Hi,

I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard.

I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the same analysis in v5.3.0 (snowleopard) didn't overlay on the brain in a sensible way, and only after I searched the mailing list did I realize that I needed to use -no-subcort-mask. Using this option gave me the same results as with v.5.2.0. Searching through freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask = 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing things the right way...

Thanks in advance,

Leila