Dear Bruce, My questions is just to learn and to improve my understanding. The commands recon-all and dt-recon are routinely generating the statistics at the end of there running and we can check the results in aseg.stats (the output of recon-all) and fa.stats (the output of dt-recon for FA). In those files we have the white matter volume for many different parts of the brain like the right and left cerebral white matter. If we check the volumes in those files we can see that we have differences between the numbers and I can explain that by the following: in aseg.stats the white matter volume is derived from the T1 segmentation in the structural space and in fa.stats the white matter volume is derived from the FA map in diffusion space and the difference between the volumes is the difference between the accuracy of the images in different spaces. Now: 1. If we want to study the relationship between the FA and the right hemispheric white matter volume for example, we should not care about the volumes in fa.stasts because it is not accurate?! in this case what is the optimal and correct method in freeSurfer to do such like this comparison, is it by moving the FA map to the structural space by registering the FA map to T1 or by using the volumes in aseg.stats and the metrics values from fa.stats? or we can use the fa values and the volumes from fa.stats? 2.What is the exact usage for the volumes mentioned in FA.stats 3. What is the meaning and the exact usage of min-max intensity range (intensity of what) in aseg.stats and fa.stats
So Sorry for this long email but as always I am looking forward to learn from you Thanks Mohamad
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