# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=294

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

**Page:** 295

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## [SimpleITK import error](https://discourse.slicer.org/t/simpleitk-import-error/7294)

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**Author:** [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Replies:** 25\
**Last updated:** [March 2, 2021, 4:59am UTC](https://discourse.slicer.org/t/simpleitk-import-error/7294 "2021-03-02T04:59:59Z")

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Hi all, I’ve been getting this error for a while on mac. This is from the latest nightly. Please let me know if you’d like me to report it on the issue tracker. Python 3.6.7 (default, Jun 23 2019, 23:06:42) \[GCC 4.2.1…

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## [Alignment of two images in physical space prior to landmark registration](https://discourse.slicer.org/t/alignment-of-two-images-in-physical-space-prior-to-landmark-registration/16292)

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**Author:** [@songbird](https://discourse.slicer.org/u/songbird)\
**Replies:** 1\
**Last updated:** [March 1, 2021, 5:56pm UTC](https://discourse.slicer.org/t/alignment-of-two-images-in-physical-space-prior-to-landmark-registration/16292 "2021-03-01T17:56:55Z")

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Hello, I am very new to Slicer and would like to register a phantom to a patient image (same image dimensions) using the Landmark Registration module. However, they are not in the same orientation: the patient image is …

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## [SegmentEditorExtraEffects not building for latest stable snapshot](https://discourse.slicer.org/t/segmenteditorextraeffects-not-building-for-latest-stable-snapshot/16291)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 5\
**Last updated:** [March 1, 2021, 5:53pm UTC](https://discourse.slicer.org/t/segmenteditorextraeffects-not-building-for-latest-stable-snapshot/16291 "2021-03-01T17:53:31Z")

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An error about MaskVolume: https://slicer.cdash.org/build/2166922/configure @lassoan

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## [Surfece Registration: superimposition of two model - SlicerCMF ](https://discourse.slicer.org/t/surfece-registration-superimposition-of-two-model-slicercmf/16290)

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**Author:** [@Fede](https://discourse.slicer.org/u/Fede)\
**Replies:** 0\
**Last updated:** [March 1, 2021, 4:44pm UTC](https://discourse.slicer.org/t/surfece-registration-superimposition-of-two-model-slicercmf/16290 "2021-03-01T16:44:59Z")

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Hi, I have a problem and I need help. I need to superimpose a 3d model (an stl file imported as segmentation) to a CT segmentation and I would like to use the SlicerCMF plug-in. The problem is that when I select the modu…

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## [Grey values (GV) to HU units conversion](https://discourse.slicer.org/t/grey-values-gv-to-hu-units-conversion/16277)

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**Author:** [@nithin](https://discourse.slicer.org/u/nithin)\
**Replies:** 1\
**Last updated:** [March 1, 2021, 3:53pm UTC](https://discourse.slicer.org/t/grey-values-gv-to-hu-units-conversion/16277 "2021-03-01T15:53:00Z")

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Hi, Can anyone please let me know how to view image intensity in HU units, currently, I am getting values in greyscale only? Thanks & Regards,

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## [Issue with version inconsistency](https://discourse.slicer.org/t/issue-with-version-inconsistency/16283)

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**Author:** [@justomont](https://discourse.slicer.org/u/justomont)\
**Replies:** 1\
**Last updated:** [March 1, 2021, 2:18pm UTC](https://discourse.slicer.org/t/issue-with-version-inconsistency/16283 "2021-03-01T14:18:46Z")

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Hello everybody! I’m having a problem with my code when I run it in slicer v4.10.2, and it worked fine on v4.10.1. This is the code, in which I select a segmentation (already in the scene) and convert it to a LabelmapV…

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## [Inaccurate drawing on registered MRI](https://discourse.slicer.org/t/inaccurate-drawing-on-registered-mri/16286)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 2\
**Last updated:** [March 1, 2021, 1:51pm UTC](https://discourse.slicer.org/t/inaccurate-drawing-on-registered-mri/16286 "2021-03-01T13:51:38Z")

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im trying to segment a register axial MRI using BRAIN im using drawing too but the result is pixelated with inaccurate borders is there a way to improve it ? thanks

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## [Visualization in SlicerRT](https://discourse.slicer.org/t/visualization-in-slicerrt/16282)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 1\
**Last updated:** [March 1, 2021, 1:03pm UTC](https://discourse.slicer.org/t/visualization-in-slicerrt/16282 "2021-03-01T13:03:37Z")

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Is there a specific type of medical images that must be used in SlicerRT, because the segmentation performed in 3D slicer and exported as DICOM-RT for other purposes like 3D reconstruction often fails especially with i…

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## [Issue with level tracing](https://discourse.slicer.org/t/issue-with-level-tracing/16284)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [March 1, 2021, 12:52pm UTC](https://discourse.slicer.org/t/issue-with-level-tracing/16284 "2021-03-01T12:52:33Z")

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i heve the level tracing only showing axial regardless of the view im trying to segment i had this issue for a while , now it is not working properly anymore

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## [Segmentation to labelmap via commandline](https://discourse.slicer.org/t/segmentation-to-labelmap-via-commandline/16209)

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**Author:** [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Replies:** 3\
**Last updated:** [March 1, 2021, 12:32pm UTC](https://discourse.slicer.org/t/segmentation-to-labelmap-via-commandline/16209 "2021-03-01T12:32:51Z")

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Hi all, is there a way for converting a segmentation into a labelmap via command line? The labelmap should fit the shape of an anatomical image, so this would be another parameter to specify. In addition: can I apply …

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## [Trying to update a slicer volume node from SimpleITKImage](https://discourse.slicer.org/t/trying-to-update-a-slicer-volume-node-from-simpleitkimage/2032)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 6\
**Last updated:** [March 1, 2021, 11:07am UTC](https://discourse.slicer.org/t/trying-to-update-a-slicer-volume-node-from-simpleitkimage/2032 "2021-03-01T11:07:09Z")

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Operating system: Window 7 Slicer version: 4.8.1 Hi All, I am a newbie. I am trying to develop a segmentation module using python. The main function takes as input a vtkMRMLLabelMapVolumeNode and a vtkMRMLScalarVolum…

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## [Get average deformation from model to model](https://discourse.slicer.org/t/get-average-deformation-from-model-to-model/16271)

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**Author:** [@BORIPHAT](https://discourse.slicer.org/u/BORIPHAT)\
**Replies:** 2\
**Last updated:** [March 1, 2021, 10:56am UTC](https://discourse.slicer.org/t/get-average-deformation-from-model-to-model/16271 "2021-03-01T10:56:19Z")

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Hello, Lassoan I would like to get the average deformation from model to model, too. Now I install SlicerSALT and which module use for analyzing? and what’s kind of file that I must attach to the input and output direct…

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## [Issue with brush or eraser](https://discourse.slicer.org/t/issue-with-brush-or-eraser/16270)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 3\
**Last updated:** [March 1, 2021, 4:33am UTC](https://discourse.slicer.org/t/issue-with-brush-or-eraser/16270 "2021-03-01T04:33:01Z")

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i frequently have the paint or eraser forced or stuck on a certain selection that i didn’t do actually, and wether i cancel and retry or not, it won’t “unstuck till ill let it take effect then undo " command z” the att…

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## [Interactive lobe segmentation on Chest Imaging Platform](https://discourse.slicer.org/t/interactive-lobe-segmentation-on-chest-imaging-platform/15374)

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**Author:** [@JMC](https://discourse.slicer.org/u/JMC)\
**Replies:** 8\
**Last updated:** [February 28, 2021, 7:47pm UTC](https://discourse.slicer.org/t/interactive-lobe-segmentation-on-chest-imaging-platform/15374 "2021-02-28T19:47:51Z")

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Hello everyone, I have created a lung lobe segmentation using Interactive lobe segmentation on Chest Imaging Platform but I don’t know how to calculate the volume of each lung and each lobe. Is there a way to get the vo…

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## [Local threshold and other effects ](https://discourse.slicer.org/t/local-threshold-and-other-effects/16273)

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**Author:** [@vijayaraj](https://discourse.slicer.org/u/vijayaraj)\
**Replies:** 1\
**Last updated:** [February 28, 2021, 3:41pm UTC](https://discourse.slicer.org/t/local-threshold-and-other-effects/16273 "2021-02-28T15:41:09Z")

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Hi how to and where to download local threshold and other effects Slicer 4.11.2

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## [ACPC Transform for MRI scans- Slicer 4.11](https://discourse.slicer.org/t/acpc-transform-for-mri-scans-slicer-4-11/15762)

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**Author:** [@shebaelena](https://discourse.slicer.org/u/shebaelena)\
**Replies:** 18\
**Last updated:** [February 28, 2021, 3:23pm UTC](https://discourse.slicer.org/t/acpc-transform-for-mri-scans-slicer-4-11/15762 "2021-02-28T15:23:55Z")

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Hi, I am trying to do an ACPC transform on Slicer 4.11, and have been unable to determine how to do so. I recently updated from an older version in which I used to be able to complete the transform, but lately it had no…

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## [Calculating the average deformations from Model to Model Distance](https://discourse.slicer.org/t/calculating-the-average-deformations-from-model-to-model-distance/6539)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 5\
**Last updated:** [April 26, 2019, 5:40pm UTC](https://discourse.slicer.org/t/calculating-the-average-deformations-from-model-to-model-distance/6539 "2019-04-26T17:40:05Z")

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Is there a way to compute the average Hausdorf distances between models so that you can show the average displacement? Also, can you create an average model, or a minimum/maximum model given specified points such as a st…

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## [Spinal cord segmentation MRI](https://discourse.slicer.org/t/spinal-cord-segmentation-mri/16249)

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**Author:** [@gloria](https://discourse.slicer.org/u/gloria)\
**Replies:** 4\
**Last updated:** [February 28, 2021, 3:45am UTC](https://discourse.slicer.org/t/spinal-cord-segmentation-mri/16249 "2021-02-28T03:45:34Z")

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Hello! Hopefully someone can help me. I need to segment a rat’s spinal cord. From T8-T10 and obtain volumes of gray matter and white matter as well as total volume of the spinal cord, from MRI. I used segment editor f…

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## [Cannot download Slicer 2021 Feb 27](https://discourse.slicer.org/t/cannot-download-slicer-2021-feb-27/16259)

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**Author:** [@arevell](https://discourse.slicer.org/u/arevell)\
**Replies:** 4\
**Last updated:** [February 28, 2021, 1:15am UTC](https://discourse.slicer.org/t/cannot-download-slicer-2021-feb-27/16259 "2021-02-28T01:15:13Z")

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An error occurred All three OS’s download links at https://download.slicer.org seem to have a SQL error. I have all three OS’s on different computers and irrespective on which computer I am on, I get this error: The sys…

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## [Setting an MNI origo to a volume](https://discourse.slicer.org/t/setting-an-mni-origo-to-a-volume/16164)

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**Author:** [@Kalman](https://discourse.slicer.org/u/Kalman)\
**Replies:** 6\
**Last updated:** [February 27, 2021, 6:12pm UTC](https://discourse.slicer.org/t/setting-an-mni-origo-to-a-volume/16164 "2021-02-27T18:12:43Z")

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I would like to ask whether there is a possibility to set and/or visualize of the MNI-origo of a volume. A bit more detail about the question: I’m working with MRI images of different (mostly dog) brains. Looking at …

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## [Modify other segment in mask selection](https://discourse.slicer.org/t/modify-other-segment-in-mask-selection/16255)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 6\
**Last updated:** [February 27, 2021, 3:51pm UTC](https://discourse.slicer.org/t/modify-other-segment-in-mask-selection/16255 "2021-02-27T15:51:47Z")

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im srtuggling with the new feature of " modify other segments in mask selection " is there a way to disable it??? in my workflow, i don’t want to modify other segments. i choose outside all segments but still get issu…

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## [Sudden slowing in slicer](https://discourse.slicer.org/t/sudden-slowing-in-slicer/16257)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 4\
**Last updated:** [February 27, 2021, 2:13pm UTC](https://discourse.slicer.org/t/sudden-slowing-in-slicer/16257 "2021-02-27T14:13:30Z")

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after a long process of segementation i face significant slowing in any thing i do even scrolling through slices . any suggestion ? thanks

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## [The Python source code of the Transform module](https://discourse.slicer.org/t/the-python-source-code-of-the-transform-module/16256)

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**Author:** [@Carl098](https://discourse.slicer.org/u/Carl098)\
**Replies:** 2\
**Last updated:** [February 27, 2021, 1:30pm UTC](https://discourse.slicer.org/t/the-python-source-code-of-the-transform-module/16256 "2021-02-27T13:30:12Z")

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I would like to ask where the Python source code of the Transform module is, and I want to learn it.

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## [Get normal vector of a model mesh at fiducial marker](https://discourse.slicer.org/t/get-normal-vector-of-a-model-mesh-at-fiducial-marker/16192)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 3\
**Last updated:** [February 27, 2021, 1:20am UTC](https://discourse.slicer.org/t/get-normal-vector-of-a-model-mesh-at-fiducial-marker/16192 "2021-02-27T01:20:36Z")

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Hi everyone! I´d like to get the normal vector of a model surface at a marked point with a fiducial. Is there any example in the script repository for this task? Thanks on advance…

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## [CpuRaycasting too pixelated for small voxel data](https://discourse.slicer.org/t/cpuraycasting-too-pixelated-for-small-voxel-data/16245)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [February 26, 2021, 8:41pm UTC](https://discourse.slicer.org/t/cpuraycasting-too-pixelated-for-small-voxel-data/16245 "2021-02-26T20:41:21Z")

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We will be running our SlicerMOrph workshop using cloud resources, which doesn’t have a GPU. I have been testing CPUraycasting. While large voxel spacing rendering quality is good. For small voxel data seems very noisy. …

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## [Slicer 4.11 on M1 not loading .mrb file](https://discourse.slicer.org/t/slicer-4-11-on-m1-not-loading-mrb-file/16228)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 9\
**Last updated:** [February 26, 2021, 5:43pm UTC](https://discourse.slicer.org/t/slicer-4-11-on-m1-not-loading-mrb-file/16228 "2021-02-26T17:43:55Z")

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Problem report for Slicer 4.11.20200930 macosx-amd64: \[please describe expected and actual behavior\] i cant load the file , the hierarchy shows nothing being loaded as well . its quite frustrating ! i need urgent help …

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## [Slicer ACPC Transformation Instructions](https://discourse.slicer.org/t/slicer-acpc-transformation-instructions/16244)

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**Author:** [@shebaelena](https://discourse.slicer.org/u/shebaelena)\
**Replies:** 0\
**Last updated:** [February 26, 2021, 4:55pm UTC](https://discourse.slicer.org/t/slicer-acpc-transformation-instructions/16244 "2021-02-26T16:55:19Z")

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Begin by opening the ACPC module in the upper left. Under the ‘Transform Panel’, create a new markups line. Use this line to define the posterior border of the anterior commissure as well as the anterior border o…

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## [CBCT too slow to segment](https://discourse.slicer.org/t/cbct-too-slow-to-segment/16243)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 3\
**Last updated:** [February 26, 2021, 4:30pm UTC](https://discourse.slicer.org/t/cbct-too-slow-to-segment/16243 "2021-02-26T16:30:24Z")

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i noticed that segmenting CBCT is way slower than Medical CT although the latter being way smaller in size . any suggestion to make segmenting CBCT faster ? thanks

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## [Convert RT structure to Nrrd](https://discourse.slicer.org/t/convert-rt-structure-to-nrrd/16241)

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**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 0\
**Last updated:** [February 26, 2021, 3:02pm UTC](https://discourse.slicer.org/t/convert-rt-structure-to-nrrd/16241 "2021-02-26T15:02:53Z")

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Hi everyone, I’m trying to convert the RT structure to nrrd using the script BatchStructureSetConversion.py from the SlicerRT module. I executed the script from terminal in this way: /path/to/Slicer/Slicer-4.11.0-2020-…

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## [elastix\_matlab\_Nifti data](https://discourse.slicer.org/t/elastix-matlab-nifti-data/16239)

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**Author:** [@sara\_sharifi](https://discourse.slicer.org/u/sara_sharifi)\
**Replies:** 0\
**Last updated:** [February 26, 2021, 2:01pm UTC](https://discourse.slicer.org/t/elastix-matlab-nifti-data/16239 "2021-02-26T14:01:41Z")

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Hi if anyone is familiar with Elastix, I need help on how to import Nifti data to MATLAB, ie I need an example with 3D data with Elastix code.

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