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