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.
