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Dear all,
I am currently running a Mass-Univariate LME analysis in Freesurfer. I have
some doubts about the last steps and I was wondering whether someone could
help me figure them out and also check what I have done so far (sorry for
the long email).
My study has 2 time points (baseline, follow-up), 3 groups (controls,
patients without cognitive problems, patients with cognitive problems) and
2 covariates of no interest (age, sex).
I am interested in looking at the interactions between group and time
(mainly whether the 2 patient groups show more cortical thinning over time
compared to controls).
These are the commands I have ran so far through terminal or in matlab:
1)
mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh
--meas thickness --out lh.thickness.mgh
mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi rh
--meas thickness --out rh.thickness.mgh
2)
mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval
lh.thickness_sm15.mgh --fwhm-trg 15 --cortex --noreshape
mri_surf2surf --hemi rh --s fsaverage --sval rh.thickness.mgh --tval
rh.thickness_sm15.mgh --fwhm-trg 15 --cortex --noreshape
3)
[Y,mri] = fs_read_Y('lh.thickness_sm15.mgh');
[Y,mri] = fs_read_Y('rh.thickness_sm15.mgh');
4)
lhsphere = fs_read_surf('fsaverage/surf/lh.sphere')
rhsphere = fs_read_surf('fsaverage/surf/rh.sphere')
lhcortex = fs_read_label('fsaverage/label/lh.cortex.label')
rhcortex = fs_read_label('fsaverage/label/rh.cortex.label')
5) Create X matrix in matlab, here is a sample:
intercept time group2 group2*time group3 group3*time
age sex
1 0 0 0 0
0 41 1
1 2.42 0 0 0
0 41 1
1 0 1 0 0
0 53 1
1 2.5 1 2.5 0
0 53 1
1 0 0 0 0
0 54 2
1 5.25 0 0 0
0 54 2
5)
lhstats = lme_mass_fit_vw(X, [1], Y, ni, lhcortex);
rhstats = lme_mass_fit_vw(X, [1], Y, ni, rhcortex);
6)
I entered 3 contrasts separately to check the interaction group*time.
CM.C1 = [0 0 0 1 0 0 0 0]; this contrast will show if group 1 and 2 show a
different cortical thinning pattern over time
CM.C2 = [0 0 0 0 0 1 0 0]; this contrast will show if group 1 and 3 show a
different cortical thinning pattern over time
CM.C3 = [0 0 0 -1 0 1 0 0]; this contrast will show if group 2 and 3 show a
different cortical thinning pattern over time
7)
For each of the previous contrasts, i did the following:
F_lhstats = lme_mass_F(lhstats, CM);
F_rhstats = lme_mass_F(rhstats, CM);
fs_write_fstats(F_lhstats, mri,' sigL.mgh', 'sig');
fs_write_fstats(F_rhstats, mri,' sigR.mgh', 'sig');
mri.volsz(4) = 1
[detvtx,sided_pval,pth] =
lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0);
[detvtx,sided_pval,pth] =
lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);
8)
fs_write_Y(sided_pval,mri,'spval_lh.mgh');
fs_write_Y(sided_pval,mri,'spval_rh.mgh');
mri_surfcluster --subject fsaverage --hemi lh --in spval_lh.mgh
--cwpvalthresh 0.05 --fdr 0.05 --sign pos --o lh_time_cluster --sum
lh_time_cluster_sum
mri_surfcluster --subject fsaverage --hemi rh --in spval_rh.mgh
--cwpvalthresh 0.05 --fdr 0.05 --sign pos --o rh_time_cluster --sum
rh_time_cluster_sum
*My questions are:*
- Is the order of the steps (1-8) correct?
- How can I visualize the significant FDR-corrected results?
- Is there any way I can apply a Monte Carlo correction using the generated
files?
Thank you so much!
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