Hi,
i ran about 260 subjects and got good results for all but 30. the 30 that failed all seemed to have the same problem with normalization. the original were done with v5.1 i reran one with 5.3 and the problem was reduced. I attached a slice of the T1 from each. the 5.3 rerun produced a good quality brainmask.mgz, the originalrun with 5.1 failed to produce the brainmask.mgz
the original orig.mgz volumes look fairly decent, they were aquired on a good 1.5T scanner. since it ran much better on 5.3 im thinking some defaults were changed and perhaps i can add some flags with new default values to get 5.1 to produce usable results, i.e. the 230 other subjects have been inspected and im thinking they really really don't want to reinspect all of them after running on 5.3
can you suggest options/flags that i can try to rerun with 5.1
thanks
greg
