Dear Douglas,

Thank you very much for your rapid response. I have another question.

I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd.

However, in the FS Group Analysis tutorial, it says that you must include "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with recon-all with the -qcache option, which was my case. As I am doing longitudinal analyses, do I have to skip this option and just follow the Repeated Measures tutorial or do I have to include the --cache option?

Thank you very much.

Best regards,

Agurne

Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es

Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)

El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:

In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it.

On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
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Dear Freesurfer experts,

I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).

Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares.

I am trying to follow the tutorial MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova, but I have several doubts when designing the FSGD file as well as the contrasts.

How should it be the FSGD file?

I have seen in a previous post the following design for the same number fo groups and time points:

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables                                             Tp1vsTp2.GrExp    Tp1vsTp2.GrControl

Input Subject1_time1 Subject1         1                                 0

Input Subject1_time2 Subject1        -1                                0

Input   Subject2_time1 Subject2         0                                 1

Input Subject2_time2 Subject02      0                                 -1

Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1

Contrasts (.mtx files):

Tp1vsTp2.GrExp 0 0 1 0

Tp1vsTp2.GrControl 0 0 0 -1

Interaction 0 0 1 -1

Would this design be the correct one to use in this case?

Alternatively, could it be this the correct one?

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables                                             Tp1vsTp2          Groupxtime

Input Subject1_time1 Subject1         1                                1

Input Subject1_time2 Subject1        -1                               -1

Input   Subject2_time1 Subject2         1                                -1

Input Subject2_time2 Subject02      -1                              1

Design matrix:

1 0 1 1

1 0 -1 -1

0 1 1 -1

0 1 -1 1

Contrasts (.mtx files):

Tp1vsTp2        0 0 1 0

Groupxtime Interaction 0 0 0 1

Thank you very much in advance.

Kind regards,

Agurne

Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es

Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
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