# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=209

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

**Page:** 210

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## [How to export segmentation to STEP or IGES format?](https://discourse.slicer.org/t/how-to-export-segmentation-to-step-or-iges-format/24717)

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**Author:** [@mdear](https://discourse.slicer.org/u/mdear)\
**Replies:** 4\
**Last updated:** [August 19, 2022, 2:35am UTC](https://discourse.slicer.org/t/how-to-export-segmentation-to-step-or-iges-format/24717 "2022-08-19T02:35:14Z")

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Hello, I have a DICOM-originated CAT scan segmentation of air in a patient’s trachea and a segmentation imported from an Informatics/Curve Maker model (proposed complex tracheostomy tube design) that I want to export tog…

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## [Slicer crashes when adjusting slice intersection origin](https://discourse.slicer.org/t/slicer-crashes-when-adjusting-slice-intersection-origin/24824)

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**Author:** [@connorh](https://discourse.slicer.org/u/connorh)\
**Replies:** 1\
**Last updated:** [August 18, 2022, 9:29pm UTC](https://discourse.slicer.org/t/slicer-crashes-when-adjusting-slice-intersection-origin/24824 "2022-08-18T21:29:06Z")

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I repeatedly crash slicer when I try to place the origin of my slice intersections on top of markup point (Slicer 5.0.2). Does this happen to anyone else? It is because Slicer is trying to move my fiducial marker any my …

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## [Creating a Slicer binary for Apple Silicon M1](https://discourse.slicer.org/t/creating-a-slicer-binary-for-apple-silicon-m1/24821)

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**Author:** [@efu98](https://discourse.slicer.org/u/efu98)\
**Replies:** 3\
**Last updated:** [August 18, 2022, 4:50pm UTC](https://discourse.slicer.org/t/creating-a-slicer-binary-for-apple-silicon-m1/24821 "2022-08-18T16:50:59Z")

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Hello! I am trying to create a binary of a custom application based on Slicer for Apple Silicon M1. I have managed built Qt5 (using this tutorial) and installed the other prerequisites. However, when I try building Slic…

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## [How can I segment T1W MRI and produce its image mask?](https://discourse.slicer.org/t/how-can-i-segment-t1w-mri-and-produce-its-image-mask/24818)

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**Author:** [@das](https://discourse.slicer.org/u/das)\
**Replies:** 2\
**Last updated:** [August 18, 2022, 4:17pm UTC](https://discourse.slicer.org/t/how-can-i-segment-t1w-mri-and-produce-its-image-mask/24818 "2022-08-18T16:17:48Z")

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I currently have a task at hand which has been challenging for me. I wish to produce a mask image (to be in .nii format) from a T1-weighted image (which is in .nii format and containing a glioma region). Before producing…

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## [converting 3D nii files to 4D](https://discourse.slicer.org/t/converting-3d-nii-files-to-4d/12822)

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**Author:** [@mindmap2](https://discourse.slicer.org/u/mindmap2)\
**Replies:** 2\
**Last updated:** [August 18, 2022, 3:16pm UTC](https://discourse.slicer.org/t/converting-3d-nii-files-to-4d/12822 "2022-08-18T15:16:43Z")

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Dear 3D slicer community, I have 50 3D nii files that I want to convert them to 4D nii and view it as a movie.I wonder if 3D slicer has this ability. Thanks,

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## [How to keep up with the pace of learning](https://discourse.slicer.org/t/how-to-keep-up-with-the-pace-of-learning/24820)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 1\
**Last updated:** [August 18, 2022, 2:51pm UTC](https://discourse.slicer.org/t/how-to-keep-up-with-the-pace-of-learning/24820 "2022-08-18T14:51:08Z")

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The new version of Slicer is released very fast, and the new extension modules are also very powerful. I would like to ask you how to keep up with the pace of learning. :slightly\_smiling\_face:

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## [I want to obtain x,y,z,HU from DICOM(bone regions)](https://discourse.slicer.org/t/i-want-to-obtain-x-y-z-hu-from-dicom-bone-regions/22896)

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**Author:** [@kookoo9999](https://discourse.slicer.org/u/kookoo9999)\
**Replies:** 17\
**Last updated:** [August 18, 2022, 11:48am UTC](https://discourse.slicer.org/t/i-want-to-obtain-x-y-z-hu-from-dicom-bone-regions/22896 "2022-08-18T11:48:59Z")

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I want to obtain bone regions of each coordinate(x,y,z,HU) from DICOM. You can see my source at here. I use input volume from DICOM loaded, and input segment from segment of DICOM. so I obtain x,y,z,HU and display eac…

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## [spect ct fusion](https://discourse.slicer.org/t/spect-ct-fusion/6814)

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**Author:** [@kotzasm](https://discourse.slicer.org/u/kotzasm)\
**Replies:** 7\
**Last updated:** [August 18, 2022, 2:02am UTC](https://discourse.slicer.org/t/spect-ct-fusion/6814 "2022-08-18T02:02:26Z")

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Operating system: windows Slicer version:4.10.1 Expected behavior: Actual behavior: how can I fuse SPECT and CT dcm images and perform roi segmentation simultaneously on both data sets in order to get the ROI counts? …

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## [Mask in segmentation editor is limited to specific ROI. How do I change this?](https://discourse.slicer.org/t/mask-in-segmentation-editor-is-limited-to-specific-roi-how-do-i-change-this/24817)

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**Author:** [@Brendan\_Davies](https://discourse.slicer.org/u/Brendan_Davies)\
**Replies:** 0\
**Last updated:** [August 18, 2022, 12:18am UTC](https://discourse.slicer.org/t/mask-in-segmentation-editor-is-limited-to-specific-roi-how-do-i-change-this/24817 "2022-08-18T00:18:41Z")

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## [Slicer-DeepSeg issue](https://discourse.slicer.org/t/slicer-deepseg-issue/24786)

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**Author:** [@platanus](https://discourse.slicer.org/u/platanus)\
**Replies:** 1\
**Last updated:** [August 17, 2022, 9:04pm UTC](https://discourse.slicer.org/t/slicer-deepseg-issue/24786 "2022-08-17T21:04:09Z")

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Hello, All members in 3D-Slicer Maybe… Have you ever used the Slicer-DeepSeg extension? I’m reproducting extraction of brain tumor using Slicer-DeepSeg extension based on 3D-Slicer. I’m running DeepSeg extension using…

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## [mrmlScene is not available anymore in slicer module](https://discourse.slicer.org/t/mrmlscene-is-not-available-anymore-in-slicer-module/24811)

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**Author:** [@spichardo](https://discourse.slicer.org/u/spichardo)\
**Replies:** 1\
**Last updated:** [August 17, 2022, 5:50pm UTC](https://discourse.slicer.org/t/mrmlscene-is-not-available-anymore-in-slicer-module/24811 "2022-08-17T17:50:22Z")

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Hi, I updated my Slicer installation to 5.0.3 and my scripts stopped working because the attribute mrmlScene is not available in the slice module. I tried to reinstall slicer 5.3.0, install the pre-release 5.10 version,…

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## [Slice thickness for a CT image](https://discourse.slicer.org/t/slice-thickness-for-a-ct-image/24794)

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**Author:** [@Varsha](https://discourse.slicer.org/u/Varsha)\
**Replies:** 1\
**Last updated:** [August 17, 2022, 4:46pm UTC](https://discourse.slicer.org/t/slice-thickness-for-a-ct-image/24794 "2022-08-17T16:46:41Z")

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Hi, I am currently in the process of examining various bony surface changes and correlating the same to the age of individuals using CT scans of the pelvis. I have some doubts which might seem pretty basic but I was wond…

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## [Problem changing the individual segment opacity in slice views](https://discourse.slicer.org/t/problem-changing-the-individual-segment-opacity-in-slice-views/24810)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 2\
**Last updated:** [August 17, 2022, 3:02pm UTC](https://discourse.slicer.org/t/problem-changing-the-individual-segment-opacity-in-slice-views/24810 "2022-08-17T15:02:52Z")

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I’m having trouble changing an individual segment’s opacity and was wondering if this was a bug or expected behavior. I set the segmentation wide slice fill opacity to 1.0, and then set the individual segment opacity to…

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## [Applying of low resolution transformation on a high resolution dataset](https://discourse.slicer.org/t/applying-of-low-resolution-transformation-on-a-high-resolution-dataset/24805)

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**Author:** [@Stephanie](https://discourse.slicer.org/u/Stephanie)\
**Replies:** 2\
**Last updated:** [August 17, 2022, 1:50pm UTC](https://discourse.slicer.org/t/applying-of-low-resolution-transformation-on-a-high-resolution-dataset/24805 "2022-08-17T13:50:35Z")

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Good afternoon to everyone, We use a skeleton vasculature dataset. This is a graph composed of nodes which have properties of position and radius, and edges that specify the connectivity of the former. We apply 2 trans…

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## [SegmentStatistics error](https://discourse.slicer.org/t/segmentstatistics-error/24803)

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**Author:** [@Jorge\_Wagner\_Esteves](https://discourse.slicer.org/u/Jorge_Wagner_Esteves)\
**Replies:** 2\
**Last updated:** [August 17, 2022, 11:27am UTC](https://discourse.slicer.org/t/segmentstatistics-error/24803 "2022-08-17T11:27:33Z")

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Hi there, I am starting with 3D Slicer, using version 5.0.2. I did a segmentation on CT images and tried to process it using SegmentStatistics to get organ volumes. I am running 3D Slicer on an AMD Ryzen 7 3700X with 3…

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## [Dilation erosion element type](https://discourse.slicer.org/t/dilation-erosion-element-type/23722)

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**Author:** [@massisenergy](https://discourse.slicer.org/u/massisenergy)\
**Replies:** 7\
**Last updated:** [August 17, 2022, 10:57am UTC](https://discourse.slicer.org/t/dilation-erosion-element-type/23722 "2022-08-17T10:57:31Z")

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Dear, Does 3DSlicer offer any more element types (sphere, circle, rectangle etc.) than squared pixels? For example, I have a tomography image which is high resolution (very small pixel size). That, upon surface-export,…

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## [Grayscale Model Maker input selection issues](https://discourse.slicer.org/t/grayscale-model-maker-input-selection-issues/24799)

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**Author:** [@Stephane\_Beaudin](https://discourse.slicer.org/u/Stephane_Beaudin)\
**Replies:** 0\
**Last updated:** [August 17, 2022, 10:27am UTC](https://discourse.slicer.org/t/grayscale-model-maker-input-selection-issues/24799 "2022-08-17T10:27:16Z")

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Operating system:Windows 10 Slicer version:5.0.3 Expected behavior: Starting from an image sequence dataset, I have created a volume that displays both in the 3D viewer and as an available choice in such modules as Vol…

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## [How to generate 4D cine MRI?](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743)

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**Author:** [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Replies:** 4\
**Last updated:** [August 17, 2022, 2:15am UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743 "2022-08-17T02:15:10Z")

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Dear Dr, Lasso, Currently, I have cine MRI images (25 phases a cardiac cycle, at 2-, 3-, 4 chamber and short-axis view (9 slices from the apex to the base) \[total 300 pictures\]. I tried to “Reconstruct 4D volume from ci…

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## [Axial, Sagittal, and Coronal views saved as a JPEG, but can’t upload all.](https://discourse.slicer.org/t/axial-sagittal-and-coronal-views-saved-as-a-jpeg-but-can-t-upload-all/24788)

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**Author:** [@Qferreira](https://discourse.slicer.org/u/Qferreira)\
**Replies:** 0\
**Last updated:** [August 16, 2022, 3:53pm UTC](https://discourse.slicer.org/t/axial-sagittal-and-coronal-views-saved-as-a-jpeg-but-can-t-upload-all/24788 "2022-08-16T15:53:21Z")

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Hi all! New to the community here but hoping someone can provide some guidance. I was handed a case with the axial, sagittal, and coronal views were in separate folders saved as a JPEG. I am looking to segment the mand…

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## [Problem: How can i transform nifti files forever?](https://discourse.slicer.org/t/problem-how-can-i-transform-nifti-files-forever/24771)

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**Author:** [@nikkos](https://discourse.slicer.org/u/nikkos)\
**Replies:** 1\
**Last updated:** [August 16, 2022, 2:01pm UTC](https://discourse.slicer.org/t/problem-how-can-i-transform-nifti-files-forever/24771 "2022-08-16T14:01:18Z")

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Hello dear slicer community, I have the following problem when transforming Nifti files. Because they are not transfomed correctly. My procedure is the following: I open the nifti file. I go to the Transform tab , cre…

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## [Loading vector fields (.vf)](https://discourse.slicer.org/t/loading-vector-fields-vf/15660)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 10\
**Last updated:** [August 16, 2022, 12:24pm UTC](https://discourse.slicer.org/t/loading-vector-fields-vf/15660 "2022-08-16T12:24:02Z")

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Hello everyone, Is it possible to load vector fields with .vf extension? I tried to load them in the preview release 3D Slicer version but I couldn’t do it. I would appreciate any help. Thank you.

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## [OpenIGTLinkIF module is not loaded](https://discourse.slicer.org/t/openigtlinkif-module-is-not-loaded/20441)

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**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 3\
**Last updated:** [August 16, 2022, 9:56am UTC](https://discourse.slicer.org/t/openigtlinkif-module-is-not-loaded/20441 "2022-08-16T09:56:26Z")

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Hi, I built Slicer 4.13.0 in Ubuntu 20.04.3 LTS and then I installed the following extensions using the Extensions Manager: After the installation, I restarted Slicer but I noticed that only some IGT modules are pr…

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## [Venous 3d reconstruction](https://discourse.slicer.org/t/venous-3d-reconstruction/1253)

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**Author:** [@Keno\_Mentor](https://discourse.slicer.org/u/Keno_Mentor)\
**Replies:** 5\
**Last updated:** [August 16, 2022, 6:00am UTC](https://discourse.slicer.org/t/venous-3d-reconstruction/1253 "2022-08-16T06:00:15Z")

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Operating system: macOS Slicer version: 4.5 Expected behavior: Actual behavior: Good day all, I am trying to create a 3D reconstruction of the portal vein and related structures. I have a CT with liver portal phase. …

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## [Search for the Ultrasound device that can connect to Plus（Slicer）](https://discourse.slicer.org/t/search-for-the-ultrasound-device-that-can-connect-to-plus-slicer/24779)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 0\
**Last updated:** [August 16, 2022, 4:20am UTC](https://discourse.slicer.org/t/search-for-the-ultrasound-device-that-can-connect-to-plus-slicer/24779 "2022-08-16T04:20:44Z")

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Dear all, Here I want to use slicer’s segmentation module to extract a small segment of femoral veins, please recommend an ultrasound probe that can be directly connected to Slicer(Plus), or some Handheld Ultrasound Equ…

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## [Reading correct orientations of Analyze 7.5 data into 3D Slicer](https://discourse.slicer.org/t/reading-correct-orientations-of-analyze-7-5-data-into-3d-slicer/24770)

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**Author:** [@jsother](https://discourse.slicer.org/u/jsother)\
**Replies:** 1\
**Last updated:** [August 15, 2022, 9:37pm UTC](https://discourse.slicer.org/t/reading-correct-orientations-of-analyze-7-5-data-into-3d-slicer/24770 "2022-08-15T21:37:34Z")

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Problem report for Slicer 5.0.2 win-amd64: \[please describe expected and actual behavior\] When loading an axial Analyze 7.5 dataset (\*.img, \*.hdr), anterior/posterior directions are incorrectly flipped. I know document…

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## [Slicer keeps crashing "faulty module"](https://discourse.slicer.org/t/slicer-keeps-crashing-faulty-module/24631)

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**Author:** [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Replies:** 5\
**Last updated:** [August 14, 2022, 8:47am UTC](https://discourse.slicer.org/t/slicer-keeps-crashing-faulty-module/24631 "2022-08-14T08:47:05Z")

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I have both of the latest stable and preview releases installed. Both started crashing immediately after loading a scene. The event viewer shows either one of these errors (below). I have already tried reinstalling but i…

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## [How to Work on a DICOM file with Burned In Segmentation ](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740)

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**Author:** [@PrinceAla93](https://discourse.slicer.org/u/PrinceAla93)\
**Replies:** 4\
**Last updated:** [August 13, 2022, 9:23pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740 "2022-08-13T21:23:34Z")

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Hello All, I have obtained a dicom image set with the segmented objects of interest burnt in (ie: for red nucleus, the image just shows up as white around that area). I am wondering if 3D slicer can take that Burnt in d…

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## [How to fill small holes in segmentations](https://discourse.slicer.org/t/how-to-fill-small-holes-in-segmentations/24701)

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**Author:** [@tomdillon97](https://discourse.slicer.org/u/tomdillon97)\
**Replies:** 8\
**Last updated:** [August 13, 2022, 8:57pm UTC](https://discourse.slicer.org/t/how-to-fill-small-holes-in-segmentations/24701 "2022-08-13T20:57:59Z")

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Hi, I’m having trouble filling the small voids in this model. I’ve tried using the “closing” operation as visualized in the photo, though it seems to have no effect. Does anyone know of alternative tools I could use her…

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## [103: Processed Images \[Scalar Volume\]: Reference image in series does not contain geometry information. Please use caution.](https://discourse.slicer.org/t/103-processed-images-scalar-volume-reference-image-in-series-does-not-contain-geometry-information-please-use-caution/24739)

<div class="topic-metadata">

**Author:** [@usmanqadir91](https://discourse.slicer.org/u/usmanqadir91)\
**Replies:** 1\
**Last updated:** [August 13, 2022, 6:30pm UTC](https://discourse.slicer.org/t/103-processed-images-scalar-volume-reference-image-in-series-does-not-contain-geometry-information-please-use-caution/24739 "2022-08-13T18:30:20Z")

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Hi I have DICOM data and I am attempting to read the data using import DICOM files. The examine feature in the DICOM database presents warning “Reference image in series does not contain geometry information. Please use…

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## [Segmentation from 3D CT](https://discourse.slicer.org/t/segmentation-from-3d-ct/24726)

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**Author:** [@francesca\_flore](https://discourse.slicer.org/u/francesca_flore)\
**Replies:** 4\
**Last updated:** [August 13, 2022, 8:45am UTC](https://discourse.slicer.org/t/segmentation-from-3d-ct/24726 "2022-08-13T08:45:03Z")

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Anyone know how to segment a 3D CT scan? Exist any extension to do this?

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