SCIRun User Mailing List

Text archives Help


Chronological Thread 
  • From: Petar Petrov <>
  • To:
  • Subject: [SCIRUN-USERS] Biomesh3D
  • Date: Mon, 19 Apr 2010 12:10:11 +0200
  • Domainkey-signature: a=rsa-sha1; c=nofws;; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type; b=hLTMhScRQ0Gz5e0YUbX03lVv5H5PifE12pocW11zRy5LW1bbUSYGc+WCf3n5B3ou8/ XvVKhO3eWKcVCdxDuxEo1MKJ5J4C+8EcdPvYu4ZcahNyRCGBiM43WLMsgVlFDWdXIkZI 13t+P8Yv0vubQ8YjQCGWM5Wn3vJbmOG7yEOBY=

hello all,
I have some  issues with the meshing pipeline coming along with scirun.
to start with I am doing a brain 3dmesh of 4tissue types skull,csf,gm,wm, coming from 3.5 tesla MRI 256x256x256:volume
My first try with 3tissue types was successful it run in decent less than 24h on 3xAMD with 6GB ram.
However running scirun on thw 4tissue type turned to be such a pain.
at one stage or another the pipeline got stacked on some operation which takes like forever.

and as forever I mean issues like:

[1]- Run Particles system takes prohibitive time to execute:
max sf: 20.55
Binning structure radius = 35.5936
Initializing with a mesh...
Reading particle file...
  number of particles = 309870
Done intializing
Rebuilding Neighborhoods
ApproximateNeighborhoods::optimize iteration: 16785.8 seconds.
Rebuilding Neighborhoods
ApproximateNeighborhoods::optimize iteration: 15472.9 seconds.
Writing point file 9 ...
Writing particle file 9 ...

this 16 thousands seconds for lets say 100 (forget 400) iterations will take a bit long for just 309870 or even up to a  million particles which is to be expected
note the high value of sizing field = 20. which should produce less of a tetrahedra, which also mean less of particles at stage 6 , right?

[2]- tetgen never finishes on stage 7:
SCIRun_SVN/bin/tetgen" junctions/particle-union.node
Opening junctions/particle-union.node.
Constructing Delaunay tetrahedralization.
Warning:  Point #709479 is duplicated with Point #190379. Ignored!
Warning:  Point #698163 is duplicated with Point #171285. Ignored!
Warning:  Point #749986 is duplicated with Point #213475. Ignored!
Warning:  Point #784349 is duplicated with Point #234481. Ignored!

after 2 days on 1 CPU = 100% it continues while the memory consumption is 24Mb !

stage 8 never really reached :(

I did some modification on the code coming from SVN, as you can see i got some debug info out, which i recommend to be able to show with some '-d' debug flag on the shell.
second big improvement was to do smarter scheduling of the spawned sub-processes at stage 6, to keep up to 3 running processes thus scale nicely with my triple core CPU, and insure I dont run out of physical memory. using virtual memory must be avoided at all cost with the speeds I am reporting :(((

I can provide the nrrd file of my segmentation,(~500kb) if someone is willing to give it a try.

It is really frustrating as I cannot seem to pin whats the core of the issue here. does medial axis refinement reflect the number of particles or tets in the final mesh?
i found out there is a hardcoded limit of atleast 3 steps in the medial axis refinement shell utility, something not documented!

I appreciate any inside you might give.

All the best,

Archive powered by MHonArc 2.6.16.

Top of page