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