On May 28, 2020, at 3:13 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Hi,

It seems this script will process VTK data.

ShapeWorks/Examples/Scripts/FullPrepPipeline/FullPipelinePrepRunMeshtoDT.sh

However this sub script:

RasterizationVolumeOriginAndSize.sh 

Does not spit out the two files needed next:

# convert meshes to distance transforms

if [ $doMeshesToVolumes -eq 1 ]

then

    origin_filename=${parentDir}origin_size/origin_sp${spacing}_nb${narrow_band}.txt

    size_filename=${parentDir}origin_size/size_sp${spacing}_nb${narrow_band}.txt

I see the names in an xml file but not sure what to make of that. 

So at this point I am pretty lost. As such it would be really good to have a zoom chat so I can understand the pipeline. Especially as parts of the pipeline are not going to be needed - the data is located and oriented. But the bounding box is different. But for now I would just like to have and understand a working pipeline.

I can supply two VTK files that can be used for the initial setup. I have time tomorrow anytime to meet.

Cheers,

Allen

Allen Sanderson

SCI Institute

University of Utah

On May 27, 2020, at 2:49 PM, Allen Sanderson <allen@sci.utah.edu> wrote:

Hi Shireen,

Though a bit late, happy Eid-ul-Fitr. Years ago I was in Egypt for Eid-ul-Fitr, then spent three weeks traveling around. I had a great time as it was the start of a three month tour around the Mediterranean Sea.

I am finally working through all of the parts of ShapeWorks. I went through the ellipse example and now working with some of my VTK data. But I am not seeing documentation on starting with VTK files.  Just nrrd data. I have files that describe a closed surface (and as a volume elements) that I wanted to use for some initial testing and to familiarize myself with all the tools and steps.

I pinged Cam and Alan but they did not reply or did not know. Any pointers??


Cheers,

Allen