Sorry I had to be more clear.
Yes, I did first_flirt both on the raw (as proposed by your
website) and on the standardized image (as I tried to avoid the
noise problem).
However the difference between the HC volumes obtained from
the standardized image was 1.8 times larger than the volume
obtained from the native image.
I think cropping the neck would fix the failing cases.
If you like I can send you a sample data.
Cheers
Naj
On Mon, 24 Sep 2007, Brian Patenaude wrote:
> Hi,
>
> To clarify, "The average 1.8 scaling factor is not explained by the
> transformation parameters.". Are you saying that the transformation matrix
> calculated from first_flirt differs in the scale component to that applied
> to get the standardized image by a factor of 1.8.
>
> If so, did you look at the output of first_flirt? Did it clearly fail?
> If so, the failure may be due to the neck or possibly bias field? If the
> neck is the problem, it may be corrected by masking the neck out. Did you
> try and apply first_flirt to the standardized image?
>
> Cheers,
>
> Brian
>
>
>
> > Hi Brian,
> >
> > Yes, I mean the amount of noise in the original data prior to
> > any noise reduction.
> >
> > The other question is:
> > result of FIRST on standardized data > result of FIRST on
> > native.
> >
> > The average 1.8 scaling factor is not explained by the
> > transformation parameters.
> >
> > Any ideas?
> >
> > Naj
> >
> >
> >
> >
> > On Mon, 24 Sep 2007, Brian Patenaude wrote:
> >
> >> Hi,
> >>
> >> The only disadvantage is that you've interpolated the data during the
> >> transofrmation to MNI152 space. By senstive to the noise in the raw
> >> image, are you meaning prior to non-uniformity correction?
> >>
> >> When applying FIRST to the pre-processed data, you should still use
> >> first_flirt to re-align the image since it uses the sub-cortical mask
> >> (the segmentation will be in the original MNI152 space).
> >>
> >> The volumes are do take into account the boundary correction for the
> >> set threshold.
> >>
> >> Cheers,
> >>
> >> Brian
> >>
> >>
> >> > Hi,
> >> >
> >> > I am interested in comparing the results of FIRST with manual
> >> > segmentation.
> >> >
> >> > Is there an impediment to doing FIRST on data that has
> >> > undergone: non-uniformity correction, neck cropping and 12
> >> > param-affine registeration to MNI152 space? (The reason: 1)
> >> > FISRT is sensitive to noise in the raw image; 2) our manual
> >> > segmentation is done in standard space.)
> >> >
> >> > Also, would you be considering the boundary in calculation of
> >> > the structure's volume?
> >> >
> >> > Many thanks
> >> > Naj
> >>
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