Does y.mgh exist? y.mgh is the stack of data that should be created by qdec. I think it's called y.mgh and I think that it is in the GLM dir, but it might be in the directory just above it. doug
Cat Chong wrote: > Hi Doug, > I spoke too soon. I tried to follow your advice and run either command: > > > In a terminal, cd to the GLM directory inside qdec directory and then > cd to the folder of the contrast of interest and run > mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh > --sum yourlabel.sum > the output yourlabel.sum will have information about the label > including the mean gamma (gamma is a map of the contrast values). > > Along those same lines, you can run > > mri_segstats --id 1 --slabel fsaverage lh yourlabel --i y.mgh --avgwf > yourlabel.dat > y.mgh should be there already and is a stack of thickness maps for all > your subjects > the output yourlabel.dat will be a single column with the average > thicknesses for each subject > > ..... however the error message I receive is that y.mgh could not be > opened...and I also don't seem to have a gamma.mgh file? > > Here is the error message, I received: > > mri_segstats --id 1 --slabel fsaverage lh lh.Temporal_lobe.label --i > y.mgh --avgwf lh.Temporal_lobe.label.dat > sysname Darwin > hostname fmris-Mac-Pro-2.local > machine x86_64 > user fmri > Constructing seg from label > Loading y.mgh > mghRead(/8000_series/8000_series/qdec/example_contrast/y.mgh , -1): > could not open file. > Filename extension must be .mgh, .mgh.gz or .mgz > ERROR: loading y.mgh > fmris-Mac-Pro-2:example_contrast fmri$ ls > X.mat lh-Avg-Intercept-thickness qdec.fsgd > Xg.dat lh-Avg-thickness-Age-Cor rstd.mgh > beta.mgh lh-Diff-1-0-Cor-thickness-Age rvar.mgh > contrasts lh-Diff-1-0-Intercept-thickness sar1.mgh > contrasts.sig.mgh lh.Temporal_lobe.label surface > dof.dat lh.Temporal_lobe.label.dat y.fsgd > error.log mask.mgh y.mgh > fwhm.dat mri_glmfit.log > > thanks so much for your help: > cat > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
