Hello Experts: In qdec, I would like to analyze if the thickness- entorhinal volume correlation differs between APOE positive and negative subjects accounting for age. I have chosen age as a nuisance variable and entorhinal volume as a covartiate. ( hope this is correct)
Results show me several clusters of group differences following FDR correction. Here is my question: I would like to know what the mean value differences are between the groups for various clusters. And I would also like to know which group shows less of a correlation for certain clusters. Could you tell me where I would find those values?
Best Regards, Catherine
Hi Cat, first create and save a label of your cluster.
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
doug
Cat Chong wrote:
Hello Experts: In qdec, I would like to analyze if the thickness- entorhinal volume correlation differs between APOE positive and negative subjects accounting for age. I have chosen age as a nuisance variable and entorhinal volume as a covartiate. ( hope this is correct) Results show me several clusters of group differences following FDR correction. Here is my question: I would like to know what the mean value differences are between the groups for various clusters. And I would also like to know which group shows less of a correlation for certain clusters. Could you tell me where I would find those values?
Best Regards, Catherine
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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
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
freesurfer@nmr.mgh.harvard.edu
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Cat Chong -
Douglas N Greve