# Algorithms

**URL:** https://discourse.itk.org/c/algorithms/7.md?no_subcategories=false&page=18

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**Page:** 19

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## [What is the standard deviation (sigma) used to compute the Hessian in SimpleITK's ObjectnessMeasure](https://discourse.itk.org/t/what-is-the-standard-deviation-sigma-used-to-compute-the-hessian-in-simpleitks-objectnessmeasure/822)

<div class="topic-metadata">

**Author:** [@nicoco](https://discourse.itk.org/u/nicoco)\
**Replies:** 2\
**Last updated:** [April 3, 2018, 2:54pm UTC](https://discourse.itk.org/t/what-is-the-standard-deviation-sigma-used-to-compute-the-hessian-in-simpleitks-objectnessmeasure/822 "2018-04-03T14:54:16Z")

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Hello all, I’m trying to use the brand new SimpleITK procedural interface to the ObjectnessMeasureFilter. Since it automatically computes the Hessian Matrix of the image, I’d like to know which sigma value is used for …

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## [extracting a surface from a segmentation](https://discourse.itk.org/t/extracting-a-surface-from-a-segmentation/816)

<div class="topic-metadata">

**Author:** [@ibr](https://discourse.itk.org/u/ibr)\
**Replies:** 3\
**Last updated:** [April 2, 2018, 8:45pm UTC](https://discourse.itk.org/t/extracting-a-surface-from-a-segmentation/816 "2018-04-02T20:45:22Z")

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Hi, Is there a any itk filter to do this? I tried getting the edges but the surface was not good despite a good manual segmentation. By surface I mean the outer border of a 3D object (the contor). e.g. if I have a hand …

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## [PeriodicBoundaryCondition](https://discourse.itk.org/t/periodicboundarycondition/698)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 14\
**Last updated:** [March 15, 2018, 2:47pm UTC](https://discourse.itk.org/t/periodicboundarycondition/698 "2018-03-15T14:47:53Z")

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Hello, Is there an example of how to use a PeriodicBoundaryCondition anywhere? I had hoped it was as simple as changing the definition of my NeighborhoodIterator to ConstNeighborhoodIterator\<TImage, PeriodicBoundaryCon…

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## [Query regarding implementation of itkGeometricJacobianDeterminantImageFilter.hxx](https://discourse.itk.org/t/query-regarding-implementation-of-itkgeometricjacobiandeterminantimagefilter-hxx/748)

<div class="topic-metadata">

**Author:** [@Mageshwar](https://discourse.itk.org/u/Mageshwar)\
**Replies:** 2\
**Last updated:** [March 14, 2018, 1:49pm UTC](https://discourse.itk.org/t/query-regarding-implementation-of-itkgeometricjacobiandeterminantimagefilter-hxx/748 "2018-03-14T13:49:50Z")

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I want to have a deeper insight into the implementation of jacobian determinant in itkGeometricJacobianDeterminantImageFilter.hxx, but I’m unable to find some theory which explains on what basis this code is implemented.…

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## [ITK 4.13 changes](https://discourse.itk.org/t/itk-4-13-changes/757)

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**Author:** [@mstaring](https://discourse.itk.org/u/mstaring)\
**Replies:** 6\
**Last updated:** [March 14, 2018, 9:15am UTC](https://discourse.itk.org/t/itk-4-13-changes/757 "2018-03-14T09:15:12Z")

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Hi all, Our image registration software elastix depends on ITK. I recently updated the ITK version from ITK 4.12 to 4.13 and noticed this changed the results in some of our regression tests: https://my.cdash.org/viewTe…

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## [initial contour/surface as the zero level set](https://discourse.itk.org/t/initial-contour-surface-as-the-zero-level-set/751)

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**Author:** [@Abdelkhalek\_Bakkari](https://discourse.itk.org/u/Abdelkhalek_Bakkari)\
**Replies:** 1\
**Last updated:** [March 9, 2018, 8:21pm UTC](https://discourse.itk.org/t/initial-contour-surface-as-the-zero-level-set/751 "2018-03-09T20:21:14Z")

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Dear All, I am trying to adopt the eodesicActiveContourLevelSetImage Filter. However, I don’t know how to create the initial contour/surface using ITK and Qt. Could you please help me? Kind regards,

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## [Add itkIntegralImageFilter](https://discourse.itk.org/t/add-itkintegralimagefilter/744)

<div class="topic-metadata">

**Author:** [@Besler](https://discourse.itk.org/u/Besler)\
**Replies:** 1\
**Last updated:** [March 7, 2018, 9:50pm UTC](https://discourse.itk.org/t/add-itkintegralimagefilter/744 "2018-03-07T21:50:13Z")

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Hi Everyone! I am interested in using some Haar-like features for an object recognition task. I think an integral image is the way to go for computational performance. (I need to take the features further after this whi…

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## [Manual creation of FEMObject](https://discourse.itk.org/t/manual-creation-of-femobject/720)

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**Author:** [@Urban\_Simoncic](https://discourse.itk.org/u/Urban_Simoncic)\
**Replies:** 0\
**Last updated:** [February 27, 2018, 2:57pm UTC](https://discourse.itk.org/t/manual-creation-of-femobject/720 "2018-02-27T14:57:49Z")

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Hi, I am trying to use ITK for simple FEM elasticity problems, where FEM models would be derived from the medical image. However, I don’t want uniform mesh, so I will need to somehow create FEMObject myself. Is there an…

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## [Which Interpolator to Resample Image and its segmentation Mask](https://discourse.itk.org/t/which-interpolator-to-resample-image-and-its-segmentation-mask/689)

<div class="topic-metadata">

**Author:** [@Jsphine](https://discourse.itk.org/u/Jsphine)\
**Replies:** 4\
**Last updated:** [February 20, 2018, 3:12pm UTC](https://discourse.itk.org/t/which-interpolator-to-resample-image-and-its-segmentation-mask/689 "2018-02-20T15:12:44Z")

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Dear community, I have a set of CT images and their masks (segmentations). What I want to do is to rotate/resample them without losing the correspondence between the image and the mask. Using the LinearInterpolator yie…

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## [STL files](https://discourse.itk.org/t/stl-files/650)

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**Author:** [@Scleri](https://discourse.itk.org/u/Scleri)\
**Replies:** 2\
**Last updated:** [February 7, 2018, 1:45pm UTC](https://discourse.itk.org/t/stl-files/650 "2018-02-07T13:45:27Z")

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Hi there, I need to store points of a STL file in a container, I found this class: itkSTLMeshIO, But I’m not able to store point of the input STL file in a container. Should I use ReadDataPoint? I don’t understand ho…

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## [Mean of Complex Vector Image](https://discourse.itk.org/t/mean-of-complex-vector-image/632)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 4\
**Last updated:** [February 2, 2018, 7:50pm UTC](https://discourse.itk.org/t/mean-of-complex-vector-image/632 "2018-02-02T19:50:03Z")

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Hi, I need to take the average (mean) of a complex-valued vector image (i.e. the output should also be a complex vector). I am trying to do this with itk::StatisticsImageFilter, however, I am getting the following compi…

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## [Crash caused by itk.PDEDeformableRegistrationFilter](https://discourse.itk.org/t/crash-caused-by-itk-pdedeformableregistrationfilter/611)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 7\
**Last updated:** [January 29, 2018, 12:18am UTC](https://discourse.itk.org/t/crash-caused-by-itk-pdedeformableregistrationfilter/611 "2018-01-29T00:18:00Z")

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Hi all, When I used itk.PDEDeformableRegistrationFilter to perform deformable registration on two 3D images using python supported ITK, “Segmentation fault (core dumped)” appeared. Other deformable registration methods …

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## [Gradient magnitude filter](https://discourse.itk.org/t/gradient-magnitude-filter/603)

<div class="topic-metadata">

**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 2\
**Last updated:** [January 19, 2018, 9:11pm UTC](https://discourse.itk.org/t/gradient-magnitude-filter/603 "2018-01-19T21:11:15Z")

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Hello, Is there any difference between the gradients calculated by GradientMagnitudeImageFilter and GradientImageFilter? I took a quick look at the source expecting the former filter to call the latter + AbsImageFilter…

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## [Set values for a displacement field](https://discourse.itk.org/t/set-values-for-a-displacement-field/586)

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**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 1\
**Last updated:** [January 12, 2018, 7:01pm UTC](https://discourse.itk.org/t/set-values-for-a-displacement-field/586 "2018-01-12T19:01:40Z")

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Hello! I want to set values for a displacement field. If the position is on a grid point, i.e. something like \[2,3,4\], I will just use SetPixel(). However, sometimes the position is not on a grid point, like \[0.5, 1.7, …

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## [Difference between two displacement fields](https://discourse.itk.org/t/difference-between-two-displacement-fields/582)

<div class="topic-metadata">

**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 1\
**Last updated:** [January 10, 2018, 8:03pm UTC](https://discourse.itk.org/t/difference-between-two-displacement-fields/582 "2018-01-10T20:03:13Z")

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Hello! Given two displacement fields df1 and df2, does ITK provide a way to compute the difference between the two displacement fields? i.e. || df1-df2 || Thanks. -Ray

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## [Some thing slow down itkMaskNeighborhoodOperatorImageFilter](https://discourse.itk.org/t/some-thing-slow-down-itkmaskneighborhoodoperatorimagefilter/537)

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**Author:** [@Rock\_Lin](https://discourse.itk.org/u/Rock_Lin)\
**Replies:** 4\
**Last updated:** [January 8, 2018, 4:13pm UTC](https://discourse.itk.org/t/some-thing-slow-down-itkmaskneighborhoodoperatorimagefilter/537 "2018-01-08T16:13:10Z")

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Hi, ITK developers, I am working for implementing a fast convolution process and I found some thing seems incorrect in the itkMaskNeighborhoodOperatorImageFilter . I made a MaskConvolutionImageFilter using itkMaskNeig…

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## [Run length matrices](https://discourse.itk.org/t/run-length-matrices/548)

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**Author:** [@Francisco\_Oliveira](https://discourse.itk.org/u/Francisco_Oliveira)\
**Replies:** 3\
**Last updated:** [December 26, 2017, 10:19am UTC](https://discourse.itk.org/t/run-length-matrices/548 "2017-12-26T10:19:19Z")

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Hello, I want to use the itk filter ScalarImageToRunLengthMatrixFilter for texture analysis. But I think there something with the filter that does not make sense for me. The filter only allows to set the same number of …

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## [Multi Object Segmentation by Level Set Method](https://discourse.itk.org/t/multi-object-segmentation-by-level-set-method/534)

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**Author:** [@arwtyxouymz](https://discourse.itk.org/u/arwtyxouymz)\
**Replies:** 1\
**Last updated:** [December 18, 2017, 2:00pm UTC](https://discourse.itk.org/t/multi-object-segmentation-by-level-set-method/534 "2017-12-18T14:00:14Z")

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Hi, Although I wonder if I should ask here, I have a question about level set method. Is it possible to detect multi object contour by using level set method? Or, supposing there are 3 object, is the contour detectio…

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## [BSpline on multi-level registration](https://discourse.itk.org/t/bspline-on-multi-level-registration/512)

<div class="topic-metadata">

**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 3\
**Last updated:** [December 18, 2017, 1:18pm UTC](https://discourse.itk.org/t/bspline-on-multi-level-registration/512 "2017-12-18T13:18:59Z")

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Hello! I’m trying to understand multi-level BSpline registration in ITK. I’m using itk::BSplineTransform as my transformation model. I set the mesh size to be 8x8x8. If I run a 2-level registration with shrinking factor…

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## [Why is numberOfGridNodesInOneDimension not equal to meshsize in BSpline transformation?](https://discourse.itk.org/t/why-is-numberofgridnodesinonedimension-not-equal-to-meshsize-in-bspline-transformation/495)

<div class="topic-metadata">

**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 1\
**Last updated:** [December 10, 2017, 5:53am UTC](https://discourse.itk.org/t/why-is-numberofgridnodesinonedimension-not-equal-to-meshsize-in-bspline-transformation/495 "2017-12-10T05:53:04Z")

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Why is numberOfGridNodesInOneDimension not equal to meshsize in BSpline transformation? The example code shows numberOfGridNodesInOneDimension = SplineOrder + meshSize (of one dimension). Why do we have this? unsigned i…

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## [Segmentation Fault style error during Casting](https://discourse.itk.org/t/segmentation-fault-style-error-during-casting/485)

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**Author:** [@WillScottJackson](https://discourse.itk.org/u/WillScottJackson)\
**Replies:** 11\
**Last updated:** [December 6, 2017, 4:05pm UTC](https://discourse.itk.org/t/segmentation-fault-style-error-during-casting/485 "2017-12-06T16:05:58Z")

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Hi there I’m debugging some code to perform a process on 3D MRI data and I’m getting hung up on a crash I keep encountering when my application is performing a type cast from an unsigned short image to a float. The rel…

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## [Image Stamping](https://discourse.itk.org/t/image-stamping/447)

<div class="topic-metadata">

**Author:** [@NHPatterson](https://discourse.itk.org/u/NHPatterson)\
**Replies:** 1\
**Last updated:** [November 21, 2017, 8:56pm UTC](https://discourse.itk.org/t/image-stamping/447 "2017-11-21T20:56:17Z")

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Hello, I am trying to do a sort of morphological filtering on an image. I am not sure how to call this sort of filter, but perhaps it is already known in ITK. Let’s suppose we have a 2000x2000 2D image, this filter woul…

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## [Neighborhood Cross Correlation](https://discourse.itk.org/t/neighborhood-cross-correlation/443)

<div class="topic-metadata">

**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 0\
**Last updated:** [November 21, 2017, 6:08pm UTC](https://discourse.itk.org/t/neighborhood-cross-correlation/443 "2017-11-21T18:08:58Z")

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This is a function in itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx to compute cross correlation in a local window. I think if fabs(sFixedFixed\_sMovingMoving) \< NumericTraits\< LocalR…

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## [flipping transform in ITK](https://discourse.itk.org/t/flipping-transform-in-itk/437)

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**Author:** [@asertyuio](https://discourse.itk.org/u/asertyuio)\
**Replies:** 2\
**Last updated:** [November 21, 2017, 10:55am UTC](https://discourse.itk.org/t/flipping-transform-in-itk/437 "2017-11-21T10:55:58Z")

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Hi everyone, Is there by any change a way of having a flipping, or mirroring transform ? A transform, not a filter. I have looking for it, but no match for now. As I’m working with 2D images, I’ve tried to use a 3D Eule…

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## [Automatic femur segmentation edge closing](https://discourse.itk.org/t/automatic-femur-segmentation-edge-closing/428)

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**Author:** [@Pythonsegmenter](https://discourse.itk.org/u/Pythonsegmenter)\
**Replies:** 7\
**Last updated:** [November 18, 2017, 12:56am UTC](https://discourse.itk.org/t/automatic-femur-segmentation-edge-closing/428 "2017-11-18T00:56:40Z")

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Hi all, I’m doing a project in which I need to automatically segment the femur. It seemed like an easy job (great difference between bone and soft tissue) but I’ve been stuck for a while. I’ve already written a basic al…

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## [Unstable iteration for registration](https://discourse.itk.org/t/unstable-iteration-for-registration/410)

<div class="topic-metadata">

**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 12\
**Last updated:** [November 17, 2017, 4:53am UTC](https://discourse.itk.org/t/unstable-iteration-for-registration/410 "2017-11-17T04:53:40Z")

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Hi all, I am using itk.RegularStepGradientDescentOptimizerv4 to perform a multiresolution translation registration between two images. I ran my code in the same computation environment for the same two images at differe…

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## [Generate inverse warp images](https://discourse.itk.org/t/generate-inverse-warp-images/401)

<div class="topic-metadata">

**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 1\
**Last updated:** [November 8, 2017, 8:55pm UTC](https://discourse.itk.org/t/generate-inverse-warp-images/401 "2017-11-08T20:55:35Z")

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I use rigid registration to get a transformation estimation represented by six numbers (three for rotation, three for translation). And I use the following code to generate the corresponding warp image. I wonder if there…

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## [Change optimizer parameters for multiresolution image registration](https://discourse.itk.org/t/change-optimizer-parameters-for-multiresolution-image-registration/397)

<div class="topic-metadata">

**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 5\
**Last updated:** [November 12, 2017, 2:23pm UTC](https://discourse.itk.org/t/change-optimizer-parameters-for-multiresolution-image-registration/397 "2017-11-12T14:23:08Z")

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Hi all, I saw the example of MultiResImageRegistration1.cxx can change the optimizer parameters (e.g learning rate) for different level of a image pyramid. But when I learnt from it to write python-supported ITK code, t…

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## [GDCMImageIO](https://discourse.itk.org/t/gdcmimageio/402)

<div class="topic-metadata">

**Author:** [@coertmetz](https://discourse.itk.org/u/coertmetz)\
**Replies:** 0\
**Last updated:** [November 9, 2017, 2:25pm UTC](https://discourse.itk.org/t/gdcmimageio/402 "2017-11-09T14:25:17Z")

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GDCMImageIO seems to use GDCM’s default for the transfer syntax, which is an implicit one. Is there a way to make it use explicit transfer syntax?

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## [itk FEM Solver](https://discourse.itk.org/t/itk-fem-solver/339)

<div class="topic-metadata">

**Author:** [@nasil122002](https://discourse.itk.org/u/nasil122002)\
**Replies:** 4\
**Last updated:** [November 9, 2017, 2:10pm UTC](https://discourse.itk.org/t/itk-fem-solver/339 "2017-11-09T14:10:44Z")

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Dear ITK community, I want to deform a 3D model using itk’s FEM module. For this I have implemented the following workflow: Read CT data-set and create 3D iso-surface using vtkMarchingCubes (output is polydata) Extrac…

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