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| Follow these steps to run mris_glm for computing contrasts: | In order to compute the contrats you will first need to change to the tutorial data directory and setup SUBJECTS_DIR: |
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# change to the tutorial data directory and setup SUBJECTS_DIR: cd $FREESURFER_HOME/subjects/buckner_public_distribution/FsTutorialDataSet/group_analysis_tutorial |
cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial |
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}}} Change into the directory you ran the estimation step in, most likely called 'stats': {{{ |
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--beta_in ./beta_doss-thickness-100lh bfloat \ --var_in ./var_doss-thickness-100lh.w paint \ |
--beta_in ./beta_doss-thickness-100lh.mgz \ --var_in ./var_doss-thickness-100lh.mgz \ |
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--ces ./ces_Age_doss-thickness-100lh.w paint \ --t ./t_Age_doss-thickness-100lh.w paint \ --sigt ./sigt_Age_doss-thickness-100lh.w paint |
--ces ./ces_Age_doss-thickness-100lh.mgz \ --t ./t_Age_doss-thickness-100lh.mgz \ --sigt ./sigt_Age_doss-thickness-100lh.mgz |
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--beta_in ./beta_doss-thickness-100rh bfloat \ --var_in ./var_doss-thickness-100rh.w paint \ |
--beta_in ./beta_doss-thickness-100rh.mgz \ --var_in ./var_doss-thickness-100rh.mgz \ |
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--ces ./ces_Age_doss-thickness-100rh.w paint \ --t ./t_Age_doss-thickness-100rh.w paint \ --sigt ./sigt_Age_doss-thickness-100rh.w paint |
--ces ./ces_Age_doss-thickness-100rh.mgz \ --t ./t_Age_doss-thickness-100rh.mgz \ --sigt ./sigt_Age_doss-thickness-100rh.mgz |
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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-100lh.mgz ls -l t_Age_doss-thickness-100lh.mgz ls -l sigt_Age_doss-thickness-100lh.mgz |
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ls -l ces_Age_doss-thickness-100rh.w ls -l t_Age_doss-thickness-100rh.w ls -l sigt_Age_doss-thickness-100rh.w |
ls -l ces_Age_doss-thickness-100rh.mgz ls -l t_Age_doss-thickness-100rh.mgz ls -l sigt_Age_doss-thickness-100rh.mgz |
[wiki:FsTutorial top] | [wiki:FsTutorial/GroupAnalysis previous]
Run mris_glm to compute contrast
In order to compute the contrats you will first need to change to the tutorial data directory and setup SUBJECTS_DIR:
cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial
setenv SUBJECTS_DIR ${PWD}Change into the directory you ran the estimation step in, most likely called 'stats':
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.mgz \
--var_in ./var_doss-thickness-100lh.mgz \
--gcv 0 0 1 \
--ces ./ces_Age_doss-thickness-100lh.mgz \
--t ./t_Age_doss-thickness-100lh.mgz \
--sigt ./sigt_Age_doss-thickness-100lh.mgz# For the right hemisphere
mris_glm --hemi rh \
--trgsubj average \
--fsgd ./my_gender_age_fsgd.txt doss \
--beta_in ./beta_doss-thickness-100rh.mgz \
--var_in ./var_doss-thickness-100rh.mgz \
--gcv 0 0 1 \
--ces ./ces_Age_doss-thickness-100rh.mgz \
--t ./t_Age_doss-thickness-100rh.mgz \
--sigt ./sigt_Age_doss-thickness-100rh.mgz 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.mgz ls -l t_Age_doss-thickness-100lh.mgz ls -l sigt_Age_doss-thickness-100lh.mgz ls -l ces_Age_doss-thickness-100rh.mgz ls -l t_Age_doss-thickness-100rh.mgz ls -l sigt_Age_doss-thickness-100rh.mgz
in that directory.