Dear FSL experts,
I am trying to normalize volumes by ICV in order to make group comparisons. After looking through many threads on calculating ICV, it seems that using the VSCALING value from sienax as a normalization factor is the best approach. So, I have run sienax on my subjects, but I am noticing problems with the output from some subjects.
1. For a few subjects, it appears that the individual structural scans are going into standard space in the wrong orientation. The BET results look good (I think), but the FLIRT standard space registration results are oriented wrong.
2. The other issue is that for about half of my subjects, the standard brain mask is smaller than the BET-derived brain mask (and smaller than the subject's brain). Therefore, when I look at the "Field of view and standard space masking" in the html output, there is a ring of blue (from the BET-derived brain mask) showing the part of the BET mask that does not overlap with the standard space mask. The result of this seems to be that the whole-brain segmentation cuts off part of the brain, so I imagine that the size of the brain is being underestimated, which worries me when using the VSCALING value.
Does anyone know how I can fix these problems? Also, if someone could tell me how to attach the images from the html output without exceeding the size limits for posts, that would be very helpful, as I think seeing the output would help convey the issues.
Thank you very much!
-Deanna
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