Hi Dusan,
On the RepeatedMeasuresAnova page you sent, the last command doesn't include the --surface flag. You can try running your command without that part:
mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd doss --C contrast.mtx --C contrast2.mtx --C mean.mtx
Best, Lee
On Tue, 29 Sep 2015, Dusan Hirjak wrote:
Dear Freesurfer Experts, I am trying to run a longitudinal analysis. I have done the first three steps of the analysis. Now, I am trying to visualize my results.
However, I am having trouble doing the last step of the analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
bash-3.2$ mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd doss --surface lh.thickness.sm15.mgh --C contrast.mtx --C contrast2.mtx --C mean.mtx
gdfReadHeader: reading long.table.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 TP1-vs-TP2 0 1
Class Means of each Continuous Variable
1 Subject1 0.0000
2 Subject2 0.0000
3 Subject3 0.0000
4 Subject4 0.0000
5 Subject5 0.0000
6 Subject6 0.0000
7 Subject7 0.0000
8 Subject8 0.0000
9 Subject9 0.0000
10 Subject10 0.0000
11 Subject11 0.0000
INFO: gd2mtx_method is doss
Reading source surface /users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx
MRISread(/users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx): could not open file
Not a directory
mri_glmfit: could not read surface /users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx
Not a directory
Any suggestions what I should do??? I dont understand what/which surface shoul I use?
Many thanks!
Dusan