Ricardo,

This is a good feature suggestion, but I believe one that currently is not supported.  The simple reason why is that for some datasets there is not a clear "air" material to exclude. 

However, that said, it's fairly easy to filter the output mesh to exclude tets with a particular label.  Especially if you use .node/.ele files you can just extract the lines of interest and recount.  I hope this offers a quick workaround.  

Thanks a lot for these emails---these are exactly the kind of features we'd like to implement to simplify future users' experiences. 

Regards,

Josh 

On Sep 24, 2013, at 8:37 AM, Ricardo Ortiz <ricardo.ortiz@kitware.com> wrote:

Joshua -

Thanks for the feedback.  I got it to work with your suggestion and using padded volume!

Although it seems that with the padded volume option "air" is meshed as well.  Is there a way around this?

Thank you,

/Ricardo

On Sun, Sep 22, 2013 at 1:10 PM, Joshua Levine <jlevine@sci.utah.edu> wrote:

Hi Ricardo,

For your particular dataset, you'll need a separate nrrd file for each
indicator function.  You've given us the label map, where each voxel
is labeled by material.  What cleaver expects is a distance field per
label, as in the frog example you can find on the cleaver website.

Converting between the two is not super tricky, and is in fact
something we've discussed supporting in the code itself.  Jonathan
Bronson might in fact have this feature hidden in a development
version of Cleaver.  I believe this is the currently unimplemented
"loadNRRDLabelMap()" function in release 1.5.3.

Regards,
Josh

On Fri, Sep 20, 2013 at 9:15 AM, Ricardo Ortiz
<ricardo.ortiz@kitware.com> wrote:

> Hello,
>
> We are testing cleaver to generate a mesh on the following volumetric
> dataset. I get the following output:
>
>> Input Dimensions: 128 x 170 x 335
>> Creating Mesh with Volume Size [128, 170, 335]
>> ...
>> Worst Angles:
>> min: 180
>> max: 0
>> Writing settings file: man-arm-2mm-3labels-clean.info
>> ...
>> Cleaning up.
>> Done.
>
>
> Note the max worst angle is 0.  There is no error message nor warning and
> the output files are pretty much empty.
> Is there something I am missing parameter wise?
> I am using the defaults for -as and -al.
>
> Any help will be very much appreciated.
>
> Thanks,
> /Ricardo
>
> --
> Ricardo Ortiz, Ph.D.
> R&D Engineer
> Kitware, Inc.
> 101 East Weaver St. G4
> Carrboro, NC 27510
> Phone: (919) 869-8870
> Fax: (919) 969-6910
>

--
Ricardo Ortiz, Ph.D.
R&D Engineer
Kitware, Inc.

101 East Weaver St. G4

Carrboro, NC 27510

Phone: (919) 869-8870

Fax: (919) 969-6910