Hi,

First, thanks for the clearly-coded and very useful scripts! I have some questions about the 4_segment.sh script. Although the script ran well, my resulting wm_mask and csf_mask are much more limited than I would expect and I also am having trouble examining how they overlap with the images that they are based upon using AFNI. A general question is about the value of finding the overlap with priors. It seems that this is the step where things are going strange, so I was curious why this is recommended as opposed to just jumping right to the binarizing step. A more specific question has to do with the appropriateness of the priors for my population (very young children). I assume the priors are from 152 adults? The most specific question has to do with my attempts to examine all the different outputs along the segmentation pathway. For some reason, AFNI doesn't seem to think that the priors or the _masked and _mask datasets are in standard space because the GUI will not allow me to overlay these onto func2standard. This last question may be one for the AFNI messageboard, but I would appreciate any thoughts about these issues you may have.

Lisa