Hi Dan and Michael,<br><br>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,
<br><br>Charlotte<br><br><div><span class="gmail_quote">On 9/28/07, <b class="gmail_sendername">Dan Mueller</b> <<a href="mailto:dan.muel@gmail.com">dan.muel@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Charlotte,<br><br>On 29/09/2007, Charlotte Curtis <<a href="mailto:curtisc@uoguelph.ca">curtisc@uoguelph.ca</a>> wrote:<br>> I've put up my speed image and original at<br>> <a href="http://www.uoguelph.ca/~curtisc/">
http://www.uoguelph.ca/~curtisc/</a> in dicom format (seemed to<br>> be the only one I could get to work properly). However, I didn't have much<br>> luck getting a list of my seed points - I could only get them in "world"
<br>> coordinates, which isn't much help. Basically, I just seeded several<br>> locations on the inside of one of the bones, and I experimented with several<br>> different bones, seed points, and number of seed points.
<br>><br>> What should I be looking for to make sure the speed function is in the<br>> correct range? Once again, thank you very much for your help,<br><br>The first thing I notice is that the speed image you uploaded is of
<br>type signed short in the range [12,499]. This means that you *must*<br>use the NormalizationFactor (probably with a value of ~500) to convert<br>the speed to be in the range [0.0,1.0] (if you use<br>NormalizationFactor=500, the range will be [
0.024,0.996]).<br>Alternatively you could use the RescaleIntensityImageFilter (which is<br>what I used) to explicitly rescale the image.<br><br>Once this was done, the Fast Marching worked fine for me (note that I<br>was using ITK directly, not through MeVisLab). I placed a single seed
<br>on one of the bones and received expected results. For your reference<br>I have temporarily uploaded my results (so you can understand what to<br>expect):<br> <a href="https://fileshare.qut.edu.au/public/muellerd/FastMarching.png">
https://fileshare.qut.edu.au/public/muellerd/FastMarching.png</a><br> <a href="https://fileshare.qut.edu.au/public/muellerd/FastMarching.mha">https://fileshare.qut.edu.au/public/muellerd/FastMarching.mha</a><br><br>If you still can't get the method to work, perhaps try the MeVisLab
<br>mailing list... Everything seems to be working on the ITK end.<br><br>HTH<br><br>Cheers, Dan<br><br>> Charlotte<br>><br>><br>> On 9/27/07, Charlotte Curtis <<a href="mailto:curtisc@uoguelph.ca">curtisc@uoguelph.ca
</a>> wrote:<br>> > Thanks Dan, I'll see if I can save those images and put them up tomorrow<br>> when I get back to school. I really do hope it's something I'm doing wrong<br>> and not a problem with the program.
<br>> ><br>> ><br>> ><br>> > On 9/27/07, Dan Mueller <<a href="mailto:dan.muel@gmail.com">dan.muel@gmail.com</a>> wrote:<br>> > > On 28/09/2007, Charlotte Curtis <<a href="mailto:curtisc@uoguelph.ca">
curtisc@uoguelph.ca</a>> wrote:<br>> > > > I'm using ITK filters through MeVisLab, it comes with nearly all of<br>> them<br>> > > > implemented as modules.<br>> > ><br>> > > Okay.
<br>> > ><br>> > > > It was my understanding that the stopping value should be somewhere<br>> around<br>> > > > the values of the voxels at the edge of the region, which for me is<br>> > > > somewhere between 200 and 1000 HU. I've tried using very large
<br>> numbers, but<br>> > > > I still get nothing output.<br>> > ><br>> > > The stopping value has nothing to do with the intensity range of the<br>> > > input image -- it tells the algorithm at what *arrival value* the
<br>> > > processing should stop. If you are not sure, make the value large or<br>> > > use the default (which will force the algorithm to take longer to<br>> > > execute, but guarantee you a result).
<br>> > ><br>> > > > I posted a screenshot from the program showing (left to right): the<br>> input<br>> > > > image, the FastMarching dialogue box, and the speed image. It can be<br>> found
<br>> > > > at<br>> <a href="http://www.uoguelph.ca/~curtisc/MeVisScreenshot.png">http://www.uoguelph.ca/~curtisc/MeVisScreenshot.png</a>.<br>> > ><br>> > > Unfortunately a screenshot doesn't help very much. It is best to
<br>> > > inspect the raw data (especially the speed function to ensure it is in<br>> > > the correct range). Can you temporarily save the speed function you<br>> > > are using and post this? Also, the initial trial seed/region would be
<br>> > > helpful.<br>> > ><br>> > > Cheers, Dan<br></blockquote></div><br>