# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=341

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

**Page:** 342

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## [Importing segmented MR image in NIfTI format to 3D](https://discourse.slicer.org/t/importing-segmented-mr-image-in-nifti-format-to-3d/11021)

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**Author:** [@Bassam](https://discourse.slicer.org/u/Bassam)\
**Replies:** 1\
**Last updated:** [April 6, 2020, 11:15pm UTC](https://discourse.slicer.org/t/importing-segmented-mr-image-in-nifti-format-to-3d/11021 "2020-04-06T23:15:55Z")

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Hi, I am experiencing a problem in importing mask file in NIfTI format, which is segmented using ITK SNAP, to the 3D slicer for extracting the features. I converted the extension to DICOM format, but unfortunately the p…

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## [Cardiac CT evaluation](https://discourse.slicer.org/t/cardiac-ct-evaluation/11500)

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**Author:** [@opetne](https://discourse.slicer.org/u/opetne)\
**Replies:** 0\
**Last updated:** [May 12, 2020, 8:10am UTC](https://discourse.slicer.org/t/cardiac-ct-evaluation/11500 "2020-05-12T08:10:49Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: I have 15 dog cardiac CT scans of the full cardiac cycle. Some of them has motion artifacts but there should be an evaluation made for the left AV…

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## [CommonTK website broken when going to URLs with www prefix](https://discourse.slicer.org/t/commontk-website-broken-when-going-to-urls-with-www-prefix/11422)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 3\
**Last updated:** [May 12, 2020, 4:28am UTC](https://discourse.slicer.org/t/commontk-website-broken-when-going-to-urls-with-www-prefix/11422 "2020-05-12T04:28:58Z")

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Posting this here because Slicer uses CTK and generally maintained by the same people: http://www.commontk.org/ doesn’t work as a link, though the site is accessible through http://commontk.org/. The www hyperlink vers…

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## ["How to" for a really newbie having a MRI CDRom?](https://discourse.slicer.org/t/how-to-for-a-really-newbie-having-a-mri-cdrom/11450)

<div class="topic-metadata">

**Author:** [@janolap1](https://discourse.slicer.org/u/janolap1)\
**Replies:** 4\
**Last updated:** [May 11, 2020, 12:03pm UTC](https://discourse.slicer.org/t/how-to-for-a-really-newbie-having-a-mri-cdrom/11450 "2020-05-11T12:03:17Z")

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Operating system: Win10 Slicer version: 4.10.2 Expected behavior: Obtaining 3D model of my head Actual behavior: Seeing images but not sure the good way Hi, I’m really new to 3D Slicer and all of those MRI stuff. I’…

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## [Threshold picking up too many voxels. How do I segment different areas with same voxels without having to manually paint it? ](https://discourse.slicer.org/t/threshold-picking-up-too-many-voxels-how-do-i-segment-different-areas-with-same-voxels-without-having-to-manually-paint-it/11476)

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**Author:** [@Demi\_Trimino](https://discourse.slicer.org/u/Demi_Trimino)\
**Replies:** 1\
**Last updated:** [May 10, 2020, 11:35am UTC](https://discourse.slicer.org/t/threshold-picking-up-too-many-voxels-how-do-i-segment-different-areas-with-same-voxels-without-having-to-manually-paint-it/11476 "2020-05-10T11:35:42Z")

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Operating system: Mac Slicer version: 4-11-0 Expected behavior: Actual behavior: I want to just segment the outline (cuticle) but the inner muscles are too similar in intensity and threshold keeps picking them up. H…

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## [How to import cardiac MRI](https://discourse.slicer.org/t/how-to-import-cardiac-mri/11408)

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**Author:** [@Calin](https://discourse.slicer.org/u/Calin)\
**Replies:** 3\
**Last updated:** [May 10, 2020, 10:50am UTC](https://discourse.slicer.org/t/how-to-import-cardiac-mri/11408 "2020-05-10T10:50:54Z")

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## [N4ITK MRI Bias correction standard error:  The number of control points must be greater than the spline order.](https://discourse.slicer.org/t/n4itk-mri-bias-correction-standard-error-the-number-of-control-points-must-be-greater-than-the-spline-order/11474)

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**Author:** [@Igcha](https://discourse.slicer.org/u/Igcha)\
**Replies:** 2\
**Last updated:** [May 10, 2020, 7:12am UTC](https://discourse.slicer.org/t/n4itk-mri-bias-correction-standard-error-the-number-of-control-points-must-be-greater-than-the-spline-order/11474 "2020-05-10T07:12:19Z")

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Operating system: Windows 10 Slicer version: 4.10.2 r28257 Expected behavior: N4ITK MRI Bias correction filtering on images Actual behavior: The N4ITK MRI Bias correction filter on .png Angio X ray images doesn’t wor…

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## [Using open3d within Slicer](https://discourse.slicer.org/t/using-open3d-within-slicer/11475)

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**Author:** [@agporto](https://discourse.slicer.org/u/agporto)\
**Replies:** 4\
**Last updated:** [May 10, 2020, 2:35am UTC](https://discourse.slicer.org/t/using-open3d-within-slicer/11475 "2020-05-10T02:35:34Z")

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I recently joined the SlicerMorph team and I have been developing an algorithm that makes heavy use of the open3d library (https://github.com/intel-isl/Open3D). I was able to install it within Slicer using pip, but when …

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## [color STL surface](https://discourse.slicer.org/t/color-stl-surface/11481)

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**Author:** [@A\_Bonifacio](https://discourse.slicer.org/u/A_Bonifacio)\
**Replies:** 1\
**Last updated:** [May 9, 2020, 3:21pm UTC](https://discourse.slicer.org/t/color-stl-surface/11481 "2020-05-09T15:21:22Z")

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Hi, I’m new to 3D slicer and i was wondering if was possible to export an STL file with different color for each surface (as in 3-Matic using Autocolor Surface). Thank you!

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## [Splitting Diffusion Volume into multiple b-values](https://discourse.slicer.org/t/splitting-diffusion-volume-into-multiple-b-values/11478)

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**Author:** [@Margherita\_Mottola](https://discourse.slicer.org/u/Margherita_Mottola)\
**Replies:** 1\
**Last updated:** [May 9, 2020, 2:56pm UTC](https://discourse.slicer.org/t/splitting-diffusion-volume-into-multiple-b-values/11478 "2020-05-09T14:56:27Z")

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Hi all, I have some troubles with an enhanced dicom files contaning 9-b-values diffusion volume. When loading the Dicom file, in Examine-\>Reader, it is written “Diffusion volume-please see DWI Convert module for advanced…

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## [Pre/post-op CBCT matching](https://discourse.slicer.org/t/pre-post-op-cbct-matching/11438)

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**Author:** [@Aras\_J](https://discourse.slicer.org/u/Aras_J)\
**Replies:** 4\
**Last updated:** [May 9, 2020, 11:14am UTC](https://discourse.slicer.org/t/pre-post-op-cbct-matching/11438 "2020-05-09T11:14:13Z")

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Hello everyone, I am very new to Slicer and clicking myself through the basic tutorials learning this amazing tool step by step. But: what do i have to search for or is the any tutorial for following task: Loading pre-…

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## [Slicer app crashing when SegmentEditor Islands effect is run on an empty segment](https://discourse.slicer.org/t/slicer-app-crashing-when-segmenteditor-islands-effect-is-run-on-an-empty-segment/10348)

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**Author:** [@ezgimercan](https://discourse.slicer.org/u/ezgimercan)\
**Replies:** 8\
**Last updated:** [May 8, 2020, 6:07pm UTC](https://discourse.slicer.org/t/slicer-app-crashing-when-segmenteditor-islands-effect-is-run-on-an-empty-segment/10348 "2020-05-08T18:07:13Z")

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Slicer Preview version 4.11.0-2020-02-17, on both Windows 10 and Mac OS X. All extensions disabled. When I download sample data, MRHead, create a segmentation, add a segment, and run Islands tool with any of the enabled…

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## [How to update from Python 2.7 to 3.7?](https://discourse.slicer.org/t/how-to-update-from-python-2-7-to-3-7/11443)

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**Author:** [@katjx](https://discourse.slicer.org/u/katjx)\
**Replies:** 8\
**Last updated:** [May 8, 2020, 1:16pm UTC](https://discourse.slicer.org/t/how-to-update-from-python-2-7-to-3-7/11443 "2020-05-08T13:16:40Z")

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Hi! I 'm very new with DICOM images processing and with Python I have 3DSlicer version 4.10.2 installed and the Python version I see in Python Interactor is: Python 2.7.13 (default, May 16 2019, 14:27:45) \[MSC v.1900…

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## [STL measured values editable?](https://discourse.slicer.org/t/stl-measured-values-editable/11439)

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**Author:** [@Hina1](https://discourse.slicer.org/u/Hina1)\
**Replies:** 2\
**Last updated:** [May 8, 2020, 4:49am UTC](https://discourse.slicer.org/t/stl-measured-values-editable/11439 "2020-05-08T04:49:37Z")

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Hi all, I am a 3D slicer beginner. Actually I am using png OCT images. And as we know field of view of OCT is 6 mm ( from L to R) and 2 to 1.5 mm (from A to P). After all the steps when I get my stl file and measuring t…

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## [Removing legacy modules and rarely used features from Slicer5](https://discourse.slicer.org/t/removing-legacy-modules-and-rarely-used-features-from-slicer5/11371)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 20\
**Last updated:** [May 8, 2020, 4:01am UTC](https://discourse.slicer.org/t/removing-legacy-modules-and-rarely-used-features-from-slicer5/11371 "2020-05-08T04:01:12Z")

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We plan to release Slicer 5.0 soon. This is a major version change, which happens in about every 5 years and brings lots of new features and also trimming of old features that have been replaced by alternative solutions. …

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## [SUV quantification modules and segment statistics--negative SUV values?](https://discourse.slicer.org/t/suv-quantification-modules-and-segment-statistics-negative-suv-values/11457)

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**Author:** [@eap](https://discourse.slicer.org/u/eap)\
**Replies:** 0\
**Last updated:** [May 7, 2020, 11:12pm UTC](https://discourse.slicer.org/t/suv-quantification-modules-and-segment-statistics-negative-suv-values/11457 "2020-05-07T23:12:29Z")

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I’m trying to calculate SUVmean and SUVmax for segments I’ve created as labelmaps on my PET-CT. I’ve been running these through quantitative indices module with my PET or the SUVbw image that was automatically created th…

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## [Display different images and models in different views](https://discourse.slicer.org/t/display-different-images-and-models-in-different-views/11442)

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**Author:** [@kristjanq](https://discourse.slicer.org/u/kristjanq)\
**Replies:** 6\
**Last updated:** [May 7, 2020, 10:14pm UTC](https://discourse.slicer.org/t/display-different-images-and-models-in-different-views/11442 "2020-05-07T22:14:29Z")

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Dear Slicer community, I am trying to build a training phantom for Interventional Cardiologists making use of tracked Ultrasound using PlusToolkit from @lassoan et al, as part of my master thesis. To give a big picture:…

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## [Python wrapping (some elements missing)](https://discourse.slicer.org/t/python-wrapping-some-elements-missing/10457)

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**Author:** [@RafaelPalomar](https://discourse.slicer.org/u/RafaelPalomar)\
**Replies:** 11\
**Last updated:** [May 7, 2020, 8:31am UTC](https://discourse.slicer.org/t/python-wrapping-some-elements-missing/10457 "2020-05-07T08:31:45Z")

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Hello, I’m playing with building slicer with SLICER\_SUPERBUILD=OFF and trying to get a modular and installable version of slicer in linux. So far, I managed to build the dependencies from the superbuild, 3D Slicer libs,…

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## [No extensions in Windows preview release](https://discourse.slicer.org/t/no-extensions-in-windows-preview-release/11433)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 2\
**Last updated:** [May 6, 2020, 2:36pm UTC](https://discourse.slicer.org/t/no-extensions-in-windows-preview-release/11433 "2020-05-06T14:36:59Z")

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I just downloaded the Windows preview version 29049 and there are no extensions showing up in the extension manager. I checked cdash and see Linux and Mac builds for our extension but no Windows. It doesn’t look like the…

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## [Brain tumor volumetric segmentation](https://discourse.slicer.org/t/brain-tumor-volumetric-segmentation/11193)

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**Author:** [@kalpathi](https://discourse.slicer.org/u/kalpathi)\
**Replies:** 7\
**Last updated:** [May 6, 2020, 2:57am UTC](https://discourse.slicer.org/t/brain-tumor-volumetric-segmentation/11193 "2020-05-06T02:57:38Z")

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I watched a Slicer video on a brain tumor segmentation - that video used a Volumetric Segmentation module (Slicer3D 4.6.x). I dont find it in the latest version. What has replaced that? Are there more detailed documen…

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## [Jump to line node and view both endpoints](https://discourse.slicer.org/t/jump-to-line-node-and-view-both-endpoints/11421)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 2\
**Last updated:** [May 5, 2020, 7:54pm UTC](https://discourse.slicer.org/t/jump-to-line-node-and-view-both-endpoints/11421 "2020-05-05T19:54:21Z")

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I haven’t been able to figure out a way in the GUI yet to jump to a LineNode object where both end points are visible in the same view. When the line node is drawn across axis in 3D space or you’ve reformatted views aft…

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## [How do I get a model of a spine from DICOM files](https://discourse.slicer.org/t/how-do-i-get-a-model-of-a-spine-from-dicom-files/11423)

<div class="topic-metadata">

**Author:** [@CHRIS\_HUYNH](https://discourse.slicer.org/u/CHRIS_HUYNH)\
**Replies:** 0\
**Last updated:** [May 5, 2020, 7:12pm UTC](https://discourse.slicer.org/t/how-do-i-get-a-model-of-a-spine-from-dicom-files/11423 "2020-05-05T19:12:12Z")

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I’ve got DICOM files for a phantom spine I’m working with. I want to use these DICOM files to generate a model in 3D slicer, such that it shows up as an stl model in the models tab, with the ability to see the different …

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## [Masked volume loosing contrast outside of the masked area](https://discourse.slicer.org/t/masked-volume-loosing-contrast-outside-of-the-masked-area/11418)

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**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 1\
**Last updated:** [May 5, 2020, 3:36pm UTC](https://discourse.slicer.org/t/masked-volume-loosing-contrast-outside-of-the-masked-area/11418 "2020-05-05T15:36:59Z")

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Hi, I created a segment that I use to mask my volume, filling inside with -1000, creating a new renamed volume (and affecting all segments in my case). Unfortunately the result seem to suffer a rise of the overall ‘lig…

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## [A way to automatically export stl files from many mrb files?](https://discourse.slicer.org/t/a-way-to-automatically-export-stl-files-from-many-mrb-files/11416)

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**Author:** [@Aoz](https://discourse.slicer.org/u/Aoz)\
**Replies:** 1\
**Last updated:** [May 5, 2020, 3:36pm UTC](https://discourse.slicer.org/t/a-way-to-automatically-export-stl-files-from-many-mrb-files/11416 "2020-05-05T15:36:25Z")

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Hi, I have got a bunch of mrb files (\>100), generated using 3DSlicer v4.1.1. For each of those files, I can export the stl files corresponding to the included segmentations. But is there a way to process all the mrb fi…

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## [Change size of pictures with SlicerFab](https://discourse.slicer.org/t/change-size-of-pictures-with-slicerfab/11412)

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**Author:** [@Mathias](https://discourse.slicer.org/u/Mathias)\
**Replies:** 7\
**Last updated:** [May 5, 2020, 3:34pm UTC](https://discourse.slicer.org/t/change-size-of-pictures-with-slicerfab/11412 "2020-05-05T15:34:18Z")

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Hello, I’m working on a project, I need to add my .stl file and convert this file into an image set with the extension SlicerFab. But when I “generate bitmaps”, the pictures I obtain are too zoomed, how can I change th…

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## [Model to segment](https://discourse.slicer.org/t/model-to-segment/11403)

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**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 4\
**Last updated:** [May 5, 2020, 2:13pm UTC](https://discourse.slicer.org/t/model-to-segment/11403 "2020-05-05T14:13:38Z")

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Hello, I followed a topic about the way to import a model (.stl or .obj in my case) as a segment through the ‘Add data’ window of importation. The segmentation is well visible in my data and in the segments of this volu…

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## [How do I add robot arm STL into a scene?](https://discourse.slicer.org/t/how-do-i-add-robot-arm-stl-into-a-scene/11395)

<div class="topic-metadata">

**Author:** [@CHRIS\_HUYNH](https://discourse.slicer.org/u/CHRIS_HUYNH)\
**Replies:** 3\
**Last updated:** [May 5, 2020, 7:58am UTC](https://discourse.slicer.org/t/how-do-i-add-robot-arm-stl-into-a-scene/11395 "2020-05-05T07:58:58Z")

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Hi, I’ve just created a scene for a phantom spine I’m working with seen below. I want to now add an ABB IRB 120 robotic arm into the scene with all its links connected in correct order similar to Junichi Tokuda’s ex…

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## [Spine segmentation](https://discourse.slicer.org/t/spine-segmentation/11393)

<div class="topic-metadata">

**Author:** [@TMrt](https://discourse.slicer.org/u/TMrt)\
**Replies:** 2\
**Last updated:** [May 4, 2020, 9:36pm UTC](https://discourse.slicer.org/t/spine-segmentation/11393 "2020-05-04T21:36:21Z")

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## [Adding drop down menu](https://discourse.slicer.org/t/adding-drop-down-menu/11404)

<div class="topic-metadata">

**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 1\
**Last updated:** [May 4, 2020, 9:23pm UTC](https://discourse.slicer.org/t/adding-drop-down-menu/11404 "2020-05-04T21:23:12Z")

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I’m currently developing a Python scripted module. Shortly after the module starts running, it pauses to allow the user to select a region of interest from an image by adjusting a vtkMRMLAnnotationROINode. I would like t…

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## [UFK Tractography - Fiber Bundle Selection](https://discourse.slicer.org/t/ufk-tractography-fiber-bundle-selection/11406)

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**Author:** [@flavceschi](https://discourse.slicer.org/u/flavceschi)\
**Replies:** 0\
**Last updated:** [May 4, 2020, 6:44pm UTC](https://discourse.slicer.org/t/ufk-tractography-fiber-bundle-selection/11406 "2020-05-04T18:44:10Z")

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Hello, I have to extract several fiber bundles by Multiple-Manual ROI Labeling. What I am doing after having converted the DICOMs into NRRD is to create a brain mask create a whole-brain UKF tractography using as inp…

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