Dear Martin,

Yes I think so, and I run the mri_glmfit with fsaverage as the subject like:

mri_glmfit --glmdir lh.thickness.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C tp1-vs-tp2.mtx --C tp1-vs-tp3.mtx --C tp2-vs-tp3.mtx --C tp-effect.mtx --C mean.mtx --surf fsaverage lh

it reports:

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y /Freesurfer/k/lh.thickness.sm05.mgh

logyflag 0

usedti 0

FSGD rmanova.fsgd

labelmask /Freesurfer//fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.thickness.rmanova

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.thickness.rmanova

Loading y from /Freesurfer/k/lh.thickness.sm05.mgh

INFO: gd2mtx_method is doss

Saving design matrix to lh.thickness.rmanova/Xg.dat

Normalized matrix condition is 1.73205

Matrix condition is 1.73205

Found 149955 points in label.

Pruning voxels by thr: 0.000000

Found 149955 voxels in mask

Saving mask to lh.thickness.rmanova/mask.mgh

Reshaping mriglm->mask...

search space = 74612.965197

DOF = 0

ERROR: DOF = 0

It seems still something wrong was ignored.

Also if I call the preproc or surf2surf commands with the base subject, i.e. k, instead of fsaverage, will it work? or even better?

mris_preproc --target k --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd

mri_surf2surf --s k --hemi lh --fwhm 5 --sval lh.thickness.mgh --tval lh.thickness.sm05.mgh

Thanks,

Kaiming

On Thu, Jan 30, 2014 at 3:18 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Your data was probably mapped to fsaverage when you call the preproc or surf2surf commands? If so you should specify fsaverage as the subject nane.

Best Martin

Sent via my smartphone, please excuse brevity.

-------- Original message --------
From: Kaiming Yin
Date:01/29/2014 9:07 PM (GMT-05:00)
To: FreeSurfer Mailing List
Subject: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi"

Dear FreeSurfer guys,

I am using longitudinal processing stream and with the RepeatedMeasuresAnova.

I follow the instruction here from http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova

my fsgd file is:

GroupDescriptorFile 1

Title k_longitudinal

Class k

Variables TP1-vs-TP2 TP1-vs-TP3

Input k_1 k 1 1

Input k_2 k -1 0

Input k_3 k 0 -1

contrasts is:

tp1-vs-tp2.mtx tp1-vs-tp3.mtx tp2-vs-tp3.mtx tp-effect.mtx mean.mtx
0 1 0 0 0 1 0 -1 1 0 1 0 1 0 0

0 0 1

I run the mris_preproc and mri_surf2surf commands as the same for left hemi thickness,

but when I run the mri_glmfit command it reports "ERROR: you must use '--surface subject hemi' with surface data". if i add the flag as:

mri_glmfit ...(as the same before)... --surface k lh

or --surface k lh thickness

or --surface k_1.long.k lh

or --surface k_1.long.k lh thickness

or --surface k_1 lh

or --surface k_1 lh thickness

it still goes wrong and even not make an output folder.

Any problems there?

thanks,

Kaiming

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