Does /8000_series/8000_series/qdec/example_contrast/y.mgh exist? doug

Cat Chong wrote:

yes, it does exist..

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*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Cat Chong cavecreekcutter@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

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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