Sorry, there is nothing here (ie, no fsgd file, no images). Did you mean to attached?
On 7/10/2024 5:31 AM, Josefine Tingdal Taube Danielsen wrote:
External Email - Use Caution
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:
- Have we been using the right contrasts?
- Do the results look realistic?
- 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
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