7/13/2019 11:47 AM, FAST Study wrote:

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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 — mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh (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. It is not corrected for multiple comparisons. Use mri_glmfit-sim (there is a tutorial for this). At this point, you can either do multiple comp corrections or visualize the uncorrected maps. There is not a lot to talk about in the terminal output.

mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh 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.eduhttp://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$

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