[Insight-users] fast marching algorithm very time consuming?

[Dan Mueller]

Hi Won-Ki,

As Luis said: the results you get seem normal. In the case I
previously described, the whole dataset was not processed: the speed
function restricted the expanding front to certain areas. The speed
function heavily influences the computational time -- the more areas
that are 0.0, the faster the process.

Anyway, hope this helps.

Cheers, Dan

On 28/08/07, Won-Ki Jeong <graphor at gmail.com> wrote:
> Dear Dan
>
> I found your message in the itk mailing list threads. I also have a
> question about the performance of FM in itk. I run a very simple
> example, as follows
>
> Volume 256x256x256
> Speed is 1.0 everywhere
> Seed is at the center of the volume
>
> I use itk 3.2 and my machine is Intel Core 2 Duo 2.4GHz with 3G
> memory. I did not use stopping value so it runs all over the volume.
> Mine took about 60 seconds, which looks slower than your case (your
> volume is 8 times larger). My code is compiled in release mode. Do you
> think my code have some problem?
>
> Won-Ki
>
>
> On 8/13/07, Dan Mueller <dan.muel at gmail.com> wrote:
> > Hi Michal,
> >
> > I too use the Fast Marching method for segmenting the heart (from CTA
> > images). I can process 512x512x512 datasets with Fast Marching in
> > under 60 sec on an Intel Xeon, 2.66 GHz, 8 MB RAM, Windows XP.
> >
> > Are you compiling your program in Debug or Release mode? Sometimes
> > debug mode can be very slow...
> >
> > Also, your speed function can alter the stopping value: for example,
> > if the speed function has many small values (near say 0.0001), larger
> > arrival times will be produced (requiring more time to reach your
> > stopping value). Are you rescaling your speed function to fill the
> > entire range between [0, 1]? Perhaps you could upload your speed image
> > (or a few slices of it) to a public datastore and post the link on
> > this list?
> >
> > Cheers, Dan
> >
> > On 14/08/07, Michal Plotkowiak <michal.plotkowiak at bnc.ox.ac.uk> wrote:
> > > In message <46C06E15.7050200 at kitware.com> Luis Ibanez <luis.ibanez at kitware.com>
> > > writes:
> > > >
> > >
> > > as far as I see, the fact that I increased the treshold value allowed me to
> > > store the result in the final output. Previously I was reading results from the
> > > intermediate output 4. But still to get a complite segmentation i need to set
> > > my values to around 2000 (this value is also suggested by my output map).
> > > Again, it takes very long to get any results.
> > >
> > > michal
> > >
> > > > Hi Michael,
> > > >
> > > > FastMarching should take only seconds in that size of data set.
> > > >
> > > > You are requesting a stopping time of 2000 and thresholding at 100,
> > > > that means that all the times from 101 to 2000 are going to waste.
> > > >
> > > > If you are going to threshold at 100, you can just set the stopping
> > > > time to a value slightly above the threshold. For example, you could
> > > > stop at 110.
> > > >
> > > > The heuristic for choosing the stopping time relates to the size of
> > > > the object that you want to segment and to the average value of the
> > > > speed image in the region that goes from the seed points to the
> > > > boundaries of the object that you want to segment.
> > > >
> > > >
> > > >
> > > > BTW: What is the profile of your computer ?
> > > >       OS, Processor, Memory ?
> > > >
> > > >
> > > >
> > > >     Regards,
> > > >
> > > >
> > > >        Luis
> > > >
> > > > -------------------------
> > > > Michal Plotkowiak wrote:
> > > > > Hi,
> > > > >
> > > > > I'm segmenting 3D data of a heart using FastMarchingImageFilter program.
> > > The
> > > > > data size is 256x256x362. Every 5th slice I generate seed points
> > > (approximately
> > > > > 300 on a slice). My threshold time is 100 and stoping time 2000. When I ran
> > > the
> > > > > simulation only for 6 slices I get good results but after about an hour.
> > > When I
> > > > > tried to run the sumulation for all the slices (362) two days wasn't
> > > enough...
> > > > >
> > > > > Has anyone some experience with FastMarching algorithm? The time needed for
> > > the
> > > > > simulation seems to be far too long. Should I somehow change my approach to
> > > the
> > > > > problem?
> > > > >
> > > > > many thanks
> > > > > michal
> > > >
> > >
> > > --
> > > Michal Plotkowiak
> > > Doctoral Researcher
> > > Oxford University LSI DTC
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