#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
Fsgd file 1:pairs.fsgd
GroupDescriptorFile 1
Class ADEX
Input 1000_1 ADEX
Input 1000_2 ADEX
Input 1001_1 ADEX
Input 1001_2 ADEX
Input 1003_1 ADEX
Input 1003_2 ADEX
Input 1005_1 ADEX
Input 1005_2 ADEX
Input 1008_1 ADEX
Input 1008_2 ADEX
Input 1013_1 ADEX
Input 1013_2 ADEX
Input 1014_1 ADEX
Input 1014_2 ADEX
Fsgd file 2: paired_diff.fsgd
GroupDescriptorFile 1
Class ADEX
Variables Age
Input 1000 ADEX 72
Input 1001 ADEX 76
Input 1003 ADEX 72
Input 1005 ADEX 80
Input 1008 ADEX 72
Input 1013 ADEX 80
Input 1014 ADEX 80