Dear Experts,
I have run GLM group analyses with Freesurfer tools according DODS
model, with six classes ((Male,Female) ; (Control,Left,Right)) and one
age variable :
/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age
/However, I would like to consider gender as covariable of my GLM
design. So, should I as done consider gender as discret factor and part
of CLASS/group or should I consider gender as a continuous variable (0 =
male, 1 = female) and add a column on the Variables line of the FSGD
file near Age (/Variables Age Gender) ?
/Many thanks in advance for helping !
Best regards,
Matthieu/
/
On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:
Hello,
I have run GLM group analyses with Freesurfer tools according DODS
model, with six classes ((Male,Female) ; (Control,Left,Right)) and
one age variable :
/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age /
I wanted to test /Control > Left/ and /Control > Right/ on CBF maps.
I defined with help of the tutorial contrats for that :
/control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0
control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0
control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5/
My problem is that I don't know how to interpret significative
results in both /Control > Left /contrasts/:
//control-left.intercept.mtx /and///control-left.slope.mtx. /The same
for/Control > Right./ One is coding for intercept and the other for
slope, but concretely what significative results in both contrasts mean ?
Thank you in advance for helping !
Best regards,
-------------------------------------
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-11 16:51 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
the sig value is actually -log10(p)*sign(gamma) where gamma
is the
contrast (gamma.mgh). The p-value is two-tailed, and the color
indicates
what tail you are on.
doug
On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
> Dear FreeSurfer's experts,
>
> I have launched a GLM analyses following the tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
> Below the command I have used :
>
> /mri_glmfit \
> --y
>
${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
> \
> --fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
> --C
${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
> --surf fsaverage lh \
> --cortex \
> --glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
>
>
> In order to see the uncorrected results with p<.0001, I ran :
>
> /freeview -f
>
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
> -viewport 3d/
>
> However, nothing appears with this threshold and when I wanted to
> configure overlay I saw that most of my values in /sig.mgh /were
> negatives between -4 and 0...
>
> How is possible for /-log10(pvalue)/ values ? Could I obtain
> significant uncorrected values from this /sig.mgh/ file ?
>
> Please find attached my needed files : *y.fsgd, mri_glmfit.log,
> **/control-left.intercept.mtx/ and sig.mgh *
>
> Thank you in advance for helping me !!
>
> Best regards,
>
> -------------------------------------
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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