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Ross Whitaker
Ross Whitaker
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- From: Fernando Quivira <f.quivira@gmail.com>
- To: cleaver@sci.utah.edu
- Cc: "#D.Brooks #fwd" <brooks@ece.neu.edu>
- Subject: [Cleaver] Fwd: Cleaver usage and problems
- Date: Sat, 2 Feb 2013 14:01:10 -0500
Dear Cleaver developers:
My name is Fernando Quivira. I work with Dana in the Breast Imaging Research Lab at the Mass. General Hospital. I don't know how much has Dana told you about what we do, but we basically need meshing software to create high quality meshes of breast tomosynthesis data for our finite element simulations.
I started using Cleaver with simple datasets, but I have encountered a couple of problems. Here is the info I have compiled for you
System details:
thanks! I hope this is of help
- Fernando
My name is Fernando Quivira. I work with Dana in the Breast Imaging Research Lab at the Mass. General Hospital. I don't know how much has Dana told you about what we do, but we basically need meshing software to create high quality meshes of breast tomosynthesis data for our finite element simulations.
I started using Cleaver with simple datasets, but I have encountered a couple of problems. Here is the info I have compiled for you
System details:
Ubuntu 12.04 - 64 bits
Nvidia GTX 480
GCC 4.6.3 (program did not work with 4.4)
48 GB RAM
(let me know if you need more system info)
Installation:Nvidia GTX 480
GCC 4.6.3 (program did not work with 4.4)
48 GB RAM
(let me know if you need more system info)
Everything went smoothly
Usage:I tried writing NRRD files from Matlab. I found a .m file in the Slicer plugin website, but it did not work. Do you guys have Matlab tools to write NRRD files?
Then, I wrote a simple NRRD writer. However, cleaver was stuck while reading the file. The file used a simple header:
My next step was to save my data as a .mat file, and use Seg3D to convert it to nrrd. This seemed to work as Cleaver did not get stuck in the reading file process.
Doing this with Seg3D was somewhat difficult since it kept crashing with a seg fault everytime I tried to write data as NRRD. Only occasionally was I able to do it.
Cleaver finished executing with the NRRD data from Seg3D, but the matlab output is empty. Cleaver log shows that the mesh contains 0 elements.
The command I ran was:
I have attached the data and results as a .rar file.
test.mat contains the simple block to be meshed. test.nrrd is the NRRD file from Seg3D. the files test2.* are the outputs from cleaver
Here is the output from the command line:
I don't know what I'm doing wrong. Let me know if there is more information you need. Is there some documentation I can read regarding cleaver usage?Then, I wrote a simple NRRD writer. However, cleaver was stuck while reading the file. The file used a simple header:
NRRD0001
type: int8
dimension: 3
sizes: 441 280 95
encoding: raw
type: int8
dimension: 3
sizes: 441 280 95
encoding: raw
My next step was to save my data as a .mat file, and use Seg3D to convert it to nrrd. This seemed to work as Cleaver did not get stuck in the reading file process.
Doing this with Seg3D was somewhat difficult since it kept crashing with a seg fault everytime I tried to write data as NRRD. Only occasionally was I able to do it.
Cleaver finished executing with the NRRD data from Seg3D, but the matlab output is empty. Cleaver log shows that the mesh contains 0 elements.
The command I ran was:
cleaver -i ./test.nrrd -o test2 -f matlab
I have attached the data and results as a .rar file.
test.mat contains the simple block to be meshed. test.nrrd is the NRRD file from Seg3D. the files test2.* are the outputs from cleaver
Here is the output from the command line:
Reading File: ./test.nrrd
Input Dimensions: 441 x 280 x 95
Creating Mesh with Volume Size [441, 280, 95]
Cuts Computed
Triples Computed
Quads Computed
Tets Generalized
Phase 1 Complete
Phase 2 Complete
Phase 3 Complete
Stenciling Complete
Mesh Construction Complete
Total Time: 0 s
Worst Angles:
min: 180
max: 0
Writing settings file: test2.info
Writing mesh matlab file: test2.mat
Writing mesh ply file: test2.ply
Cleaning up.
Done.
Input Dimensions: 441 x 280 x 95
Creating Mesh with Volume Size [441, 280, 95]
Cuts Computed
Triples Computed
Quads Computed
Tets Generalized
Phase 1 Complete
Phase 2 Complete
Phase 3 Complete
Stenciling Complete
Mesh Construction Complete
Total Time: 0 s
Worst Angles:
min: 180
max: 0
Writing settings file: test2.info
Writing mesh matlab file: test2.mat
Writing mesh ply file: test2.ply
Cleaning up.
Done.
thanks! I hope this is of help
- Fernando
Attachment:
Cleaver_test.zip
Description: Zip archive
- [Cleaver] Fwd: Cleaver usage and problems, Fernando Quivira, 02/02/2013
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