Continue with what you have done, do not model it as a continuous variable. doug
On 06/02/2015 04:03 PM, Matthieu Vanhoutte wrote: > 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 >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://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 >>> <mailto: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. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> 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. > > > > _______________________________________________ > 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