Hello FreeSurfer Developers, I am attempting to repeat the group analysis with the tutorial data on FreeSurfer website, as described on the FsTutorial/GroupAnalysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). But I received an error message when running the mri_glmfit command lines.
At first, the command lines that I types: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh \—-cortex —glmdir xiuyi_lh.gender_age.glmdir Errors: MRISread(/Users/xiuyi/Documents/tutorial_data/buckner_data/tutorial_subjs/ group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex): could not open file No such file or directory mri_glmfit: could not read surface /Users/xiuyi/Documents/tutorial_data/ buckner_data/tutorial_subjs/group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex No such file or directory Then I changed the command lines, replacing "surf fsaverage lh.white" with "surf fsaverage lh". The exact command lines are: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh.white \—-cortex —glmdir xiuyi_lh.gender_age.glmdir The error message is: gdfReadHeader: reading gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 57.175 26.6006 Class Means of each Continuous Variable 1 genderFemale 59.1429 2 genderMale 55.0000 INFO: gd2mtx_method is dods *ERROR: Option fsaverage unknown.* I have searched the list and found this type of error has been reported by another person but no reply was found.(https://mail.nmr.mgh. harvard.edu/pipermail//freesurfer/2010-May/014401.html) 1) FreeSurfer Version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Flatform: macOS Sierra version 10:12 Thank you for your reply. Xiuyi
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