Hi,

I have used a linear mixed model for longitudinal data analysis on a FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04.

I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape.

I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses.

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I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model.

I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email.

The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ).

Any idea what went wrong here?

Thank you!

Best regards, Knut Jørgen