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| == Run mris_glm to compute contrast == | == Group Analysis command lines == |
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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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| 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: | Upon successful completion of the make_average_subject command you should have an average subject in your SUBJECTS_DIR. After successfully completing [wiki:Self:FsTutorial/CreateFsgdFile Exercise A.] and [wiki:Self:FsTutorial/CreateContrastVectors Exercise B.] you should have an FSGD file called my_gender_age.txt and a contrast file called age.mat, both in your SUBJECTS_DIR/stats directory . The following are sample commands, that can be used with the data, to complete a group analysis: |
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| 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 |
mris_preproc --fsgd my_gender_age.txt --target average --hemi lh -- meas thickness --out lh.my_gender_age.thickness.mgh |
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Once this completes, you can do the smoothing step: |
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| # 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 |
mri_surf2surf --hemi lh --s average --sval lh.my_gender_age.thickness.mgh --fwhm 10 --tval lh.my_gender_age.thickness.10.mgh |
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| 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. | |
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| Upon completion, make sure that the following files are available in the directory from which mris_glm was run by typing: | Once this is complete, you can move on to test your contrast vector: |
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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 |
mri_glmfit --y lh.my_gender_age.thickness.10.mgh --fsgd my_gender_age.txt --glmdir lh.my_gender_age.glmdir --pca --surf --average lh --C age.mat }}} |
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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 }}} in that directory. |
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| The commands are the same for the right hemisphere, replacing every '''lh''' with an '''rh'''. |
[wiki:FsTutorial top] | [wiki:FsTutorial/GroupAnalysis previous]
Group Analysis command lines
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 make_average_subject command you should have an average subject in your SUBJECTS_DIR. After successfully completing [wiki:FsTutorial/CreateFsgdFile Exercise A.] and [wiki:FsTutorial/CreateContrastVectors Exercise B.] you should have an FSGD file called my_gender_age.txt and a contrast file called age.mat, both in your SUBJECTS_DIR/stats directory . The following are sample commands, that can be used with the data, to complete a group analysis:
# For the left hemisphere mris_preproc --fsgd my_gender_age.txt --target average --hemi lh -- meas thickness --out lh.my_gender_age.thickness.mgh
Once this completes, you can do the smoothing step:
mri_surf2surf --hemi lh --s average --sval lh.my_gender_age.thickness.mgh --fwhm 10 --tval lh.my_gender_age.thickness.10.mgh
Once this is complete, you can move on to test your contrast vector:
mri_glmfit --y lh.my_gender_age.thickness.10.mgh --fsgd my_gender_age.txt --glmdir lh.my_gender_age.glmdir --pca --surf --average lh --C age.mat
The commands are the same for the right hemisphere, replacing every lh with an rh.