Thanks, but I not understand if the follow step that you suggested me should be used also for FS-FAST analysis.

Specifically, I'm refferring to:

1Sample each individual's surface onto the average surface. 
2Compute the difference between each of the pairs in the average surface space. 
3Concatenate the differences into one file. 
4Smooth on the surface (optional)
5Perform analysis with mri_glmfit on this file

Importantly, should I create the two fsgd files as reported in the web page and below? Or only the second is due?

One is:
GroupDescriptorFile 1
Class Main
Input subject1      Main
Input subject1match Main
Input subject2      Main
Input subject2match Main
Input subject3      Main
Input subject3match Main
Input subject3      Main
Input subject3match Main

the other is:
GroupDescriptorFile 1
Class Main
Variables Age
Input subject1pair   Main 30
Input subject2pair   Main 40
Input subject3pair   Main 50
Input subject4pair   Main 60

Thanks

Regards


Stefano
----Messaggio originale----
Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
Data: 18-set-2017 0.13
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] FS-FAST longitudinal analyis

That looks correct. You can also checkout the instructions here:

https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis


On 9/17/17 6:07 PM, stdp82@virgilio.it wrote:
Hi list,

I'm not sure that the files reported below are correct to assess the longitudinal difference between T1 and T2.
Please, could you check it? The result which I have obtained bu running mri_glmfit is too strange.
Thanks
Best regards
Stefano

1) PAIRWISE.fsgd file
-------------------
GroupDescriptorFile 1
Class subj1
Class subj2
...
Class subjN
Variables TP1-vs-TP2
Input subj1_tp1 subj1 1
Input subj1_tp2 subj1 -1
Input subj2_tp1 subj2 1
Input subj2_tp2 subj2 -1
...
Input subjN_tp1 subjN 1
Input subjN_tp2 subjN -1
----------------------------

2) mean.mtx
1 1 ... 1 0
------------------------------
3) tp-effect.mtx
0 0 ... 0 1
------------------------------
4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd PAIRWISE.fsgd doss --C mean.mtx --C tp-effect.mtx


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