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Run mris_glm to compute contrast

Follow these steps to run mris_glm for computing contrasts: 

# change to the tutorial data directory and setup SUBJECTS_DIR:
cd $FREESURFER_HOME/subjects/buckner_public_distribution/FsTutorialDataSet/group_analysis_tutorial
setenv SUBJECTS_DIR ${PWD}
cd stats

Upon successful completion of the estimation step (computed in a prior exercise), mris_glm may be configured on command line with proper options to perform contrast computation: 

# For the left hemisphere
mris_glm --hemi lh \
         --trgsubj average \
         --fsgd ./my_gender_age_fsgd.txt doss \
         --beta_in ./beta_doss-thickness-100lh bfloat \
         --var_in ./var_doss-thickness-100lh.w paint \
         --gcv 0 0 1 \
         --ces ./ces_Age_doss-thickness-100lh.w paint \
         --t ./t_Age_doss-thickness-100lh.w paint \
         --sigt ./sigt_Age_doss-thickness-100lh.w paint

# For the right hemisphere
mris_glm --hemi rh \
         --trgsubj average \
         --fsgd ./my_gender_age_fsgd.txt doss \
         --beta_in ./beta_doss-thickness-100rh bfloat \
         --var_in ./var_doss-thickness-100rh.w paint \
         --gcv 0 0 1 \
         --ces ./ces_Age_doss-thickness-100rh.w paint \
         --t ./t_Age_doss-thickness-100rh.w paint \
         --sigt ./sigt_Age_doss-thickness-100rh.w paint

With the above configuration, mris_glm tests the given subjects for straight correlation between thickness and age. The command will read in the regression coefficients (--beta_in) and noise variance (--var_in) that were generated from the estimation process, and save the contrast effect size (ces), t-ratio of the contrast, and the significance of the t-ratio (i.e., t-test) in the same directory, all in paint format.

Upon completion, make sure that the following files are available in the directory from which mris_glm was run by typing: 

ls -l ces_Age_doss-thickness-100lh.w
ls -l t_Age_doss-thickness-100lh.w
ls -l sigt_Age_doss-thickness-100lh.w

ls -l ces_Age_doss-thickness-100rh.w
ls -l t_Age_doss-thickness-100rh.w
ls -l sigt_Age_doss-thickness-100rh.w

in that directory.