# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=199

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

**Page:** 200

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## [Merge dicom or nrrd or nii images](https://discourse.slicer.org/t/merge-dicom-or-nrrd-or-nii-images/1566)

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**Author:** [@Daniel\_Frenzel](https://discourse.slicer.org/u/Daniel_Frenzel)\
**Replies:** 11\
**Last updated:** [October 20, 2022, 3:10pm UTC](https://discourse.slicer.org/t/merge-dicom-or-nrrd-or-nii-images/1566 "2022-10-20T15:10:43Z")

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I want to merge sub-MRI images of a patient to one bigger file. I noticed that neither MITK nor ITK-Snap are suitable to merge images. C3d also fails because the sub-images have different sizes. Is it possible to merg…

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## [Join image series together](https://discourse.slicer.org/t/join-image-series-together/22226)

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**Author:** [@lmboop](https://discourse.slicer.org/u/lmboop)\
**Replies:** 4\
**Last updated:** [October 20, 2022, 3:09pm UTC](https://discourse.slicer.org/t/join-image-series-together/22226 "2022-10-20T15:09:51Z")

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Operating system: Windows Slicer version: 4.11.2021 Expected behavior: N/A Actual behavior: N/A Due to the 50+ year age of equipment, we believe our scanner has a limit of ~230 images per series. While it is not unma…

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## [Stitching overlapping volumes](https://discourse.slicer.org/t/stitching-overlapping-volumes/21337)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 3\
**Last updated:** [October 20, 2022, 3:08pm UTC](https://discourse.slicer.org/t/stitching-overlapping-volumes/21337 "2022-10-20T15:08:08Z")

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I have a case of lesion extending from neck to lungs I have both ct chest and ct neck. I’m trying to merge both through the registration method with no success. any other way to do it? thanks ahead

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## [Problem Importing CT-Scan ](https://discourse.slicer.org/t/problem-importing-ct-scan/25812)

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**Author:** [@Jan\_Mehl](https://discourse.slicer.org/u/Jan_Mehl)\
**Replies:** 0\
**Last updated:** [October 20, 2022, 2:41pm UTC](https://discourse.slicer.org/t/problem-importing-ct-scan/25812 "2022-10-20T14:41:18Z")

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Hey Guys, I have a little problem when I want to import a CT-Scan to Slicer. If I do so, only a short and small part of the CT-scan appears. If I try to import it to other softwares like invesalius or ITK-Snap, it works…

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## [Crop Volume in Z direction](https://discourse.slicer.org/t/crop-volume-in-z-direction/25799)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 1\
**Last updated:** [October 20, 2022, 1:02pm UTC](https://discourse.slicer.org/t/crop-volume-in-z-direction/25799 "2022-10-20T13:02:18Z")

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Hi all, I want to obtain more resolution but only in z direction. Let’s say I have a volume of 512x512x256 and I want to obtain a volume of 512x512x600. Is it possible? Thanks,

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## [Controlling the rotation handles with a python script](https://discourse.slicer.org/t/controlling-the-rotation-handles-with-a-python-script/25804)

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**Author:** [@AMK](https://discourse.slicer.org/u/AMK)\
**Replies:** 0\
**Last updated:** [October 20, 2022, 10:56am UTC](https://discourse.slicer.org/t/controlling-the-rotation-handles-with-a-python-script/25804 "2022-10-20T10:56:04Z")

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Hi, Is it possible to programitically control the rotation handles to rotate the plane. I have created a plane. B = slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLMarkupsPlaneNode”) B.SetOrigin(\[0,0,0\]) B.SetNormal(\[0,0…

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## [Create shortcut to toggle editable intensity range](https://discourse.slicer.org/t/create-shortcut-to-toggle-editable-intensity-range/25787)

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**Author:** [@Alex\_Shen](https://discourse.slicer.org/u/Alex_Shen)\
**Replies:** 6\
**Last updated:** [October 20, 2022, 10:47am UTC](https://discourse.slicer.org/t/create-shortcut-to-toggle-editable-intensity-range/25787 "2022-10-20T10:47:51Z")

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Hi, I’m currently working on customising a few things to make segmentation in slicer faster. I want to customize a shortcut to toggle paint with an editable intensity range. e.g. when I press ALT while I paint, it will…

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## [Cropping a ROI in a sequence node using python](https://discourse.slicer.org/t/cropping-a-roi-in-a-sequence-node-using-python/25802)

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**Author:** [@Karl-Philippe](https://discourse.slicer.org/u/Karl-Philippe)\
**Replies:** 0\
**Last updated:** [October 20, 2022, 8:52am UTC](https://discourse.slicer.org/t/cropping-a-roi-in-a-sequence-node-using-python/25802 "2022-10-20T08:52:00Z")

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Hello, I am working with large ultrasound tracking sequences (.mha files) and I need to crop the ultrasound signal from the monitor background. I have tried the “Crop volume” extension to crop the image sequence as a vo…

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## [SKULL STRIPPING USING "HDBrainExtraction"](https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795)

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**Author:** [@D.Prasad](https://discourse.slicer.org/u/D.Prasad)\
**Replies:** 1\
**Last updated:** [October 20, 2022, 6:16am UTC](https://discourse.slicer.org/t/skull-stripping-using-hdbrainextraction/25795 "2022-10-20T06:16:05Z")

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Operating system: windows 11 Slicer version: 5.0.3 r30893/7eaof43 Expected behavior: skull stripping Actual behavior: Failed to compute results. Command '\['C:/Users/admin/AppData/Local/NA-MIC/Slicer 5.0.3/bin/../bi…

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## [How to get a linear or affine transform from Elastix?](https://discourse.slicer.org/t/how-to-get-a-linear-or-affine-transform-from-elastix/25791)

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**Author:** [@tdchen](https://discourse.slicer.org/u/tdchen)\
**Replies:** 1\
**Last updated:** [October 20, 2022, 5:22am UTC](https://discourse.slicer.org/t/how-to-get-a-linear-or-affine-transform-from-elastix/25791 "2022-10-20T05:22:51Z")

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It works fine but always output a b-spline transform even I selected the generic rigid (all) preset. What else should be done? I use Slicer 5.0.3 Thx.

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## [Problem with Elastix](https://discourse.slicer.org/t/problem-with-elastix/25762)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 13\
**Last updated:** [October 19, 2022, 10:39pm UTC](https://discourse.slicer.org/t/problem-with-elastix/25762 "2022-10-19T22:39:05Z")

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I have a problem lately with elastix, it doesn’t execute anything. Traceback (most recent call last): File "/home/alex/GIT/opendose3d/OpenDose3D/OpenDose3D.py", line 944, in onRunTestButton self.test.FullTest\_posi…

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## [Export of SequenceRegistration output: save each individual transformed Model](https://discourse.slicer.org/t/export-of-sequenceregistration-output-save-each-individual-transformed-model/25761)

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**Author:** [@scarpma](https://discourse.slicer.org/u/scarpma)\
**Replies:** 2\
**Last updated:** [October 19, 2022, 3:01pm UTC](https://discourse.slicer.org/t/export-of-sequenceregistration-output-save-each-individual-transformed-model/25761 "2022-10-19T15:01:16Z")

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Hello, I run SequenceRegistration module on a 4d cardiac CT. As a result i have a sequence of transformations. I apply the transformations to a segmentation node or to a surface model. How can I save these two as nrrd …

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## [How to get the normalized image (file)?](https://discourse.slicer.org/t/how-to-get-the-normalized-image-file/25709)

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**Author:** [@Josefa\_Garcia](https://discourse.slicer.org/u/Josefa_Garcia)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 1:45pm UTC](https://discourse.slicer.org/t/how-to-get-the-normalized-image-file/25709 "2022-10-19T13:45:04Z")

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Hi, is there an option to get the image normalized?, because after run the feature extraction I checked the histogram of the image from which I extracted the features and it didn’t change. (I have normalize enabled in th…

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## [Curved planar reformatting](https://discourse.slicer.org/t/curved-planar-reformatting/25759)

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**Author:** [@anusree\_sunilkumar](https://discourse.slicer.org/u/anusree_sunilkumar)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 1:23pm UTC](https://discourse.slicer.org/t/curved-planar-reformatting/25759 "2022-10-19T13:23:32Z")

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I have been trying to implement curved planar reformatting using the code from this github link Computing a panoramic X-ray from a cone-beam dental CT. Demonstration of how an image can be resampled along a curve - the c…

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## [Straight long gaps when segmenting](https://discourse.slicer.org/t/straight-long-gaps-when-segmenting/25758)

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**Author:** [@vvalle](https://discourse.slicer.org/u/vvalle)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 9:23am UTC](https://discourse.slicer.org/t/straight-long-gaps-when-segmenting/25758 "2022-10-19T09:23:24Z")

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When I use the ‘draw’ function in Segment Editor, sometimes these long gaps occur (see picture). Does anyone know why and how to correct this? Thanks for any advice! Best, Vanessa

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## [Quantification based on centerline curve or centerline model?](https://discourse.slicer.org/t/quantification-based-on-centerline-curve-or-centerline-model/25676)

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**Author:** [@JBierens](https://discourse.slicer.org/u/JBierens)\
**Replies:** 4\
**Last updated:** [October 19, 2022, 7:59am UTC](https://discourse.slicer.org/t/quantification-based-on-centerline-curve-or-centerline-model/25676 "2022-10-19T07:59:53Z")

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I am wondering if the Centerline quantification table is based on the properties of the centerline model or centerline curves. Sometimes when I extract the centerline, I only get one centerline curve, that is only coveri…

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## [PlaneToWorld: set position of plane to world coordinate system](https://discourse.slicer.org/t/planetoworld-set-position-of-plane-to-world-coordinate-system/25639)

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**Author:** [@jegberink](https://discourse.slicer.org/u/jegberink)\
**Replies:** 1\
**Last updated:** [October 19, 2022, 6:28am UTC](https://discourse.slicer.org/t/planetoworld-set-position-of-plane-to-world-coordinate-system/25639 "2022-10-19T06:28:49Z")

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Hello Everyone, I’m trying to create a coordinate system relative to the femur. I have selected three points to create a plane which will now represent the new coordinate system. Because i work with slicermorphs automa…

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## [Reading Multi-energy CT data in 3D Slicer](https://discourse.slicer.org/t/reading-multi-energy-ct-data-in-3d-slicer/25704)

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**Author:** [@khyatisethia](https://discourse.slicer.org/u/khyatisethia)\
**Replies:** 2\
**Last updated:** [October 19, 2022, 6:07am UTC](https://discourse.slicer.org/t/reading-multi-energy-ct-data-in-3d-slicer/25704 "2022-10-19T06:07:15Z")

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Hi Slicer Community, I have Multi-energy CT data from Siemens Hardware and would like to visualize it in Slicer. I want to visualize different materials like (iodine, calcium) from this CT. But I am not sure how it can …

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## [Change segmentation oversampling factor](https://discourse.slicer.org/t/change-segmentation-oversampling-factor/19025)

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**Author:** [@PJ\_Yu](https://discourse.slicer.org/u/PJ_Yu)\
**Replies:** 5\
**Last updated:** [October 14, 2022, 8:23pm UTC](https://discourse.slicer.org/t/change-segmentation-oversampling-factor/19025 "2022-10-14T20:23:53Z")

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Hello, I have been trying to mimic SegmentationGeometryWidget in python. In the widget, I can select a segmentation node and give a oversampling factor. After pressing the OK button, I will get a modified segmentation. …

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## [How to get multiple scalars using Probe Volume With Model?](https://discourse.slicer.org/t/how-to-get-multiple-scalars-using-probe-volume-with-model/25708)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 5:46am UTC](https://discourse.slicer.org/t/how-to-get-multiple-scalars-using-probe-volume-with-model/25708 "2022-10-19T05:46:18Z")

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I’ve started using Probe Volume With Model to view values from image volumes displayed on a surface model. I know from seeing some other use cases for scalars associated with models that a single model can have multiple…

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## [RVXLiverSegmentation extension questions](https://discourse.slicer.org/t/rvxliversegmentation-extension-questions/25752)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 0\
**Last updated:** [October 18, 2022, 1:46pm UTC](https://discourse.slicer.org/t/rvxliversegmentation-extension-questions/25752 "2022-10-18T13:46:15Z")

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I am trying to use your 3D Slicer RVXLiverSegmentation plug-in, but I have some problems: i) I specified all portal vein nodes. Why does the button “Extract Vessels from node tree” continue in gray color without activat…

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## [Getting viewport coordinates from world](https://discourse.slicer.org/t/getting-viewport-coordinates-from-world/25764)

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**Author:** [@dj\_96](https://discourse.slicer.org/u/dj_96)\
**Replies:** 1\
**Last updated:** [October 19, 2022, 5:26am UTC](https://discourse.slicer.org/t/getting-viewport-coordinates-from-world/25764 "2022-10-19T05:26:08Z")

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I have a 3d model loaded in vtk and I’m using vtkCellPicker to get the world coordinates for a point. But how can I keep track of the 2d position on the viewport that corresponds to that coordinate after I’ve rotated the…

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## [MarkupsDisplayNodes have different default glyph sizes on different computers](https://discourse.slicer.org/t/markupsdisplaynodes-have-different-default-glyph-sizes-on-different-computers/25768)

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**Author:** [@wrc](https://discourse.slicer.org/u/wrc)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 5:18am UTC](https://discourse.slicer.org/t/markupsdisplaynodes-have-different-default-glyph-sizes-on-different-computers/25768 "2022-10-19T05:18:11Z")

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Hello. When I am using vtkMRMLMarkupsCurveNode.CreateDefaultDisplayNodes() slicer.util.updateMarkupsControlPointsFromArray(vtkMRMLMarkupsCurveNode, Node) The default glyph size is 1% on PC and 3% on Mac. It looks goo…

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## [Editing Segmentation contained to one small region](https://discourse.slicer.org/t/editing-segmentation-contained-to-one-small-region/25765)

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**Author:** [@dbalentine](https://discourse.slicer.org/u/dbalentine)\
**Replies:** 1\
**Last updated:** [October 19, 2022, 5:11am UTC](https://discourse.slicer.org/t/editing-segmentation-contained-to-one-small-region/25765 "2022-10-19T05:11:14Z")

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Hello, I am trying to edit a segmentation in the segmentation editor. I am able to edit the segmentation to some extent, but any painting or drawing is only allowed in a small rectangle around the original segmentations…

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## [Creating an automatic US vessel segmentation algorithm using the Python interactor ](https://discourse.slicer.org/t/creating-an-automatic-us-vessel-segmentation-algorithm-using-the-python-interactor/18165)

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**Author:** [@J.vd.Zee](https://discourse.slicer.org/u/J.vd.Zee)\
**Replies:** 11\
**Last updated:** [October 19, 2022, 2:37am UTC](https://discourse.slicer.org/t/creating-an-automatic-us-vessel-segmentation-algorithm-using-the-python-interactor/18165 "2022-10-19T02:37:07Z")

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Hi all! I would like to develop an automatic vessel segmentation algorithm in Python code based on the abdominal aorta. Currently, I am stuck in the trial-and-error procedure since I really would like to avoid any manu…

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## [Surface model from segment](https://discourse.slicer.org/t/surface-model-from-segment/25743)

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**Author:** [@A\_B](https://discourse.slicer.org/u/A_B)\
**Replies:** 3\
**Last updated:** [October 18, 2022, 10:42pm UTC](https://discourse.slicer.org/t/surface-model-from-segment/25743 "2022-10-18T22:42:40Z")

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Hello, I am trying to create a model of the outer surface of a segment. I have tried wrap solidify extension, surface model module \> model maker and hollow. The only one that worked in making a surface model without int…

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## [Linear transform in image plane](https://discourse.slicer.org/t/linear-transform-in-image-plane/25725)

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**Author:** [@BraDan](https://discourse.slicer.org/u/BraDan)\
**Replies:** 3\
**Last updated:** [October 18, 2022, 5:41pm UTC](https://discourse.slicer.org/t/linear-transform-in-image-plane/25725 "2022-10-18T17:41:31Z")

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Hello everyone, This question must be trivial to you - but I would very much appreciate any help on this. Does anybody know how to translate a segmentation in the image plane using the translation sliders? The only wa…

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## [Which difference between Direction Matrices in vtkImageData and vtkMRMLScalarVolumeNode?](https://discourse.slicer.org/t/which-difference-between-direction-matrices-in-vtkimagedata-and-vtkmrmlscalarvolumenode/25760)

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**Author:** [@Cailen](https://discourse.slicer.org/u/Cailen)\
**Replies:** 1\
**Last updated:** [October 18, 2022, 4:07pm UTC](https://discourse.slicer.org/t/which-difference-between-direction-matrices-in-vtkimagedata-and-vtkmrmlscalarvolumenode/25760 "2022-10-18T16:07:11Z")

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This behavior spoils the display of the results of my algorithms, because only from the VTK it is not clear where to get the same matrix as in the slicer

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## [DICOM database not showing slice count](https://discourse.slicer.org/t/dicom-database-not-showing-slice-count/25746)

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**Author:** [@Vincebisca](https://discourse.slicer.org/u/Vincebisca)\
**Replies:** 3\
**Last updated:** [October 18, 2022, 1:11pm UTC](https://discourse.slicer.org/t/dicom-database-not-showing-slice-count/25746 "2022-10-18T13:11:11Z")

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Hi ! I have a little problem since I switched from 3D Slicer 4.11 to 5.0 : when I changed the version, the software recognized that I had an existing DICOM database loaded in 4.11 and uploaded it on 5.0. However, ever s…

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## [loading and stroring large transfer function (vp file)](https://discourse.slicer.org/t/loading-and-stroring-large-transfer-function-vp-file/25737)

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**Author:** [@Amin\_Nasim\_saravi](https://discourse.slicer.org/u/Amin_Nasim_saravi)\
**Replies:** 3\
**Last updated:** [October 17, 2022, 11:14pm UTC](https://discourse.slicer.org/t/loading-and-stroring-large-transfer-function-vp-file/25737 "2022-10-17T23:14:17Z")

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Hello, I’m working on a project to automatically create transfer functions (TF) and use Slicer as a reference and also to render the results. The approach is as follows, I generate a transfer function. I sample it and…

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