Dear Freesurfer team I am still trying to run a glm analysis between 2 surfaces but I am having weird results so I guess I missed something. So I sampled a DTI surface 2mm below the WM surface, and another intracortical surface (T2* actually) at 75% depth from the pial surface. The question I'd like to investigate is: is there a spatial relationship between DTI metrics below the WM surface and intracortical metrics here DTI in a patient population. So I run glm_fit with -pvr option. My design matrix has 2 classes (male and female) and 1 variable (age) that I entered as covariates. Here is the command: mri_glmfit --y lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh --pvr lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2

--y input is the T2* surfaces for each subject concatenated -- pvr input is the DTI surface below the WM for each subject concatenated

I wasn't so sure about the contrast, as I have 2 class, 1 variable + the pvr regressor I thought I would need 6 values (0 0 0 0 0 1) but I got an error about the contrast saying I should put 5 factors so my contrast is 0 0 0 0 1, to test the slope between T2* and DTI at each vertex, after taking into account gender and age.

The output sig.mgh doesn't give me any significant result, even at the lowest possible threshold.

So my first question would be: is it fine to correlate different surfaces that were not build at the same depth? And the 2nd question would be: is the contrast correct to test the correlation between the 2 surfaces at each vertex?

Thanks a lot for your help Celine

PS: here is the terminal output:

gdfReadHeader: reading ms_age_gender.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 43.1176 9.02534 Class Means of each Continuous Variable 1 F 43.0435 2 M 43.2727 INFO: gd2mtx_method is dods Reading source surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti cmdline mri_glmfit --y lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh --pvr lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2 sysname Linux hostname panarea machine x86_64 user celine FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh logyflag 0 usedti 0 FSGD ms_age_gender.fsgd labelmask /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/label/lh.cortex.label maskinv 0 glmdir t20.75_L1-2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory t20.75_L1-2 Loading y from /autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh INFO: gd2mtx_method is dods Saving design matrix to t20.75_L1-2/Xg.dat Normalized matrix condition is 117.356 Matrix condition is 121295 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 2487 voxels in mask Saving mask to t20.75_L1-2/mask.mgh Reshaping mriglm->mask... search space = 1064.228206 DOF = 29 Starting fit and test Fit completed in 0.0014 minutes Computing spatial AR1 on surface Residual: ar1mn=0.602743, ar1std=0.415130, gstd=0.568767, fwhm=1.339345 Writing results lh_age_gender_pvr maxvox sig=4.08 F=20.9043 at index 63635 0 0 seed=1384618381 mri_glmfit done