Dear Freesurfer support,
I find the qdec to be very pedagogic in its outlay, and would love to use it. However, I find several discrepancies as compared to results from the mri_glmfit analyses, and wonder why (see description below). 1) One discrepancy is the placement of the clusters; X, Y, Z's. Should I use: * the figures from the result summary from mri_glmfit, * the result summary from Qdec (which is almost the same as from the results summary from mri_glmfit), * or from the “Find clusters and goto max” function in the display window of Qdec (which shows very different placements than the two others)? 2) Which size should I use? The sizes of the clusters from qdec are 1-2% smaller than what are reported from the mri_glmfit analyses. I expect that the reason for the discrepancies is that I probably do something different in the mri_glmfit analyses than the standard Qdec analyses, but I can not figure out what it is. Below is information about which analyses I have done and some more information about the Qdec output. Overview analyses: We investigate difference between two groups. We have two sets of data, one with skewed age and gender distribution between groups (n = 89) (older participants and more girls in the risk group), and one with 33 extra control participants (n = 122) making the risk and control group having similar age and gender distribution. The vertex based analyses are done with mri_glmfit in Freesurfer version 5.3. I have analyzed the data both with DOSS and DODS. Both without covariates, controlling for age (demeaned continuous variable) or controlling for gender, or controlling for both age and gender. We have used smoothing fwhm 10. The results were controlled for multiple comparisons with the standard mri_glmfit-sim method in Freesurfer with cache 1.3 abs and 2spaces (did not use 2spaces when comparing mri_glmfit results with Qdec results). We have used tksurfer (DOSS and DODS) and qdec (DODS) to visualize the results, but mainly used results from cache.th13.abs.sig.cluster.summary files to compare with the analyses from SPSS. The contrast in the full DODS model in the mri_glmfit is 1 1 -1 -1 0 0 0 0, with the fsgd file being: GroupDescriptorFile 1 Title n89-33 Class group1risk_gender1girl Class group1risk_gender2boy Class group2control_gender1girl Class group2control_gender2boy Variables age Input UN001 group1control_gender2boy -1.0172131148 Etc Preproc was done with: mris_preproc --target fsaverage --hemi lh --meas area --fsgd $glm/demographicn122.fsgd --out $preproc Smoothing was done with: mri_surf2surf --hemi lh --s fsaverage --sval $preproc --fwhm 10 --cortex --tval $smoothing10 GLM was done with: mri_glmfit --glmdir $contrast --y $smoothing10 --fsgd $glm/demographicn122.fsgd --C $glm$contrast_kjal.mat --surf fsaverage lh --cortex Correction for multiple comparisons was done with: mri_glmfit-sim --glmdir $contrast --cache 1.3 abs Qdec: There are discrepancies between results from qdec and mri_glmfit. I am unsure why. I notice for example that there are small discrepancies in the fwhm.dat files from Qdec and mri_glmfit. The most important for my use is that when I compare the clusters in the file: cache.th13.abs.sig.cluster.summary from the mri_glmfit, and the clusters from the file: mc-z.abs.th13.sig.cluster.summary from qdec, I find the same four clusters of group differences in cortex areas with the same Max number and Vtxmax. However, the sizes are marginally different, with the sizes from qdec being 1-2% smaller. Most importantly for me are the differences in the placement of the clusters. The MNIX, Y and Z from mri_glmfit are not similar to the TalX, Y and Z from Qdec. The differences are not big, but still significant for us. I also note that the TalX, Y and Z's from the result file from Qdec is very different from the TalX, Y and Z's from the output one get from Qdec when one use the button “Find clusters and got max” in the visual Display window in Qdec. It seems the output from Qdec's “Find clusters and got max” shows the mean cluster placement (all Max figures are 4), whereas the output from mri_glmfit and from the resultsfile from Qdec shows the placement of masked clusters (the Max figures vary)? Kind regards, Egil Nygaard
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