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
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