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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,