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Hi Freesurfer support, 

 

I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64. freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460.


I'm trying to run longitudinal analysis using Repeated Measures Anova (https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova). 


My study has 2 groups (MM=patient group and HC=healthy controls) and 2 time points (1 and 2). I am looking at cortical thickness and cortical volume. 


Here is some information:


We have been using these Contrast files:

# Create 1-vs-2 contrast file

echo "0 0 1" > 1-vs-2.mtx

# Create group-effect contrast file
echo "0 1 0" > group-effect.mtx

# Create interaction contrast file
echo "0 1 -1" > interaction.mtx

# Create mean contrast file
echo "1 0 0" > mean.mtxfree

And then followed this:

Preproc using FSGD

mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd


Smooth data

mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.mgh --tval lh.thickness.sm05.mgh


Run GLM fit

mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss \
  --C 1-vs-2.mtx --C group-effect.mtx --C interaction.mtx --C mean.mtx \
  --surface fsaverage lh

This was our results:
INFO: gd2mtx_method is doss Reading source surface /mnt/c/CogimmunStudy/FS/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.4.1 cwd /mnt/c/CogimmunStudy/FS cmdline mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C 1-vs-2.mtx --C group-effect.mtx --C interaction.mtx --C mean.mtx --surface fsaverage lh sysname Linux hostname D56979 machine x86_64 user josdan FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/c/CogimmunStudy/FS/lh.thickness.sm05.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /mnt/c/CogimmunStudy/FS/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory lh.rmanova Loading y from /mnt/c/CogimmunStudy/FS/lh.thickness.sm05.mgh ... done reading. INFO: gd2mtx_method is doss Saving design matrix to lh.rmanova/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 3.15 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149955 voxels in mask Saving mask to lh.rmanova/mask.mgh Reshaping mriglm->mask... search space = 74612.577841 DOF = 123 Starting fit and test Fit completed in 0.0220333 minutes Computing spatial AR1 on surface Residual: ar1mn=0.986733, ar1std=0.003725, gstd=3.501824, fwhm=8.246166 Writing results 1-vs-2 maxvox sig=-2.06583 F=7.13254 at index 102162 0 0 seed=1720706961 Computing efficiency group-effect maxvox sig=114.013 F=8295.3 at index 155689 0 0 seed=1720706961 Computing efficiency interaction maxvox sig=106.775 F=6297.15 at index 64378 0 0 seed=1720706961 Computing efficiency mean maxvox sig=133.337 F=17231.6 at index 155689 0 0 seed=1720706961 Computing efficiency mri_glmfit done

Now our questions:

  1. Have we been using the right contrasts?
  2. Do the results look realistic?
  3. Is it possible to have some more information about results (e.g. summary, areas being significant, visualization, sig.mgh, t-values, p-values not i -log10)?

Thank you!

Best, 
Josefine Danielsen