Hi Livia,
groups should be 0 and 1, e.g. 0 for controls, 1 for disease.
Order of groups does not matter (as long as both X and Y are ordered that way).
You can do FDR or FDR2 on your final sig values. It is best to combine results from left and right hemisphere and do a single FDR2 correction. This is described at the end of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
Best, Martin
On 6. Jun 2017, at 04:24, Livia Liu livialiu333@gmail.com wrote:
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 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 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!
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