On 10/21/19 10:24 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hello Experts, > > I do have couple questions about using mri_glmfit and mri_glmfit-sim > for this analysis based on the tutorial page. > https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer > 1) Do i have to add any other flags when using mri_glmfit for this > analysis? > mri_glmfit --y ${results_dir}/all.mgx.subctxgm.mni305.sm05.nii.gz > --fsgd $pet_fsgd --C $matrix1 \ > --mask ${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz --glmdir > ${results_dir}/sub.pet.B6.glmdir No, that is fine > 2) When correcting for multiple comparisons, should i use --2spaces or > --3spaces? It depends on what you are doing. If only subortical, then don't include a spaces flag. If you are eventually going to be reporting sub cort, left hemi, and righ hemi, then use --3spaces
> 3) I ran a paired ttest analysis using age as regressor of no interest > for amyloid uptake. My contrast is "1 0" based on the tutorial > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. > How do i interpret the direction of contrast if I get a result from > mri_glmfit-sim (see below)? This is because it doesn't have the Max > column for surface based analysis > # Cluster Size(n) Size(mm^3) MNIX MNIY MNIZ Max > CWP CWPLow CWPHi > 1 12709 101672.0 26.00 -69.00 -41.00 > 5.46844 0.01037 0.00798 0.01316 Right-Cerebellum-White-Matter You get the sign from the input. If you computed timepoint1-timepoint2, then positive means timepoint1>timepoint2 > > > Thank you. > best, > Paul > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
