Dear Freesurfer experts,

I am conducting a cortical thickness study in three groups. After performing the between-group analyses, I would like to evaluate the possible correlation between cortical thickness and the levels of some csf measures. To do this I included one column in the FSGD file

GroupDescriptorFile 1
Title OSGM
Class N
Class AD_PREC
Class AD_PLUS
Variables CSF_A_measure
Input 4048 N 1730.00
Input 4102 N 2217.00
Input 4122 PREC 652.00
Input 4146 PREC 695.00
Input 4198 PREC 938.00
Input 5049 AD_PLUS 909.00
Input 5080 AD_PLUS 987.00
Input 5096 AD_PLUS 942.00
Input 5101 AD_PLUS 881.00

Input 5232 AD_PLUS 715.00

And so on....

In order to test the possible positive relation between the CSF_A_measure and the cortical thickness, that is, does the correlation between thickness and csf_A_measure differ from zero?, I would use the following vector and commands for the left hemisphere.

Question 1. Please, can you verify if this vector and commands are correct.

correlation_vector.mtx -----> 0 0 0 1 1 1

mris_preproc --fsgd J3.fsgd \
--cache-in thickness.fwhm10.fsaverage \
--target fsaverage \
--hemi lh \
--out lh_J3G_thickness.10.mgh \

mri_glmfit \
--y lh_J3G_thickness.10.mgh \
--fsgd J3.fsgd \
--C correlation_vector.mtx \
--surf fsaverage lh \
--cortex \
--glmdir 01_lh_thickness_results\

mri_glmfit-sim \
--glmdir 01_lh_thickness_results \
--sim mc-z 10000 2.3 mc-z.pos \
--sim-sign pos --cwpvalthresh 0.05\
--2spaces --overwrite \

Question 2: I tried to run these commands with the permutation method but the terminal gave to me a warning message saying that the matrix is not orthogonal and if I really want to run the analysis I should add the --perm-force argument, in this case should I use other method or can I use the --perm-force safetely?.

Thank you very much for your help in advance.

Best regards,

Steve,