Dear FS experts,
I are analysing longitudinal data - the difference between 2 groups (1 and 2) with 2 time points for each group (0, 1 --all the same time interval: a month).
I followed http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
and with Jorge's early reply in http://www.mail-achive.com/freesurfer@nmr.mgh.harvard.edu/msg25750.html
(1)qdec.table.dat
fsid fsid-base time group
sub04_MR1 sub04 0 1
sub04_MR2 sub04 1 1
sub05_MR1 sub05 0 1
sub05_MR1 sub05 1 1
...
con01_MR1 con01 0 2
con01_MR1 con01 1 2
con01_MR1 con01 0 2
con01_MR1 con01 1 2
...
(2) mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape
(3) [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');
lhsphere=fs_read_surf('$FsDir/freesurfer/subjects/fsaverage/surf/lh.sphere');
lhcortex=fs_read_label('$FsDir/freesurfer/subjects/fsaverage/surf/lh.cortex.label');
(4)Qdec = fReadQdec('qdec.table.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
[M,Y,ni] = sortData(M,1,Y,sID);
X = [ones(length(M),1) M M(:,1).*M(:,2)];
But when I followed wiki,code[M,Y,ni]first, matrix X will be four columns:
1-A column of 1s(intercept term)
2-The time covariate (0s and 1s)
3-The group covariate (2s and 1s,but in my table group 1 in the first, I think maybe it upside down?So I used the code X before code[M,Y,ni],then it will be 1s and 2s)
4-The group and time interaction (It is also affected by the third column to change).
Is my use correct here? I think it will be influn
(5)Then I used voxel-wise mixed model analysis following Jorge's reply.
lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
F_lhstats = lme_mass_F(lhstats,CM);
(6)fs_write_fstats(F_stats,mri,'sig.mgh','sig');
How to do correction about the result 'sig.mgh'?
May I use lme_mass_FDR or lme_mass_FDR2? How to do?
And if I can have a file including clusters' massage like summary file?
I can't do a mri_glmfit-sim or mc-z in QDEC, and FDR in QDEC, maybe the t-value to high,there are nothing left.
Please give me some help.Thank you very much, and looking forward to your reply!