Hi,
Actually (sorry to clutter the list) I think this example shows the problem better.
# environment setup setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR cd $SUBJECTS_DIR source /usr/local/freesurfer/nmr-dev-env
# 1. showing that the ROI differs from the unrestricted version mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca \ --fwhm 4.6
mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca \ --fwhm 4.6
# 2. taking out smoothing, whole surface version is fuzzier, still nothing in ROI version mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca
mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca
# 1. showing that the ROI differs from the unrestricted version (nothing in ROI version) mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Com_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca \ --fwhm 4.6
mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca \ --fwhm 4.6
# 2. taking out smoothing: whole surface version is fuzzier, still nothing in ROI version mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Com_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca
mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca
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Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy@nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078
