# Latest

**URL:** https://discourse.itk.org/latest.md?page=19

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

**Page:** 20

---

## [SimpleITK incorrectly identifies DICOM pixel type](https://discourse.itk.org/t/simpleitk-incorrectly-identifies-dicom-pixel-type/6185)

<div class="topic-metadata">

**Author:** [@mherron](https://discourse.itk.org/u/mherron)\
**Replies:** 6\
**Last updated:** [September 12, 2023, 8:45pm UTC](https://discourse.itk.org/t/simpleitk-incorrectly-identifies-dicom-pixel-type/6185 "2023-09-12T20:45:38Z")

</div>

I’m a developer on a software package that has started using SimpleITK to read in various image types. We have an explicit list of pixel types that we support, and if, after reading an image using SimpleITK, we find that…

---

## [Fail to install SimpleElastix due to multiple definition](https://discourse.itk.org/t/fail-to-install-simpleelastix-due-to-multiple-definition/6194)

<div class="topic-metadata">

**Author:** [@Siji-chl](https://discourse.itk.org/u/Siji-chl)\
**Replies:** 1\
**Last updated:** [September 12, 2023, 2:47pm UTC](https://discourse.itk.org/t/fail-to-install-simpleelastix-due-to-multiple-definition/6194 "2023-09-12T14:47:34Z")

</div>

I follow the instruction from the official website $ git clone https://github.com/SuperElastix/SimpleElastix $ mkdir build $ cd build $ cmake ../SimpleElastix/SuperBuild $ make -j4 the make -j4 instructions did not wor…

---

## [Pip install locally built ITK remote module?](https://discourse.itk.org/t/pip-install-locally-built-itk-remote-module/6191)

<div class="topic-metadata">

**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 1\
**Last updated:** [September 12, 2023, 11:24am UTC](https://discourse.itk.org/t/pip-install-locally-built-itk-remote-module/6191 "2023-09-12T11:24:38Z")

</div>

Hi I am developing tools for my workflows using ITK remote modules. To test these from Python I have so far used the wheels generated by the CI (github action), or eventually from PyPI. Unfortunately, this no longer wo…

---

## [How to change VascularNetwork.tre file from TubeTK into 0-1 mask?](https://discourse.itk.org/t/how-to-change-vascularnetwork-tre-file-from-tubetk-into-0-1-mask/6188)

<div class="topic-metadata">

**Author:** [@rzjiang0603](https://discourse.itk.org/u/rzjiang0603)\
**Replies:** 3\
**Last updated:** [September 11, 2023, 6:26pm UTC](https://discourse.itk.org/t/how-to-change-vascularnetwork-tre-file-from-tubetk-into-0-1-mask/6188 "2023-09-11T18:26:30Z")

</div>

I am trying to use the TubeTK dataset here https://public.kitware.com/Wiki/TubeTK/Data to do some intracranial vasculature segmentation task. Thus i need to use the VascularNetwork.tre file as the ground truth. The prob…

---

## [Resample to same Spacing and Size and Align to same Origin](https://discourse.itk.org/t/resample-to-same-spacing-and-size-and-align-to-same-origin/1378)

<div class="topic-metadata">

**Author:** [@ral\_san](https://discourse.itk.org/u/ral_san)\
**Replies:** 27\
**Last updated:** [September 8, 2023, 3:42pm UTC](https://discourse.itk.org/t/resample-to-same-spacing-and-size-and-align-to-same-origin/1378 "2023-09-08T15:42:04Z")

</div>

I have a set of 4 DICOM CT Volumes which I am reading with SimpleITK ImageSeriesReader. Two of the images represent the CT of patient before and after the surgery. The other two images are binary segmentation masks segme…

---

## [How to set center z if the 3D image is rotated along z axis with ITK::affineTransform?](https://discourse.itk.org/t/how-to-set-center-z-if-the-3d-image-is-rotated-along-z-axis-with-itk-affinetransform/6186)

<div class="topic-metadata">

**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 0\
**Last updated:** [September 8, 2023, 8:14am UTC](https://discourse.itk.org/t/how-to-set-center-z-if-the-3d-image-is-rotated-along-z-axis-with-itk-affinetransform/6186 "2023-09-08T08:14:08Z")

</div>

Hello all, I am working on 3D image rotation now. And ITK is really a great tool to do image processing. I have used affinetransform to rotate the 3D image. The rotation is done along z axis, in my view, the center on z…

---

## [Add empty slice at the end of the CT image](https://discourse.itk.org/t/add-empty-slice-at-the-end-of-the-ct-image/6182)

<div class="topic-metadata">

**Author:** [@agatadefr](https://discourse.itk.org/u/agatadefr)\
**Replies:** 3\
**Last updated:** [September 7, 2023, 12:30pm UTC](https://discourse.itk.org/t/add-empty-slice-at-the-end-of-the-ct-image/6182 "2023-09-07T12:30:17Z")

</div>

Hello, I have a simple question. i need to resize CT scan saved in nifty file. I need to add one black slice at the end of the 3D image (in Z direction). I would appreciate for any help/suggestion. How can I do that i…

---

## [How to use ITK to segment bones in osteoporotic patients](https://discourse.itk.org/t/how-to-use-itk-to-segment-bones-in-osteoporotic-patients/6181)

<div class="topic-metadata">

**Author:** [@AeBoPi](https://discourse.itk.org/u/AeBoPi)\
**Replies:** 2\
**Last updated:** [September 6, 2023, 4:12pm UTC](https://discourse.itk.org/t/how-to-use-itk-to-segment-bones-in-osteoporotic-patients/6181 "2023-09-06T16:12:28Z")

</div>

Osteoporosis reduces bone density and thus the strength of bone in the CT data set (shown in the figure), making it impossible to use traditional thresholding techniques to handle segmentation. I noticed that the M…

---

## [Bioimage analyst position @MinosBiosciences (Paris, France)](https://discourse.itk.org/t/bioimage-analyst-position-minosbiosciences-paris-france/6180)

<div class="topic-metadata">

**Author:** [@MinosBiosciences](https://discourse.itk.org/u/MinosBiosciences)\
**Replies:** 0\
**Last updated:** [September 6, 2023, 8:56am UTC](https://discourse.itk.org/t/bioimage-analyst-position-minosbiosciences-paris-france/6180 "2023-09-06T08:56:25Z")

</div>

Dear community, Minos Biosciences , a startup based in Paris, is advancing the integration of microscopy images and sequencing data, on single cells, at high throughput. We are currently searching for a talented and hi…

---

## [Setting up SimpleITK with anaconda](https://discourse.itk.org/t/setting-up-simpleitk-with-anaconda/6175)

<div class="topic-metadata">

**Author:** [@devo99](https://discourse.itk.org/u/devo99)\
**Replies:** 1\
**Last updated:** [September 4, 2023, 3:19pm UTC](https://discourse.itk.org/t/setting-up-simpleitk-with-anaconda/6175 "2023-09-04T15:19:07Z")

</div>

Hello there, I have been frustrated with getting SimpleITK working with jupyter past week. I have been following the instructions on this article : SimpleITK Tutorial . I have installed everything that is necessary. Ho…

---

## [How to ensure DRR generated image has the same size as Input Xray image during 2d/3dregistration](https://discourse.itk.org/t/how-to-ensure-drr-generated-image-has-the-same-size-as-input-xray-image-during-2d-3dregistration/3445)

<div class="topic-metadata">

**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 6\
**Last updated:** [September 4, 2023, 3:38am UTC](https://discourse.itk.org/t/how-to-ensure-drr-generated-image-has-the-same-size-as-input-xray-image-during-2d-3dregistration/3445 "2023-09-04T03:38:07Z")

</div>

Good Morning All, I have a question regarding the itk2d3dregistration module. I’m using it to register a CT liver volume to an XRay of said liver. I’ve extracted the vessels in both the 2d and 3d images and used those a…

---

## [I tried to configure itk on Linux and found an error, what is the reason](https://discourse.itk.org/t/i-tried-to-configure-itk-on-linux-and-found-an-error-what-is-the-reason/6176)

<div class="topic-metadata">

**Author:** [@ljjiayou](https://discourse.itk.org/u/ljjiayou)\
**Replies:** 0\
**Last updated:** [September 3, 2023, 1:13pm UTC](https://discourse.itk.org/t/i-tried-to-configure-itk-on-linux-and-found-an-error-what-is-the-reason/6176 "2023-09-03T13:13:29Z")

</div>

This is my step: mkdir ITK-Sandbox cd ITK-sandbox git clone GitHub - InsightSoftwareConsortium/ITK: Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing,…

---

## [ITKIOGDCM error with long dicom datasets](https://discourse.itk.org/t/itkiogdcm-error-with-long-dicom-datasets/6173)

<div class="topic-metadata">

**Author:** [@arvequina](https://discourse.itk.org/u/arvequina)\
**Replies:** 0\
**Last updated:** [September 1, 2023, 9:21am UTC](https://discourse.itk.org/t/itkiogdcm-error-with-long-dicom-datasets/6173 "2023-09-01T09:21:20Z")

</div>

Hi! First thank you to all the contributors in here as it is always super useful. Probably this one is more indicated for the GDCM guru @mathieu.malaterre :sweat\_smile: I ran into a problem using GDCM to read dicom file…

---

## [Issue with mesh points interpolation from nifti DVF image volume](https://discourse.itk.org/t/issue-with-mesh-points-interpolation-from-nifti-dvf-image-volume/6171)

<div class="topic-metadata">

**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 4\
**Last updated:** [September 1, 2023, 11:31am UTC](https://discourse.itk.org/t/issue-with-mesh-points-interpolation-from-nifti-dvf-image-volume/6171 "2023-09-01T11:31:31Z")

</div>

Hi, I have generated deformed 3D-CT versions and corresponding deformation vector field (DVF) volumes of a given nifti image volume (reference image 3D-CT volume) using another tool. I then extracted the liver mesh from…

---

## [Resample displacement field](https://discourse.itk.org/t/resample-displacement-field/6158)

<div class="topic-metadata">

**Author:** [@Xinyue](https://discourse.itk.org/u/Xinyue)\
**Replies:** 7\
**Last updated:** [September 1, 2023, 9:53am UTC](https://discourse.itk.org/t/resample-displacement-field/6158 "2023-09-01T09:53:53Z")

</div>

Hi, I am working on the image registration question, and I have my fix image, moving image and displacement field (deformation vector field). I have resampled my images to spacing 1.035003662109375, 1.035003662109375, …

---

## [Issue with Visualizing predictions and Groundtruths after numpy to sitk conversion](https://discourse.itk.org/t/issue-with-visualizing-predictions-and-groundtruths-after-numpy-to-sitk-conversion/6167)

<div class="topic-metadata">

**Author:** [@rosanajurdi](https://discourse.itk.org/u/rosanajurdi)\
**Replies:** 2\
**Last updated:** [August 29, 2023, 2:39pm UTC](https://discourse.itk.org/t/issue-with-visualizing-predictions-and-groundtruths-after-numpy-to-sitk-conversion/6167 "2023-08-29T14:39:43Z")

</div>

Hello, I am running into an error whenever I try to visualize the predictions vs ground-truths with sitk . I have a probability map correspinding to the out put of the model, and a binary groundtruth (resamppled) and a…

---

## [Composite Transform with second Transform on resampled Image](https://discourse.itk.org/t/composite-transform-with-second-transform-on-resampled-image/6163)

<div class="topic-metadata">

**Author:** [@kenrickmoke](https://discourse.itk.org/u/kenrickmoke)\
**Replies:** 3\
**Last updated:** [August 29, 2023, 8:10am UTC](https://discourse.itk.org/t/composite-transform-with-second-transform-on-resampled-image/6163 "2023-08-29T08:10:13Z")

</div>

Hello Community, my question is regarding a cleaner way to combine multiple transforms where the latter transforms are optimized over the resampled image. So what I want to do smth like this: resampled = T1(fixed,movi…

---

## [I am trying to copy all the metadata/header information from one image to another.](https://discourse.itk.org/t/i-am-trying-to-copy-all-the-metadata-header-information-from-one-image-to-another/6120)

<div class="topic-metadata">

**Author:** [@Cristobal\_Rodero](https://discourse.itk.org/u/Cristobal_Rodero)\
**Replies:** 2\
**Last updated:** [August 29, 2023, 7:29am UTC](https://discourse.itk.org/t/i-am-trying-to-copy-all-the-metadata-header-information-from-one-image-to-another/6120 "2023-08-29T07:29:24Z")

</div>

I have a segmentation (original\_image) that when I overlap it with the MRI image it comes from it overlaps as expected (comparing it in 3D Slicer, for instance). I perform some operations on Seg3D (or any other software …

---

## [Measure diameter of curved 3d tube](https://discourse.itk.org/t/measure-diameter-of-curved-3d-tube/6162)

<div class="topic-metadata">

**Author:** [@cams2b](https://discourse.itk.org/u/cams2b)\
**Replies:** 1\
**Last updated:** [August 24, 2023, 4:58pm UTC](https://discourse.itk.org/t/measure-diameter-of-curved-3d-tube/6162 "2023-08-24T16:58:26Z")

</div>

Hello everyone, I am working with a 3d curved tubular structure. I have extracted the centerline at various points and now I am trying to calculate the diameter of the tube at those points. At the curved regions, I am t…

---

## [BSplineTransform with displacement approaching zero at image boundary](https://discourse.itk.org/t/bsplinetransform-with-displacement-approaching-zero-at-image-boundary/6154)

<div class="topic-metadata">

**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 8\
**Last updated:** [August 24, 2023, 2:19am UTC](https://discourse.itk.org/t/bsplinetransform-with-displacement-approaching-zero-at-image-boundary/6154 "2023-08-24T02:19:36Z")

</div>

According to the documentation and some experiments, the BSplineTransform deformation is zero outside the support region of the coefficient images (but non-zero at the boundary, i.e. there is a discontinuity). I would l…

---

## [Setting directional cosines](https://discourse.itk.org/t/setting-directional-cosines/6156)

<div class="topic-metadata">

**Author:** [@Krishna\_Nanda](https://discourse.itk.org/u/Krishna_Nanda)\
**Replies:** 2\
**Last updated:** [August 22, 2023, 5:20pm UTC](https://discourse.itk.org/t/setting-directional-cosines/6156 "2023-08-22T17:20:05Z")

</div>

Hello, I am a little unclear on how the directional cosines are set to create a new Simple ITK image. I understand that they should be in row major order. Is this correct: If we take a 2D example, the unit vector along …

---

## [How to do a standard FDK using itk-rtk in python.](https://discourse.itk.org/t/how-to-do-a-standard-fdk-using-itk-rtk-in-python/6141)

<div class="topic-metadata">

**Author:** [@Victor\_Hu](https://discourse.itk.org/u/Victor_Hu)\
**Replies:** 4\
**Last updated:** [August 19, 2023, 5:54am UTC](https://discourse.itk.org/t/how-to-do-a-standard-fdk-using-itk-rtk-in-python/6141 "2023-08-19T05:54:44Z")

</div>

I’m new to ITK and RTK. I’m so sad since there are not enough docs of RTK (in python). What I want to do is do a simple FDK reconstruction using a number of tif images with some geometry parameters. There are 360 tif fil…

---

## [Filter is doubling allocated memory (JAVA)](https://discourse.itk.org/t/filter-is-doubling-allocated-memory-java/6144)

<div class="topic-metadata">

**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 16\
**Last updated:** [August 18, 2023, 7:50pm UTC](https://discourse.itk.org/t/filter-is-doubling-allocated-memory-java/6144 "2023-08-18T19:50:16Z")

</div>

my tests are being done with a series that has approximately 118MB. memory consumption of my software just by startup: after loading the series: this.reader.setFileNames(this.dicomFilesNames); this.series = reader…

---

## [Split deformation vector field into two deformation vector fields and apply to image in order](https://discourse.itk.org/t/split-deformation-vector-field-into-two-deformation-vector-fields-and-apply-to-image-in-order/6148)

<div class="topic-metadata">

**Author:** [@Xinyue](https://discourse.itk.org/u/Xinyue)\
**Replies:** 9\
**Last updated:** [August 16, 2023, 2:54pm UTC](https://discourse.itk.org/t/split-deformation-vector-field-into-two-deformation-vector-fields-and-apply-to-image-in-order/6148 "2023-08-16T14:54:54Z")

</div>

Hi, I am trying to split the dvf into two dvfs and apply in order. However the result of deforming with one dvf is not the same as deforming with the split two dvfs. I am wondering why is happen and how to fix it. he…

---

## [ITK python version](https://discourse.itk.org/t/itk-python-version/6147)

<div class="topic-metadata">

**Author:** [@guo7212](https://discourse.itk.org/u/guo7212)\
**Replies:** 2\
**Last updated:** [August 15, 2023, 2:12pm UTC](https://discourse.itk.org/t/itk-python-version/6147 "2023-08-15T14:12:43Z")

</div>

Hi, everyone. In ITK python version, there is a enum ChoiceMethod\_KEEP in class itkMergeLabelMapFilterEnums in the file itkMergeLabelMapFilterPython.py. In my code mergeLabelMapFilter = itk.MergeLabelMapFilter.New(lab…

---

## [how to convert a dicom series into nifity image in memory with simpleitk?](https://discourse.itk.org/t/how-to-convert-a-dicom-series-into-nifity-image-in-memory-with-simpleitk/6146)

<div class="topic-metadata">

**Author:** [@Li\_Bin](https://discourse.itk.org/u/Li_Bin)\
**Replies:** 1\
**Last updated:** [August 15, 2023, 12:50pm UTC](https://discourse.itk.org/t/how-to-convert-a-dicom-series-into-nifity-image-in-memory-with-simpleitk/6146 "2023-08-15T12:50:29Z")

</div>

Hi, there, I need to read a dicom series by network into bytes array and convert to a nifity image in memory . I see the samples which convert to nifty by save into disk by specifing the file extension .nii or .nii.gz.…

---

## [Inverse the displacement field](https://discourse.itk.org/t/inverse-the-displacement-field/6136)

<div class="topic-metadata">

**Author:** [@guo7212](https://discourse.itk.org/u/guo7212)\
**Replies:** 3\
**Last updated:** [August 15, 2023, 3:24am UTC](https://discourse.itk.org/t/inverse-the-displacement-field/6136 "2023-08-15T03:24:02Z")

</div>

In my project, I need to invert the displacement field, which is from fixed space to moving space. The inverted displacement field should be from moving space to fixed space. I tried the methods in ITK, such as itkInvert…

---

## [Is it possible to convert to Hounsfield Units in Sitk?](https://discourse.itk.org/t/is-it-possible-to-convert-to-hounsfield-units-in-sitk/5061)

<div class="topic-metadata">

**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 5\
**Last updated:** [August 14, 2023, 12:56pm UTC](https://discourse.itk.org/t/is-it-possible-to-convert-to-hounsfield-units-in-sitk/5061 "2023-08-14T12:56:09Z")

</div>

Hi, Is there a function in SITK to convert the pixel values in dicom CT images to Hounsfield Units (HU) ? This is what I currently do: def transform\_to\_hu(slices): images = np.stack(\[file.pixel\_array for file in …

---

## [How to make SmoothingRecursiveGaussianImageFilter supports RequestedRegion](https://discourse.itk.org/t/how-to-make-smoothingrecursivegaussianimagefilter-supports-requestedregion/6139)

<div class="topic-metadata">

**Author:** [@MaxMa](https://discourse.itk.org/u/MaxMa)\
**Replies:** 0\
**Last updated:** [August 11, 2023, 12:22pm UTC](https://discourse.itk.org/t/how-to-make-smoothingrecursivegaussianimagefilter-supports-requestedregion/6139 "2023-08-11T12:22:44Z")

</div>

Hi, In a nutshell, I’m trying to make SmoothingRecursiveGaussianImageFilter not overwriting the user RequestedRegion. The current behavior of the filter is that it modifies the output’s requested region to be the large…

---

## [Cuberille Mesh](https://discourse.itk.org/t/cuberille-mesh/6130)

<div class="topic-metadata">

**Author:** [@CrownMella](https://discourse.itk.org/u/CrownMella)\
**Replies:** 13\
**Last updated:** [August 10, 2023, 6:41pm UTC](https://discourse.itk.org/t/cuberille-mesh/6130 "2023-08-10T18:41:51Z")

</div>

Hi, Is there a way to convert the mesh from cuberille image to mesh filter back to an image? I saw something like itk.TriangleMeshToBinaryImageFilter but my python brain doesnt understand how instance = itk.TriangleMes…

[Previous page](https://discourse.itk.org/latest.md?page=18)

[Next page](https://discourse.itk.org/latest.md?page=20)