Hi - Thanks for your help.
I have 3 groups and am trying to run an ANOVA and series of t-tests. First, I ran mri_glmfit with two rows in my .mat file (1 -1 0, 1 0 -1) for the ANOVA. Then, before I ran into this webpage https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples, to do a follow up t-test between group 1 and group 2, I tried to mri_glmfit with a mat file of 1 -1 but it gave me an error because it was expecting any test to include all the subjects. So reran isxconcat-sess with subjects from just groups 1 and 2, and ran mri_glmfit with a mat file of 1 -1 Then I found the FSGD Examples webpage and realized I could perform all the tests in one command as long as I included a 0 in my mat file. So for the contrast between groups 1 and 2, I made a mat/mtx file with 1 -1 0. My question is, why are my results from these two similar analyses very different from each other? There are many more activations in the 1 -1 0 version than in the 1 -1 version and the activations that do exist are, for the most part, in different areas of the brain. Sorry to be ignorant of some of the statistics/analysis differences that are taking place here. I wondered why it was different and which was a more valid analysis. It seems like doing one analysis with all the tests is a better way to go then divided the data up, but I just wanted to check. Thanks again for your help, Alex Below are the mri_glmfit commands I used Directory PDSubsONLY = contains output of isxconcat-sess run on placebo and drug subjects only Directoy Analysis_Results = contains output of isxconcat-sess run all 3 subjects groups mri_glmfit --y PDSubsONLY_Results/RSF_v_NIF/tal.ces.nii --fsgd FSGD_Placebo_v_Drug.txt --C Placebo_v_Drug.mat --mask PDSubsONLY_Results/tal.mask.nii --glmdir Analysis_Results/tal.wrfx.RSF_v_NIF --nii --wls PDSubsONLY_Results/RSF_v_NIF/tal.cesvar.nii mri_glmfit --y Analysis_Results/RSF_v_NIF/tal.ces.nii --fsgd FSGD_Placebo_v_Drug_v_Control.txt --C mtx_files/placebo-drug.mtx --C mtx_files/placebo-control.mtx --C mtx_files/drug-control.mtx --C mtx_files/group_effect.mtx --C mt x_files/placebo-drug+control.mtx --C mtx_files/placebo+drug-control.mtx --mask Analysis_Results/tal.mask.nii --glmdir Analysis_Results/tal.wrfx.RSF_v_NIF --nii --wls Analysis_Results/RSF_v_NIF/tal.cesvar.nii Placebo_v_Drug.mat = 1 -1 mtx_files/placebo-drug.mtx = 1 -1 0 FSGD_Placebo_v_Drug.txt = contains only placebo and drug subjects FSGD_Placebo_v_Drug_v_Control.txt = contains placebo, drug and control subjects _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
