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Re: [shapeworks-users] segfault


Chronological Thread 
  • From: Josh Cates <cates@sci.utah.edu>
  • To: shapeworks-users@sci.utah.edu, Wei Liu <weiliu620@gmail.com>
  • Cc: Alan Morris <akenmorris@gmail.com>
  • Subject: Re: [shapeworks-users] segfault
  • Date: Wed, 9 Jul 2014 12:00:18 -0600
Hi Wei,

Yes, as Alan has pointed out, ShapeWorks assumes that your data is
co-registered in the same coordinate space with the same isotropic
pixel spacing.

Regarding different numbers of objects in different datasets: It is
possible to compute a joint statistical model of multiple objects,
i.e. sets of bones or sets of brain structures. However, you do need
to have all structures present for every individual in the sample set.
ShapeWorks will not handle cases where there are missing variables in
that context.

Josh

On Wed, Jul 9, 2014 at 11:35 AM, Wei Liu <weiliu620@gmail.com> wrote:
> Alan,
>
> Thanks for the information. Yes this particular data set seems not obtained
> under good control, so they may have different spacing. I will add the
> resampling in the preprocessing pipeline.
>
> As for the multiple components in the volume, I also noticed it and wondered
> how ShepWorks would handle it. So, thanks for pointing it out.
>
> Wei
>
>
> On Wed, Jul 9, 2014 at 11:26 AM, Alan Morris <akenmorris@gmail.com> wrote:
>>
>> Wei,
>>
>> It appears that this crash stems from the difference in spacing for the
>> different images. When I resample them to all have consistent spacing,
>> then
>> ShapeWorksRun runs to completion.
>>
>> I noticed some other issues with your data. It appears that with at least
>> some of the data, the two sides are not connected. ShapeWorks won't be
>> able
>> to model datasets where there are different numbers of objects for each
>> patient. You may be better off with a joint model of the left and right as
>> separate objects. Josh may have more ideas.
>>
>> Alan
>>
>>
>>
>> On Thu, Jul 3, 2014 at 11:59 AM, Alan Morris <akenmorris@gmail.com> wrote:
>>>
>>> Wei,
>>>
>>> Yes, the order does matter. And yes, I would put it after the auto_crop
>>> tool.
>>>
>>> I will have to take a look at the data.
>>>
>>> Alan
>>>
>>>
>>>
>>> On Thu, Jul 3, 2014 at 11:46 AM, Wei Liu <weiliu620@gmail.com> wrote:
>>>>
>>>> Alan,
>>>>
>>>> I didn't find the auto_pad option in current version of the document,
>>>> though the xml file has the parameter. I suppose I just need to add
>>>> "auto_pad" at the end of the ShapeWorkGroom preprocess1.xml command,
>>>> after
>>>> the auto_crop option? Does the order of the steps in preprocess1 matter?
>>>>
>>>> OK, I re-run the preprocess with auto_pad, and ShapeWorksRun, but still
>>>> have the segfault. The output of "Groom" now has information about the
>>>> padding, so I assume the auto_pad worked as expected.
>>>>
>>>> Thanks,
>>>> Wei
>>>>
>>>>
>>>> On Thu, Jul 3, 2014 at 10:52 AM, Alan Morris <akenmorris@gmail.com>
>>>> wrote:
>>>>>
>>>>> Wei,
>>>>>
>>>>> I will try out your data when I get a chance. In the mean time, did
>>>>> you use "auto_pad" with ShapeWorksGroom? If not, I would recommend
>>>>> using it
>>>>> with a <pad>10</pad> value in your groom parameter file. I've found
>>>>> that
>>>>> without this, the computation can sometimes runs outside the bounding
>>>>> box of
>>>>> the image (which is what it looks like is happening here).
>>>>>
>>>>> Alan
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Jul 3, 2014 at 10:41 AM, Wei Liu <weiliu620@gmail.com> wrote:
>>>>>>
>>>>>> Hi Alan,
>>>>>>
>>>>>> Thanks for the reply. I rebuilt with type "Release with Debug info",
>>>>>> and run on both 5 and 3 shapes.
>>>>>>
>>>>>> For 3 and even 4 shapes, I don't get any segfault. However, if I
>>>>>> remove the first shape in correspondence.xml and use the remaining 4,
>>>>>> I got
>>>>>> "basic_string::_S_construct null not valid" error at the very
>>>>>> beginning. If
>>>>>> I removed the second or the last files, the remaining 4 shapes will run
>>>>>> without errors. I think that might be a different issue. I previous
>>>>>> preprocess step, I used 5 shapes when running "groom". Can this be the
>>>>>> reason?
>>>>>>
>>>>>> If I use 5 shapes with the newly built executable with debug info, I
>>>>>> got the following trace when I run it in gdb (attached at the end).
>>>>>> I've
>>>>>> check the 5 distance transform volumes that I generated in previous
>>>>>> "groom"
>>>>>> step, and the files look good, i.e. not corrupted. The files at at
>>>>>> ftp://ftp.sci.utah.edu/upload/shapeworks/. Naming convention: PE105 is
>>>>>> the
>>>>>> original binary label map, PE105DT is the output of preprocess1, and
>>>>>> PE105B
>>>>>> is the output of preprocess2.
>>>>>>
>>>>>> Thanks again,
>>>>>> Wei
>>>>>>
>>>>>> ============== gdb trace for 5 shapes =======
>>>>>> Particle count: 256
>>>>>> Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Performing global step
>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>> Writing lung.1.wpts with 256points
>>>>>> Writing lung.2.wpts with 256points
>>>>>> Writing lung.3.wpts with 256points
>>>>>> Writing lung.4.wpts with 256points
>>>>>> Writing lung.0.wpts with 256points
>>>>>> Writing lung.1.wpts with 256points
>>>>>> Writing lung.2.wpts with 256points
>>>>>> Writing lung.3.wpts with 256points
>>>>>> Writing lung.4.wpts with 256points
>>>>>> ------------------------------
>>>>>> *** AddAdaptivity Step
>>>>>> ------------------------------
>>>>>> ------------------------------
>>>>>> *** Optimize Step
>>>>>> ------------------------------
>>>>>> Optimizing correspondences.
>>>>>> Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: -2.39275e-12
>>>>>> 1: 1507.72
>>>>>> 2: 6264.25
>>>>>> 3: 9221.54
>>>>>> 4: 12432.4
>>>>>> ENERGY = 6.92568 MinimumVariance = 10
>>>>>> ..........Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: -7.37188e-13
>>>>>> 1: 1751.71
>>>>>> 2: 7403.11
>>>>>> 3: 10333
>>>>>> 4: 13489.7
>>>>>> ENERGY = 7.02755 MinimumVariance = 7.94328
>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>> Writing lung.1.wpts with 256points
>>>>>> Writing lung.2.wpts with 256points
>>>>>> Writing lung.3.wpts with 256points
>>>>>> Writing lung.4.wpts with 256points
>>>>>> Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: 4.18954e-12
>>>>>> 1: 2095.34
>>>>>> 2: 8703.64
>>>>>> 3: 11476.4
>>>>>> 4: 15024.5
>>>>>> ENERGY = 7.13783 MinimumVariance = 6.30957
>>>>>> ..........Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: 2.53131e-13
>>>>>> 1: 2526.8
>>>>>> 2: 10131.4
>>>>>> 3: 12508.7
>>>>>> 4: 16966.7
>>>>>> ENERGY = 7.24689 MinimumVariance = 5.01187
>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>> Writing lung.1.wpts with 256points
>>>>>> Writing lung.2.wpts with 256points
>>>>>> Writing lung.3.wpts with 256points
>>>>>> Writing lung.4.wpts with 256points
>>>>>> Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: -3.3924e-12
>>>>>> 1: 3021.26
>>>>>> 2: 11694.5
>>>>>> 3: 13581.5
>>>>>> 4: 19224.8
>>>>>> ENERGY = 7.35258 MinimumVariance = 3.98107
>>>>>> ..........Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: -3.55715e-12
>>>>>> 1: 3568.42
>>>>>> 2: 13370.2
>>>>>> 3: 14793.5
>>>>>> 4: 21730.6
>>>>>> ENERGY = 7.45411 MinimumVariance = 3.16228
>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>> Writing lung.1.wpts with 256points
>>>>>> Writing lung.2.wpts with 256points
>>>>>> Writing lung.3.wpts with 256points
>>>>>> Writing lung.4.wpts with 256points
>>>>>> Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: 8.60201e-12
>>>>>> 1: 4187.57
>>>>>> 2: 15055.2
>>>>>> 3: 16223.1
>>>>>> 4: 24401.8
>>>>>> ENERGY = 7.5514 MinimumVariance = 2.51189
>>>>>> ..........Performing global step
>>>>>> BeforeIteration counter = 0
>>>>>> 0: -4.90941e-13
>>>>>> 1: 4883.32
>>>>>> 2: 16621.5
>>>>>> 3: 18029
>>>>>> 4: 27197.2
>>>>>> ENERGY = 7.64467 MinimumVariance = 1.99526
>>>>>> .
>>>>>> Program received signal SIGSEGV, Segmentation fault.
>>>>>> itk::LinearInterpolateImageFunction<itk::Image<float, 3u>,
>>>>>> double>::EvaluateAtContinuousIndex (this=0xbe4f40, index=...)
>>>>>> at
>>>>>> /scratch/packages/InsightToolkit-3.20.1/Code/Common/itkLinearInterpolateImageFunction.txx:150
>>>>>> 150 value += static_cast<RealType>(
>>>>>> this->GetInputImage()->GetPixel( neighIndex ) ) * overlap;
>>>>>> (gdb)
>>>>>> =========== end of gdb trace for 5 shapes ================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jul 2, 2014 at 3:51 PM, Alan Morris <akenmorris@gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Wei,
>>>>>>>
>>>>>>> Could you build ShapeWorksRun with debugging symbols and send us the
>>>>>>> stacktrace? Alternatively, if you could point us to the data, that
>>>>>>> would be
>>>>>>> great.
>>>>>>>
>>>>>>> Can you reproduce it with a smaller sample of data (e.g. 3 shapes).
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Alan
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jul 1, 2014 at 4:01 PM, Wei Liu <weiliu620@gmail.com> wrote:
>>>>>>>>
>>>>>>>> Dear shapeworks users,
>>>>>>>>
>>>>>>>> Today I got a segmentation fault when running ShapeWorksRun on my
>>>>>>>> CT image of 5 volumes. From the screen log, it seems the segfault
>>>>>>>> happened
>>>>>>>> at the "optimization step". Below I attached the log, the xml
>>>>>>>> configuration
>>>>>>>> file and the files that have been generated before the segfault
>>>>>>>> happens.
>>>>>>>>
>>>>>>>> I was monitoring the memory usage and found the allocated memory was
>>>>>>>> within the limit of my physical memory.
>>>>>>>>
>>>>>>>> Any insights on this issue? Or any flag to turn on to print more
>>>>>>>> debug information?
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>> Wei
>>>>>>>>
>>>>>>>> ========= ShapeWorksRun log ===================
>>>>>>>> weiliu@lando:/scratch/experiments/shapeworks>
>>>>>>>> /scratch/packages/shapeworks.git/build/ShapeWorksRun/ShapeWorksRun
>>>>>>>> lung.correspondence.xml
>>>>>>>> m_processing_mode = 3
>>>>>>>> m_number_of_particles = 256
>>>>>>>> m_optimization_iterations = 200
>>>>>>>> m_output_points_prefix = lung
>>>>>>>> m_output_transform_file = output_transform_file
>>>>>>>> m_domains_per_shape = 1
>>>>>>>> m_timepts_per_subject = 1
>>>>>>>> m_starting_regularization = 10
>>>>>>>> m_ending_regularization = 0.1
>>>>>>>> m_iterations_per_split = 200
>>>>>>>> m_relative_weighting = 1
>>>>>>>> m_norm_penalty_weighting = 0
>>>>>>>> m_initial_relative_weighting = 0.05
>>>>>>>> m_initial_norm_penalty_weighting = 0
>>>>>>>> m_adaptivity_strength = 0
>>>>>>>> m_attributes_per_domain = 0
>>>>>>>> m_checkpointing_interval = 20
>>>>>>>> m_transform_file =
>>>>>>>> m_prefix_transform_file =
>>>>>>>> m_procrustes_interval = 0
>>>>>>>> m_recompute_regularization_interval = 1
>>>>>>>> m_procrustes_scaling = 1
>>>>>>>> m_adaptivity_mode = 0
>>>>>>>> m_keep_checkpoints = 0
>>>>>>>> m_optimization_iterations_completed = 0
>>>>>>>> Procrustes scaling is on
>>>>>>>> Mean curvature magnitude = 0.0410644
>>>>>>>> Std deviation = 0.0386809
>>>>>>>> Mean curvature magnitude = 0.0483452
>>>>>>>> Std deviation = 0.0401311
>>>>>>>> Mean curvature magnitude = 0.0528453
>>>>>>>> Std deviation = 0.0415891
>>>>>>>> Mean curvature magnitude = 0.0442168
>>>>>>>> Std deviation = 0.0440822
>>>>>>>> Mean curvature magnitude = 0.039068
>>>>>>>> Std deviation = 0.0368917
>>>>>>>> ------------------------------
>>>>>>>> *** Initialize Step
>>>>>>>> ------------------------------
>>>>>>>>
>>>>>>>> Particle count: 2
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 2points
>>>>>>>> Writing lung.1.wpts with 2points
>>>>>>>> Writing lung.2.wpts with 2points
>>>>>>>> Writing lung.3.wpts with 2points
>>>>>>>> Writing lung.4.wpts with 2points
>>>>>>>>
>>>>>>>> Particle count: 4
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 4points
>>>>>>>> Writing lung.1.wpts with 4points
>>>>>>>> Writing lung.2.wpts with 4points
>>>>>>>> Writing lung.3.wpts with 4points
>>>>>>>> Writing lung.4.wpts with 4points
>>>>>>>>
>>>>>>>> Particle count: 8
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 8points
>>>>>>>> Writing lung.1.wpts with 8points
>>>>>>>> Writing lung.2.wpts with 8points
>>>>>>>> Writing lung.3.wpts with 8points
>>>>>>>> Writing lung.4.wpts with 8points
>>>>>>>>
>>>>>>>> Particle count: 16
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 16points
>>>>>>>> Writing lung.1.wpts with 16points
>>>>>>>> Writing lung.2.wpts with 16points
>>>>>>>> Writing lung.3.wpts with 16points
>>>>>>>> Writing lung.4.wpts with 16points
>>>>>>>>
>>>>>>>> Particle count: 32
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 32points
>>>>>>>> Writing lung.1.wpts with 32points
>>>>>>>> Writing lung.2.wpts with 32points
>>>>>>>> Writing lung.3.wpts with 32points
>>>>>>>> Writing lung.4.wpts with 32points
>>>>>>>>
>>>>>>>> Particle count: 64
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 64points
>>>>>>>> Writing lung.1.wpts with 64points
>>>>>>>> Writing lung.2.wpts with 64points
>>>>>>>> Writing lung.3.wpts with 64points
>>>>>>>> Writing lung.4.wpts with 64points
>>>>>>>>
>>>>>>>> Particle count: 128
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 128points
>>>>>>>> Writing lung.1.wpts with 128points
>>>>>>>> Writing lung.2.wpts with 128points
>>>>>>>> Writing lung.3.wpts with 128points
>>>>>>>> Writing lung.4.wpts with 128points
>>>>>>>>
>>>>>>>> Particle count: 256
>>>>>>>> Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Performing global step
>>>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>>>> Writing lung.1.wpts with 256points
>>>>>>>> Writing lung.2.wpts with 256points
>>>>>>>> Writing lung.3.wpts with 256points
>>>>>>>> Writing lung.4.wpts with 256points
>>>>>>>> Writing lung.0.wpts with 256points
>>>>>>>> Writing lung.1.wpts with 256points
>>>>>>>> Writing lung.2.wpts with 256points
>>>>>>>> Writing lung.3.wpts with 256points
>>>>>>>> Writing lung.4.wpts with 256points
>>>>>>>> ------------------------------
>>>>>>>> *** AddAdaptivity Step
>>>>>>>> ------------------------------
>>>>>>>> ------------------------------
>>>>>>>> *** Optimize Step
>>>>>>>> ------------------------------
>>>>>>>> Optimizing correspondences.
>>>>>>>> Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: -1.95399e-12
>>>>>>>> 1: 2233.63
>>>>>>>> 2: 6109.69
>>>>>>>> 3: 9130.2
>>>>>>>> 4: 13024.7
>>>>>>>> ENERGY = 7.00618 MinimumVariance = 10
>>>>>>>> ..........Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: 9.722e-12
>>>>>>>> 1: 2632.27
>>>>>>>> 2: 7232.2
>>>>>>>> 3: 10060.2
>>>>>>>> 4: 14207.3
>>>>>>>> ENERGY = 7.10904 MinimumVariance = 7.94328
>>>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>>>> Writing lung.1.wpts with 256points
>>>>>>>> Writing lung.2.wpts with 256points
>>>>>>>> Writing lung.3.wpts with 256points
>>>>>>>> Writing lung.4.wpts with 256points
>>>>>>>> Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: 1.0556e-11
>>>>>>>> 1: 3094.51
>>>>>>>> 2: 8472.64
>>>>>>>> 3: 11077.3
>>>>>>>> 4: 15777.5
>>>>>>>> ENERGY = 7.21294 MinimumVariance = 6.30957
>>>>>>>> ..........Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: 2.98161e-12
>>>>>>>> 1: 3625.51
>>>>>>>> 2: 9820.69
>>>>>>>> 3: 12145.6
>>>>>>>> 4: 17588.4
>>>>>>>> ENERGY = 7.31406 MinimumVariance = 5.01187
>>>>>>>> ..........Writing lung.0.wpts with 256points
>>>>>>>> Writing lung.1.wpts with 256points
>>>>>>>> Writing lung.2.wpts with 256points
>>>>>>>> Writing lung.3.wpts with 256points
>>>>>>>> Writing lung.4.wpts with 256points
>>>>>>>> Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: 1.29785e-11
>>>>>>>> 1: 4217.28
>>>>>>>> 2: 11188.9
>>>>>>>> 3: 13313.2
>>>>>>>> 4: 19565.2
>>>>>>>> ENERGY = 7.40989 MinimumVariance = 3.98107
>>>>>>>> ..........Performing global step
>>>>>>>> BeforeIteration counter = 0
>>>>>>>> 0: 1.87255e-11
>>>>>>>> 1: 4865.53
>>>>>>>> 2: 12485.8
>>>>>>>> 3: 14779.8
>>>>>>>> 4: 21615.6
>>>>>>>> ENERGY = 7.50115 MinimumVariance = 3.16228
>>>>>>>> .........Segmentation fault
>>>>>>>> ============ end of ShapeWorksRun log ===========
>>>>>>>>
>>>>>>>>
>>>>>>>> ============== files generated ==================
>>>>>>>>
>>>>>>>> -rw-r--r-- 1 weiliu users 6825 Jul 1 14:45 lung.0.wpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6825 Jul 1 14:45 lung.0.lpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.1.lpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.1.wpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6820 Jul 1 14:45 lung.2.wpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6820 Jul 1 14:45 lung.2.lpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6807 Jul 1 14:45 lung.3.wpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6807 Jul 1 14:45 lung.3.lpts
>>>>>>>> -rw-r--r-- 1 weiliu users 644 Jul 1 14:45
>>>>>>>> output_transform_file
>>>>>>>> -rw-r--r-- 1 weiliu users 6812 Jul 1 14:45 lung.4.wpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6812 Jul 1 14:45 lung.4.lpts
>>>>>>>> -rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.mean
>>>>>>>> -rw-r--r-- 1 weiliu users 6843 Jul 1 14:45 lung.d0.-3.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6829 Jul 1 14:45 lung.d0.-2.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6818 Jul 1 14:45 lung.d0.-1.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6809 Jul 1 14:45 lung.d0.2.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6814 Jul 1 14:45 lung.d0.1.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6791 Jul 1 14:45 lung.d0.3.0.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6793 Jul 1 14:45 lung.d0.-3.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.d0.-2.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6805 Jul 1 14:45 lung.d0.-1.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6823 Jul 1 14:45 lung.d0.2.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6804 Jul 1 14:45 lung.d0.1.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6796 Jul 1 14:45 lung.d0.3.1.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6790 Jul 1 14:45 lung.d0.-3.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6775 Jul 1 14:45 lung.d0.-2.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6795 Jul 1 14:45 lung.d0.-1.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6818 Jul 1 14:45 lung.d0.1.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6808 Jul 1 14:45 lung.d0.3.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6829 Jul 1 14:45 lung.d0.2.2.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6827 Jul 1 14:45 lung.d0.-3.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6793 Jul 1 14:45 lung.d0.-2.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6801 Jul 1 14:45 lung.d0.-1.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6798 Jul 1 14:45 lung.d0.1.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6815 Jul 1 14:45 lung.d0.3.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6806 Jul 1 14:45 lung.d0.2.3.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-3.4.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-2.4.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6816 Jul 1 14:45 lung.d0.1.4.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.-1.4.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6817 Jul 1 14:45 lung.d0.2.4.mode
>>>>>>>> -rw-r--r-- 1 weiliu users 6816 Jul 1 14:45 lung.d0.3.4.mode
>>>>>>>>
>>>>>>>> =============== configuration .xml file =====================
>>>>>>>> <?xml version="1.0" ?>
>>>>>>>>
>>>>>>>> <!-- List of files containing the set of shape surfaces. -->
>>>>>>>> <inputs>
>>>>>>>> PE105B.nii.gz
>>>>>>>> PE900B.nii.gz
>>>>>>>> PE908B.nii.gz
>>>>>>>> PE916B.nii.gz
>>>>>>>> PE919B.nii.gz
>>>>>>>> </inputs>
>>>>>>>>
>>>>>>>> <!--
>>>>>>>> OPTIONALLY we could specify a set of point files to initialize the
>>>>>>>> optimization like this:
>>>>>>>> <point_files>
>>>>>>>> torusDT.00.lpts
>>>>>>>> torusDT.01.lpts
>>>>>>>> :
>>>>>>>> .
>>>>>>>> torusDT.19.lpts
>>>>>>>> </point_files>
>>>>>>>> -->
>>>>>>>>
>>>>>>>> <!-- If point files are not specified, then the application will
>>>>>>>> initialize particles
>>>>>>>> by splitting until each shape has this total number of
>>>>>>>> particles. -->
>>>>>>>> <number_of_particles> 256 </number_of_particles>
>>>>>>>>
>>>>>>>> <!-- Iterations between splitting during initialization phase. -->
>>>>>>>> <iterations_per_split> 200 </iterations_per_split>
>>>>>>>>
>>>>>>>> <!-- Starting regularization for the entropy-based correspondence
>>>>>>>> optimization. -->
>>>>>>>> <starting_regularization> 10.0 </starting_regularization>
>>>>>>>>
>>>>>>>> <!-- Final regularization for the entropy-based correspondence. -->
>>>>>>>> <ending_regularization> 0.1 </ending_regularization>
>>>>>>>>
>>>>>>>> <!-- Number of iterations for the entropy-based correspondence. -->
>>>>>>>> <optimization_iterations> 200 </optimization_iterations>
>>>>>>>>
>>>>>>>> <!-- Number of iterations between checkpoints (iterations at which
>>>>>>>> results are saved) -->
>>>>>>>> <checkpointing_interval> 20 </checkpointing_interval>
>>>>>>>>
>>>>>>>> <!-- Prefix for the output files. -->
>>>>>>>> <output_points_prefix> lung </output_points_prefix>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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