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 MaleControlClass MaleLeftClass MaleRightClass FemaleControlClass FemaleLeftClass FemaleRightVariables 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 0control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0control-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>: > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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