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
- 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
- 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