Dear freesurfer experts and users
At the moment our group is working on longitudinal analyses for two different time points in one group. Our analyses worked well and we tried to calculate the effects of six different covariates and one fix moderator variable (we had two different MRI Scanner and tried to consider this effect) with the function mri_glmfit. We did pre-processing with mri_preproc:
mris_preproc --fsgd extra_komplett.fsgd --cache-in long.thickness-rate.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.extra_komplett.thickness.10.mgh
With the fsgd-File designed like the following example:
GroupDescriptorFile 1
Title G1V2
Class Scannertyp-Main
Variables z1 z2 z3 z4 z5 z6
Input P01 Scannertyp-Main T3 z11 z21 z31 z41 z51 z61
Because of the consideration of the variable Scanner we designed the design matrix on our own. Before calculating the effect of the covariates we calculated the main effect (for the assumed underlying regression model please refer to equation number 1 in the attached pdf). For doing this we built a contrast file (please refer to equation 2). In a longer discussion we decided to delete different covariates and get the regression model shown in equation 3 (and the contrast file for the main effect in equation 4). Surprisingly both main effects not even were similar. Therefore we tried two different models (please refer to equation 5 and 7 for the two regression models). If the underlying model is a normal linear model the first three Contrasts and regression models should gave the same results. In our analyses we have really different results, therefore we have problems in interpreting and understanding the underlying general linear model. There seems to be still an influence of the covariates even if there are modeled with 0 (which in our understanding means they were mathematically not included in the model). Is the probability dependent on the distribution of the covariates even if they are modeled with no influence? If so, how is the belonging regression model?
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
Can you help us in fixing this theoretical problem?
Thanks in advance!
Sandra
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