[Insight-users] Fast Marching Filter produces blank output

[Dan Mueller]

Hi Charlotte,

On 29/09/2007, Charlotte Curtis <curtisc at uoguelph.ca> wrote:
> I've put up my speed image and original at
> http://www.uoguelph.ca/~curtisc/ in dicom format (seemed to
> be the only one I could get to work properly).  However, I didn't have much
> luck getting a list of my seed points - I could only get them in "world"
> coordinates, which isn't much help.  Basically, I just seeded several
> locations on the inside of one of the bones, and I experimented with several
> different bones, seed points, and number of seed points.
>
> What should I be looking for to make sure the speed function is in the
> correct range?  Once again, thank you very much for your help,

The first thing I notice is that the speed image you uploaded is of
type signed short in the range [12,499]. This means that you *must*
use the NormalizationFactor (probably with a value of ~500) to convert
the speed to be in the range [0.0,1.0] (if you use
NormalizationFactor=500, the range will be [0.024,0.996]).
Alternatively you could use the RescaleIntensityImageFilter (which is
what I used) to explicitly rescale the image.

Once this was done, the Fast Marching worked fine for me (note that I
was using ITK directly, not through MeVisLab). I placed a single seed
on one of the bones and received expected results. For your reference
I have temporarily uploaded my results (so you can understand what to
expect):
   https://fileshare.qut.edu.au/public/muellerd/FastMarching.png
   https://fileshare.qut.edu.au/public/muellerd/FastMarching.mha

If you still can't get the method to work, perhaps try the MeVisLab
mailing list... Everything seems to be working on the ITK end.

HTH

Cheers, Dan

> Charlotte
>
>
> On 9/27/07, Charlotte Curtis <curtisc at uoguelph.ca> wrote:
> > Thanks Dan, I'll see if I can save those images and put them up tomorrow
> when I get back to school.  I really do hope it's something I'm doing wrong
> and not a problem with the program.
> >
> >
> >
> > On 9/27/07, Dan Mueller <dan.muel at gmail.com> wrote:
> > > On 28/09/2007, Charlotte Curtis <curtisc at uoguelph.ca> wrote:
> > > > I'm using ITK filters through MeVisLab, it comes with nearly all of
> them
> > > > implemented as modules.
> > >
> > > Okay.
> > >
> > > > It was my understanding that the stopping value should be somewhere
> around
> > > > the values of the voxels at the edge of the region, which for me is
> > > > somewhere between 200 and 1000 HU.  I've tried using very large
> numbers, but
> > > > I still get nothing output.
> > >
> > > The stopping value has nothing to do with the intensity range of the
> > > input image -- it tells the algorithm at what *arrival value* the
> > > processing should stop. If you are not sure, make the value large or
> > > use the default (which will force the algorithm to take longer to
> > > execute, but guarantee you a result).
> > >
> > > > I posted a screenshot from the program showing (left to right): the
> input
> > > > image, the FastMarching dialogue box, and the speed image.  It can be
> found
> > > > at
> http://www.uoguelph.ca/~curtisc/MeVisScreenshot.png.
> > >
> > > Unfortunately a screenshot doesn't help very much. It is best to
> > > inspect the raw data (especially the speed function to ensure it is in
> > > the correct range). Can you temporarily save the speed function you
> > > are using and post this? Also, the initial trial seed/region would be
> > > helpful.
> > >
> > > Cheers, Dan