# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=164

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

**Page:** 165

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## [Label values in manual and automated segmentation files don't match](https://discourse.slicer.org/t/label-values-in-manual-and-automated-segmentation-files-dont-match/29297)

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**Author:** [@Js165](https://discourse.slicer.org/u/Js165)\
**Replies:** 1\
**Last updated:** [May 6, 2023, 5:39pm UTC](https://discourse.slicer.org/t/label-values-in-manual-and-automated-segmentation-files-dont-match/29297 "2023-05-06T17:39:23Z")

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Hello experts, I have manual and automated segmentation files in NIFTI format. Now, I am computing some statistical measures, like Jaccard, average distance, etc. But the problem is manual and automated files have diffe…

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## [Slicer crashes when creating scalar volume node](https://discourse.slicer.org/t/slicer-crashes-when-creating-scalar-volume-node/29302)

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**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 3\
**Last updated:** [May 6, 2023, 5:09pm UTC](https://discourse.slicer.org/t/slicer-crashes-when-creating-scalar-volume-node/29302 "2023-05-06T17:09:32Z")

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I try to create a vtkMRMLScalarVolumeNode by calling slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode"), but slicer crashed after calling this method. Messages below are output of terminal: Input port 0 of a…

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## [New feature: Uniform remeshing (ACVD algorithm)](https://discourse.slicer.org/t/new-feature-uniform-remeshing-acvd-algorithm/26196)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [November 11, 2022, 2:15pm UTC](https://discourse.slicer.org/t/new-feature-uniform-remeshing-acvd-algorithm/26196 "2022-11-11T14:15:39Z")

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Models (surface meshes) exported from image segmentation often have very high point counts, which can make visualization and further editing in external software difficult. Surface Toolbox module’s Decimate feature has …

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## [ calculate the volume of cerebrospinal fluid and the volume of intracranial hemorrhage](https://discourse.slicer.org/t/calculate-the-volume-of-cerebrospinal-fluid-and-the-volume-of-intracranial-hemorrhage/29317)

<div class="topic-metadata">

**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [May 6, 2023, 2:43pm UTC](https://discourse.slicer.org/t/calculate-the-volume-of-cerebrospinal-fluid-and-the-volume-of-intracranial-hemorrhage/29317 "2023-05-06T14:43:59Z")

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Excuse me, Can you help me？I have some questions.Can 3Dslicer calculate the volume of cerebrospinal fluid and the volume of intracranial hemorrhage? If it can be calculated, which section of 3Dslicer needs to be used? I …

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## [Threshold in the segment editor](https://discourse.slicer.org/t/threshold-in-the-segment-editor/29316)

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**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [May 6, 2023, 2:40pm UTC](https://discourse.slicer.org/t/threshold-in-the-segment-editor/29316 "2023-05-06T14:40:14Z")

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What is the threshold in the segment editor? Does this threshold represent the window width of the corresponding CT value of human tissue?

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## [5.2.2 silent installer not seeming to work w10](https://discourse.slicer.org/t/5-2-2-silent-installer-not-seeming-to-work-w10/29252)

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**Author:** [@mwfee](https://discourse.slicer.org/u/mwfee)\
**Replies:** 5\
**Last updated:** [May 6, 2023, 1:04am UTC](https://discourse.slicer.org/t/5-2-2-silent-installer-not-seeming-to-work-w10/29252 "2023-05-06T01:04:12Z")

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Hi. MECM environment in a college. I see this is a NSIS installer but running theexe.exe /S is not firing away on Windows 10. I had a colleague reproduce this independently. Updating from 4.2 I see the app is fully …

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## [Failed to compute results. No module named 'torch'](https://discourse.slicer.org/t/failed-to-compute-results-no-module-named-torch/29280)

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**Author:** [@TSMemo](https://discourse.slicer.org/u/TSMemo)\
**Replies:** 2\
**Last updated:** [May 5, 2023, 6:39am UTC](https://discourse.slicer.org/t/failed-to-compute-results-no-module-named-torch/29280 "2023-05-05T06:39:58Z")

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Hi, I’m having trouble applying the program ‘Total Segmentator’. I’ve tried every possible method below Mr Anish\_Raj’s question posted on December 22, 2022 but still encountered a failure about PyTorch as mentioned in t…

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## [How to know the total pixel counts?](https://discourse.slicer.org/t/how-to-know-the-total-pixel-counts/29284)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 9\
**Last updated:** [May 4, 2023, 5:23pm UTC](https://discourse.slicer.org/t/how-to-know-the-total-pixel-counts/29284 "2023-05-04T17:23:03Z")

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Dear Sir, I did the VOI (Volume of interest) on my image. But the total counts of pixel in the VOI do not appear in the table after I did the quantification as picture attached . Anyone can help me. the data set is…

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## [How can I use Python script in Chest Imaging Platform？](https://discourse.slicer.org/t/how-can-i-use-python-script-in-chest-imaging-platform/29288)

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**Author:** [@wangjianmerci](https://discourse.slicer.org/u/wangjianmerci)\
**Replies:** 1\
**Last updated:** [May 4, 2023, 1:11pm UTC](https://discourse.slicer.org/t/how-can-i-use-python-script-in-chest-imaging-platform/29288 "2023-05-04T13:11:34Z")

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Hello everyone, I have about 200 CTvolumes to do. My procedure is as follow: Load CTfiles → Open lung CT segmenter and use lungmask LTRCLobes → Open lung CT analyzer and lobe analysis → Export csv. And I write a scri…

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## [Critical issues with binWidth setting in PARAMETERS file for Pyradiomics](https://discourse.slicer.org/t/critical-issues-with-binwidth-setting-in-parameters-file-for-pyradiomics/29286)

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**Author:** [@harad](https://discourse.slicer.org/u/harad)\
**Replies:** 0\
**Last updated:** [May 4, 2023, 10:25am UTC](https://discourse.slicer.org/t/critical-issues-with-binwidth-setting-in-parameters-file-for-pyradiomics/29286 "2023-05-04T10:25:29Z")

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I would be grateful if anyone could help with the binWidth choice. Even after the default normalization in SlicerRadiomics (normalize: true), I observe that the intensity ranges vary among different MRIs up to over five-…

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## [Moving a subset of points in a list](https://discourse.slicer.org/t/moving-a-subset-of-points-in-a-list/29198)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 5\
**Last updated:** [May 3, 2023, 10:20pm UTC](https://discourse.slicer.org/t/moving-a-subset-of-points-in-a-list/29198 "2023-05-03T22:20:39Z")

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I would like to select a subset of control points in a point list and translate/rotate these together, while the unselected points are stationary. I can make this work by copying the moving points into a new point list, …

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## [Technical issues volumes and segments](https://discourse.slicer.org/t/technical-issues-volumes-and-segments/29175)

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**Author:** [@Ennio\_Russo\_Clarisci](https://discourse.slicer.org/u/Ennio_Russo_Clarisci)\
**Replies:** 6\
**Last updated:** [May 3, 2023, 7:06pm UTC](https://discourse.slicer.org/t/technical-issues-volumes-and-segments/29175 "2023-05-03T19:06:53Z")

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Hi everybody, I am a new Slicer user with no competence in Python scripting. I am carrying out a project that aims to measure bone densities (in terms of Hounsfield) from concentric cylindrical sections. To this aim, a …

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## [LPS/RAS to voxel](https://discourse.slicer.org/t/lps-ras-to-voxel/29256)

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**Author:** [@kulasbart](https://discourse.slicer.org/u/kulasbart)\
**Replies:** 5\
**Last updated:** [May 3, 2023, 5:44pm UTC](https://discourse.slicer.org/t/lps-ras-to-voxel/29256 "2023-05-03T17:44:17Z")

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Hello, I am trying to convert a set of RAS coordinates (.fcsv) exported from slicer, into voxel units. Ideally, I would like to do this on python as part of a workflow… I’m using matmul with the coordinates \[X,Y,Z\] and…

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## [Dicom image orientation incorrect when imageorientationpatient is -1 0 0 0 -1 0](https://discourse.slicer.org/t/dicom-image-orientation-incorrect-when-imageorientationpatient-is-1-0-0-0-1-0/29268)

<div class="topic-metadata">

**Author:** [@Megan](https://discourse.slicer.org/u/Megan)\
**Replies:** 3\
**Last updated:** [May 3, 2023, 3:39pm UTC](https://discourse.slicer.org/t/dicom-image-orientation-incorrect-when-imageorientationpatient-is-1-0-0-0-1-0/29268 "2023-05-03T15:39:29Z")

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At the minute, slicer appears to load the dicom pixel data in the incorrect orientation when the dicom field, ‘imageorientationpatient’ is -1 0 0 0 -1 0. See screenshot below.

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## [Issue with HardenTransform](https://discourse.slicer.org/t/issue-with-hardentransform/29240)

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**Author:** [@Gholl](https://discourse.slicer.org/u/Gholl)\
**Replies:** 4\
**Last updated:** [May 3, 2023, 11:55am UTC](https://discourse.slicer.org/t/issue-with-hardentransform/29240 "2023-05-03T11:55:00Z")

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I’m writing a script and trying to apply HardenTransform on a segmentation node as follows. seg\_node.SetAndObserveTransformNodeID(transformNodeID.GetID()) seg\_node.HardenTransform() This works fine for most samples but…

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## [Prepopulation of measurement issue](https://discourse.slicer.org/t/prepopulation-of-measurement-issue/29090)

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**Author:** [@esomjai](https://discourse.slicer.org/u/esomjai)\
**Replies:** 6\
**Last updated:** [May 3, 2023, 11:43am UTC](https://discourse.slicer.org/t/prepopulation-of-measurement-issue/29090 "2023-05-03T11:43:19Z")

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Hi there, I am trying to reduce the number of clicks along my project after the initial allocation of hard and soft tissue landmarks and manual axes. I also save and load my landmark collections and then lock their con…

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## [Anyone help me to improve the accuracy of registration between abdominal CT and abdominal MRI](https://discourse.slicer.org/t/anyone-help-me-to-improve-the-accuracy-of-registration-between-abdominal-ct-and-abdominal-mri/29207)

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**Author:** [@guokjdaks](https://discourse.slicer.org/u/guokjdaks)\
**Replies:** 2\
**Last updated:** [May 3, 2023, 9:59am UTC](https://discourse.slicer.org/t/anyone-help-me-to-improve-the-accuracy-of-registration-between-abdominal-ct-and-abdominal-mri/29207 "2023-05-03T09:59:25Z")

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Operating system:windows Slicer version:5.0.3 Expected behavior: Actual behavior:

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## [How to show only selected control point, and hide non selected in mark ups](https://discourse.slicer.org/t/how-to-show-only-selected-control-point-and-hide-non-selected-in-mark-ups/29261)

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**Author:** [@Kae1](https://discourse.slicer.org/u/Kae1)\
**Replies:** 1\
**Last updated:** [May 3, 2023, 12:23am UTC](https://discourse.slicer.org/t/how-to-show-only-selected-control-point-and-hide-non-selected-in-mark-ups/29261 "2023-05-03T00:23:17Z")

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Is it possible to show only a selected control point on coronal, sagittal and axial slices, and hide the none selected control points? I have a range of implanted stereo EEG electrode contacts in my mark up file and am …

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## [identify a single slice file name in 3D dicom volume](https://discourse.slicer.org/t/identify-a-single-slice-file-name-in-3d-dicom-volume/29110)

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**Author:** [@sumsumin](https://discourse.slicer.org/u/sumsumin)\
**Replies:** 5\
**Last updated:** [May 2, 2023, 8:03pm UTC](https://discourse.slicer.org/t/identify-a-single-slice-file-name-in-3d-dicom-volume/29110 "2023-05-02T20:03:06Z")

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How can I identify a the file name of a single slice in a loaded 3D DICOM volume? I have loaded a DICOM directory with several hundred slices, but after I have identified a single slice of interest, I would like to know …

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## [Measuring angles on stack with defined reference plane](https://discourse.slicer.org/t/measuring-angles-on-stack-with-defined-reference-plane/21891)

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**Author:** [@Igor\_S](https://discourse.slicer.org/u/Igor_S)\
**Replies:** 9\
**Last updated:** [May 2, 2023, 7:28pm UTC](https://discourse.slicer.org/t/measuring-angles-on-stack-with-defined-reference-plane/21891 "2023-05-02T19:28:14Z")

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Hello, a beginner’s question. How could i measure an angle on CT examination (from two lines / from a line and a point) that are defined on different slices and measured in reference plane: for instance HKA line (which…

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## [Slicer crashes when applying a rigid transform to a structure set](https://discourse.slicer.org/t/slicer-crashes-when-applying-a-rigid-transform-to-a-structure-set/3517)

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**Author:** [@Lowey](https://discourse.slicer.org/u/Lowey)\
**Replies:** 4\
**Last updated:** [May 2, 2023, 7:07pm UTC](https://discourse.slicer.org/t/slicer-crashes-when-applying-a-rigid-transform-to-a-structure-set/3517 "2023-05-02T19:07:51Z")

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Operating system: Windows 7 Slicer version: 4.8.1 Expected behavior: To be able to apply a rigid 6DOF transform to a structure set, and then apply a DVF from a non-rigid registration to the same structure set Actual b…

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## [Export segmentation to PLY compatible with geomorph](https://discourse.slicer.org/t/export-segmentation-to-ply-compatible-with-geomorph/29251)

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**Author:** [@thelobsternods](https://discourse.slicer.org/u/thelobsternods)\
**Replies:** 1\
**Last updated:** [May 2, 2023, 6:34pm UTC](https://discourse.slicer.org/t/export-segmentation-to-ply-compatible-with-geomorph/29251 "2023-05-02T18:34:21Z")

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I have been using 3D Slicer to segment bones out of scans. So far we have been saving these as STL files for 3D printing. However we would like to begin 3D geometric morphometrics using geomorph in R. This requires PLY f…

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## [Volume Reconstruction Module in python](https://discourse.slicer.org/t/volume-reconstruction-module-in-python/29245)

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**Author:** [@Albags](https://discourse.slicer.org/u/Albags)\
**Replies:** 2\
**Last updated:** [May 2, 2023, 4:17pm UTC](https://discourse.slicer.org/t/volume-reconstruction-module-in-python/29245 "2023-05-02T16:17:14Z")

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Hi 3D Slicer team, I am trying to create a new module in python and for one of the functionalities that I want to implement I need as an input a reconstructed volume of live ultrasound data. I saw that I can reconstruct…

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## [16-bit segmentations appear gray after save + reload](https://discourse.slicer.org/t/16-bit-segmentations-appear-gray-after-save-reload/28633)

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**Author:** [@K-Meech](https://discourse.slicer.org/u/K-Meech)\
**Replies:** 10\
**Last updated:** [May 2, 2023, 11:55am UTC](https://discourse.slicer.org/t/16-bit-segmentations-appear-gray-after-save-reload/28633 "2023-05-02T11:55:13Z")

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Hi! I’m having an issue with using 16-bit label images in 3D slicer (saved as nrrd). I make these files externally with python or ImageJ then load them into 3D slicer - this works fine, and I can edit with the Segment E…

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## [How to insert Dicom files from an nhs disk](https://discourse.slicer.org/t/how-to-insert-dicom-files-from-an-nhs-disk/29237)

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**Author:** [@Amanghir](https://discourse.slicer.org/u/Amanghir)\
**Replies:** 1\
**Last updated:** [May 2, 2023, 4:53am UTC](https://discourse.slicer.org/t/how-to-insert-dicom-files-from-an-nhs-disk/29237 "2023-05-02T04:53:23Z")

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Hi I have an NHS encrypted disk with mri scans of my brain. I am very new to this so I am not even sure if I am doing this right. When I click on the load data button, and then choose a directory there are lots of files…

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## [How can I export 4D volume as DICOM?](https://discourse.slicer.org/t/how-can-i-export-4d-volume-as-dicom/28553)

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**Author:** [@STRF87](https://discourse.slicer.org/u/STRF87)\
**Replies:** 7\
**Last updated:** [May 2, 2023, 2:46am UTC](https://discourse.slicer.org/t/how-can-i-export-4d-volume-as-dicom/28553 "2023-05-02T02:46:50Z")

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Hello! I am fairly new to Slicer and I was hoping for some advice. I have created a sequence of volumes (4D volume) of PET data. It is for a dynamic PET kinetic modeling application. I can export the sequence as .seq.n…

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## [Remove MRI background from the threshold selection](https://discourse.slicer.org/t/remove-mri-background-from-the-threshold-selection/29231)

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**Author:** [@user\_090](https://discourse.slicer.org/u/user_090)\
**Replies:** 1\
**Last updated:** [May 1, 2023, 10:05pm UTC](https://discourse.slicer.org/t/remove-mri-background-from-the-threshold-selection/29231 "2023-05-01T22:05:25Z")

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Hi, I did a MRI and now I’m trying to extract my skull model out of it. It seems like I’ll have to do a manual work to get the unwanted selections deleted, but what makes it hard is the fact that the skull as a simil…

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## [Create a segmentation from a contour file using python](https://discourse.slicer.org/t/create-a-segmentation-from-a-contour-file-using-python/29167)

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**Author:** [@RonJones](https://discourse.slicer.org/u/RonJones)\
**Replies:** 1\
**Last updated:** [May 1, 2023, 6:43am UTC](https://discourse.slicer.org/t/create-a-segmentation-from-a-contour-file-using-python/29167 "2023-05-01T06:43:23Z")

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We have a standard workflow that uses a LabelMap file which is then converted to a Segment node. Is it possible to convert a LabelMapVolume to a Segmentation using the python API?

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## [Issues with altering/saving into DICOM format](https://discourse.slicer.org/t/issues-with-altering-saving-into-dicom-format/29187)

<div class="topic-metadata">

**Author:** [@Benjamin\_Lee](https://discourse.slicer.org/u/Benjamin_Lee)\
**Replies:** 6\
**Last updated:** [April 30, 2023, 3:43pm UTC](https://discourse.slicer.org/t/issues-with-altering-saving-into-dicom-format/29187 "2023-04-30T15:43:19Z")

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Sorry if this question is very entry level, but I have spent an entire day trying to figure this out. I am trying to rename the images in the tree structure to describe what the image shows for a dataset of about 350 th…

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## [Ultrasound to stl](https://discourse.slicer.org/t/ultrasound-to-stl/28995)

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**Author:** [@vryko](https://discourse.slicer.org/u/vryko)\
**Replies:** 3\
**Last updated:** [April 30, 2023, 1:41pm UTC](https://discourse.slicer.org/t/ultrasound-to-stl/28995 "2023-04-30T13:41:48Z")

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Hello I am new to all of this an i would like your help on an subject. Sorry if this problem has already been answered. Well i am trying to make my baby from the ultrasound to 3d model but i cant find out how. I have do…

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