On Aug 26, 2016, at 12:41 PM, Murat Maga <maga@uw.edu> wrote:

So I have a different problem now. I padded the images and they all look like this, which I think is sufficient padding.

 

<image001.png>

 

Groom successfully completed on Linux with these parameters:

<?xml version="1.0" encoding="UTF-8"?>

<blur_sigma>0.1</blur_sigma>

<antialias_iterations>100</antialias_iterations>

<background>0</background>

<foreground>1</foreground>

ShapeWorksGroom ./shapeworks.groom.xml center  isolate hole_fill antialias blur fastmarching

 

But then ShapeWorksRun fails with this command:

 

File: /root/Downloads/ITK/Modules/Core/Common/include/itkImageToImageFilter.hxx

Line: 250

Description: itk::ERROR: MaximumEntropyCorrespondenceSampler(0x15be380): Inputs do not occupy the same physical space!

InputImage Origin: [-7.2094060e+00, -9.7350384e+00, -5.6886340e+00], InputImage_1 Origin: [-7.1679193e+00, -9.7181870e+00, -5.7039522e+00]

        Tolerance: 9.6125413e-08

InputImage Spacing: [9.6125413e-02, 9.7350384e-02, 9.4810566e-02], InputImage_1 Spacing: [9.5572258e-02, 9.7181870e-02, 9.5065870e-02]

        Tolerance: 9.6125413e-08

 

When I bring the raw files into ShapeWorksStudio on Windows, it complains with this error. Yet as far as I can tell all images are of the same dimension and size (see the output from c3d below).

 

<image002.png>

 

 

What’s going on?

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4188 19.4701 11.3773]};  vox = [0.0961254, 0.0973504, 0.0948106];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3358 19.4364 11.4079]};  vox = [0.0955723, 0.0971819, 0.0950659];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3277 19.4718 11.4256]};  vox = [0.0955178, 0.0973591, 0.0952136];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3358 19.4593 11.4392]};  vox = [0.0955723, 0.0972963, 0.0953266];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3839 19.4031 11.4214]};  vox = [0.095893, 0.0970155, 0.095178];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4188 19.4579 11.4345]};  vox = [0.0961254, 0.0972894, 0.0952879];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4275 19.3802 11.4441]};  vox = [0.0961834, 0.0969009, 0.0953678];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3633 19.4461 11.3909]};  vox = [0.0957555, 0.0972306, 0.0949242];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4451 19.477 11.4043]};  vox = [0.0963004, 0.0973851, 0.0950356];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3839 19.4593 11.4392]};  vox = [0.095893, 0.0972963, 0.0953266];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3358 19.392 11.4214]};  vox = [0.0955723, 0.09696, 0.095178];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4235 19.4461 11.4842]};  vox = [0.0961569, 0.0972306, 0.0957019];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3839 19.4146 11.4043]};  vox = [0.095893, 0.0970731, 0.0950356];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3703 19.4031 11.4525]};  vox = [0.0958018, 0.0970155, 0.0954372];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3767 19.4788 11.3831]};  vox = [0.0958447, 0.0973942, 0.0948596];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4451 19.4364 11.3909]};  vox = [0.0963004, 0.0971819, 0.0949242];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3189 19.3286 11.3219]};  vox = [0.0954591, 0.0966428, 0.0943491];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4321 19.4472 11.4345]};  vox = [0.0962137, 0.097236, 0.0952879];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3563 19.4828 11.3801]};  vox = [0.0957089, 0.0974138, 0.0948343];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3767 19.4593 11.4174]};  vox = [0.0958447, 0.0972963, 0.0951446];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4275 19.3567 11.3976]};  vox = [0.0961834, 0.0967834, 0.0949802];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3421 19.3567 11.4118]};  vox = [0.0956142, 0.0967834, 0.0950982];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4321 19.4143 11.4392]};  vox = [0.0962137, 0.0970716, 0.0953266];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3899 19.5094 11.4261]};  vox = [0.0959324, 0.0975468, 0.0952173];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4106 19.4807 11.3909]};  vox = [0.0960705, 0.0974037, 0.0949242];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.4106 19.414 11.4043]};  vox = [0.0960705, 0.0970702, 0.0950356];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3698 19.5166 11.4907]};  vox = [0.095799, 0.0975828, 0.0957555];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3703 19.4031 11.4655]};  vox = [0.0958018, 0.0970155, 0.0955455];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3776 19.3802 11.4842]};  vox = [0.0958506, 0.0969009, 0.0957019];  range = [0, 1];  orient = RAI

 

Image #1: dim = [150, 200, 120];  bb = {[0 0 0], [14.3421 19.4031 11.3976]};  vox = [0.0956142, 0.0970155, 0.0949802];  range = [0, 1];  orient = RAI

 

 

From: Praful Agrawal [mailto:prafulag@cs.utah.edu] 
Sent: Friday, August 26, 2016 9:36 AM
To: Murat Maga <maga@uw.edu>
Cc: shapeworks-users@sci.utah.edu
Subject: Re: [shapeworks-users] ShapeWorksRun crashing with an itk error

 

Seems too little.

—

Regards,

Praful

http://www.sci.utah.edu/people/prafulag.html

 

On Aug 26, 2016, at 10:34 AM, Murat Maga <maga@uw.edu> wrote:

 

So what exactly is the padding issue? Too much padding, too little?

---

From: Praful Agrawal
Sent: ‎8/‎26/‎2016 9:00 AM
To: shapeworks-users@sci.utah.edu; Murat Maga
Subject: Re: [shapeworks-users] ShapeWorksRun crashing with an itk error

This seems like a padding issue as the new points generated with random seeds seem to be falling outside image domain.

 

 

—

Regards,

Praful

http://www.sci.utah.edu/people/prafulag.html

 

On Aug 26, 2016, at 1:28 AM, Murat Maga <maga@uw.edu> wrote:

 

Any ideas what might be causing this error (log file is attached, but there is not much else in it)

 

....terminate called after throwing an instance of 'itk::ExceptionObject'

  what():  /root/Downloads/shapeworks/src/ITKParticleSystem/itkPowerOfTwoPointTree.txx:125:

itk::ERROR: PowerOfTwoPointTree(0x4936160): Point [6.79247, -1.12035, -1.23879] is not contained within tree domain [-5.8547, -11.3321, -5.84979] - [5.8547, 11.3321, 5.84979]

./runSWrun.sh: line 2: 40528 Aborted                 ShapeWorksRun shapeworks.run.xml

<endo_SW.TXT>