Does /8000_series/8000_series/qdec/example_contrast/y.mgh exist? doug Cat Chong wrote: > yes, it does exist.. > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Cat Chong <cavecreekcut...@yahoo.com> > *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Thursday, January 26, 2012 9:34 AM > *Subject:* Re: [Freesurfer] qdec analysis > > 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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > 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. > > >
-- 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
