Hello Freesurfer Gurus, I have been conducting cortical thickness and LGI analyses at my lab using Qdec. We have gotten some really promising results thanks to your help! However I have a few withstanding questions which need answered to make sure our results are methodologically valid:
1) After we would display our results in Qdec, I would then run Multiple Comparison tests on the data (the FDR and Monte Carlo Simulation). However, when we would run the Monte Carlo we would get a larger surface area of significance than was shown with the original display at a threshold of +/- 2. Is this the same function that is run with mri_glmfit--sim as seen here ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons )? I understand that the area of significance may be larger post MC because the iterations allow the MAXIMUM size cluster to be shown. Is this correct? If so, how do I correctly interpret these results? Am I right in assuming that as long as the original significance area we see is still reported by the Monte Carlo to be significant then our findings are statistically significant? 2) My second question is in regard to Qdec`s inability to have discrete factors which contain more than two levels. I was trying to use handedness as a discrete factor, but since our rating has three levels (left handed, ambi, and right handed), the analysis obviously wouldn`t work. Instead, I deleted the .levels files in the qdec file and saw that Qdec then accepted handedness as a continuous variable. When I ran the analyses using Qdec as a `pseudo-continuous` variable it worked! I know I got a little creative and could have done this actually using handedness with three levels with mri_glmfit it`s just that I had very limited time to do this and wanted to see if this way worked. Is this somehow invalid? I don`t know enough about the functions Qdec runs to know. Thank you so much for your time and help! All the best, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*
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