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