[Insight-users] Fast Marching Filter produces blank output

[Charlotte Curtis]

Hi Dan and Michael,

Thank you very much for your help.  After a lot of trying to make the images
work, it turns out that my problem is that the seeds I placed are being
output by MeVisLab in "world" coordinates, and the ITK module is
interpreting them in "Voxel" coordinates, so my seed points weren't actually
in the image.  Thanks again,

Charlotte

On 9/28/07, Dan Mueller <dan.muel at gmail.com> wrote:
>
> 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
>
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