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
--
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
http://nmr.mgh.harvard.edu/manoachlab
--
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
http://nmr.mgh.harvard.edu/manoachlab