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Hi, There are a few differences in FAST 4 - especially with respect to the partial volume estimation and the fact that it uses an MRF on the mixture type (mixeltype) which tends to give more pure (100%) tissue voxels in the middle of white and grey matter. However, I am surprised to hear that there is such a large difference in your data. What do the differences between the pve images look like between the methods? That is, take the grey matter PVE in both cases and do the subtraction of them, then view this in FSLView. Does it look unusual? Does the difference tend to concentrate in some areas (e.g. deep-grey structures, border of GM and CSF, etc.)? Or is there just a general bias one way across the whole image? Knowing this info will help work out what is going on. If you cannot work out what is the predominant difference then feel free to upload the data to our upload site and we will take a look at it. All the best, Mark On 21 Jun 2009, at 18:53, Jeremy Gray wrote: > Hi all, > > I have a question about how FAST 4.1 differs from earlier versions, > esp 3.x. I get quite different results in two large samples, in > terms of grey matter to white matter ratio (ratio = 1.14 from FAST > 4.1, vs ratio = 1.67 from 3.x). This suggests big difference(s) in > classification between versions. there are many differences between > versions, obviously, but I did not expect these to impact the ratio > much if at all. I think a ratio of 1.6 is much more in line with the > literature. > > any ideas what's going on, or how to track it down? I searched the > archives but did not see anything relevant, sorry if I missed it. > > thanks in advance, > > --Jeremy > > gory details: > I ran T1 images from 114 subjects through bet (and checked that they > look reasonable after bet). I then used FAST 4.1 (on CentOS 5.3, 64- > bit) to segment them using defaults: > > fast -t 1 -o <image> <image> > > I looked at some of the resulting pve_* images and they look > reasonable in fslview. from the pve's I get CSF, grey, and white > matter volumes in mm^3 using fslstats and bc, as described on the > FAST web page (http://www.fmrib.ox.ac.uk/fsl/fast4/index.html) > > my intuition is that the grey to white matter ratio should be pretty > robust against scanner and sample differences (but maybe that's > wrong). in the sample I'm using FAST 4.1 for, the ratio of GM : WM > is 1.14. This is markedly lower that the G/W ratio of 1.67 I got in > another large sample (different scanner & subjects, but I don't > think that should have a huge impact on the ratio). this was using > FAST 3.x (again on T1 images run through bet). so think that the > version of FAST is where the difference is, and that in my hands 4.1 > is not doing what it should. > > also, there seems to be more CSF when using FAST 4.1 (~25% of intra- > skull volume, vs ~15% with 3.x). > > any ideas on how to best track down what is going on (esp with 4.1)? >