# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=377

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

**Page:** 378

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## [Can't save the scene and the segmentations - allocation ERROR, results undefined](https://discourse.slicer.org/t/cant-save-the-scene-and-the-segmentations-allocation-error-results-undefined/7782)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 18\
**Last updated:** [July 29, 2019, 3:37am UTC](https://discourse.slicer.org/t/cant-save-the-scene-and-the-segmentations-allocation-error-results-undefined/7782 "2019-07-29T03:37:46Z")

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This is the error I sadly get… This file and Segmentations are barely 1 gb while I have 16 GB on this computer. I wonder what could cause this?

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## [How to convert .xfm file to regular .tfm file to import in Slicer](https://discourse.slicer.org/t/how-to-convert-xfm-file-to-regular-tfm-file-to-import-in-slicer/7784)

<div class="topic-metadata">

**Author:** [@ljc19800331](https://discourse.slicer.org/u/ljc19800331)\
**Replies:** 2\
**Last updated:** [July 29, 2019, 4:32am UTC](https://discourse.slicer.org/t/how-to-convert-xfm-file-to-regular-tfm-file-to-import-in-slicer/7784 "2019-07-29T04:32:26Z")

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Operating system: Windows 10 Slicer version: 4.10.1 Expected behavior: Actual behavior: Hello, I have download the data and the transformation file is .xfm. Is there a good way in python or 3D slicer that I could dir…

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## [How to open Segmentation.seg.nrrd file using vtk](https://discourse.slicer.org/t/how-to-open-segmentation-seg-nrrd-file-using-vtk/7791)

<div class="topic-metadata">

**Author:** [@kscript](https://discourse.slicer.org/u/kscript)\
**Replies:** 1\
**Last updated:** [July 29, 2019, 3:21am UTC](https://discourse.slicer.org/t/how-to-open-segmentation-seg-nrrd-file-using-vtk/7791 "2019-07-29T03:21:47Z")

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Hi. I posted the following question last week. https://discourse.slicer.org/t/why-does-the-color-of-the-label-map-change-when-i-save-the-label-map/7770 And i have another question. How to Open Segmentation.seg.nrrd f…

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## [General registration(BRAINS) error"LBFGSB optimizer does not support scaling. All scales are set to one. "](https://discourse.slicer.org/t/general-registration-brains-error-lbfgsb-optimizer-does-not-support-scaling-all-scales-are-set-to-one/7780)

<div class="topic-metadata">

**Author:** [@11126](https://discourse.slicer.org/u/11126)\
**Replies:** 1\
**Last updated:** [July 28, 2019, 6:51pm UTC](https://discourse.slicer.org/t/general-registration-brains-error-lbfgsb-optimizer-does-not-support-scaling-all-scales-are-set-to-one/7780 "2019-07-28T18:51:04Z")

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I am trying to do general registration according to the tutorial. I have completed the linear transform but when I tried to apply BSpline transform it completed with error: General Registration (BRAINS) standard error: …

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## [Importing to 3Ds max or Zbrush or Maya surfaces flip and become unvisible](https://discourse.slicer.org/t/importing-to-3ds-max-or-zbrush-or-maya-surfaces-flip-and-become-unvisible/7785)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 2\
**Last updated:** [July 28, 2019, 3:53pm UTC](https://discourse.slicer.org/t/importing-to-3ds-max-or-zbrush-or-maya-surfaces-flip-and-become-unvisible/7785 "2019-07-28T15:53:31Z")

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So the surfacing is done inside out so when viewed from the outside in other software, it is transprent. What could cause this?

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## [Fill between slices](https://discourse.slicer.org/t/fill-between-slices/6276)

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**Author:** [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Replies:** 18\
**Last updated:** [July 27, 2019, 1:55pm UTC](https://discourse.slicer.org/t/fill-between-slices/6276 "2019-07-27T13:55:33Z")

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Hi all, I have a question about the function “Fill between slices” in the segment editor. How are the slices interpolated? Linear, Spline? Any intensity information used or just contours geometry? Thanks a lot. Paol…

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## [Problem downloading extensions](https://discourse.slicer.org/t/problem-downloading-extensions/7532)

<div class="topic-metadata">

**Author:** [@zahiraabdala](https://discourse.slicer.org/u/zahiraabdala)\
**Replies:** 3\
**Last updated:** [July 26, 2019, 9:16pm UTC](https://discourse.slicer.org/t/problem-downloading-extensions/7532 "2019-07-26T21:16:15Z")

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Hi all! I am having some problems downloading the extensions. I have installed 4.10.2 version for MAC. The extension manager does not work, and i do not understand the reason. I want to make a registration in brain IMR,…

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## [Segment Translated after Load segmentation](https://discourse.slicer.org/t/segment-translated-after-load-segmentation/7745)

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**Author:** [@Christina](https://discourse.slicer.org/u/Christina)\
**Replies:** 3\
**Last updated:** [July 26, 2019, 7:41pm UTC](https://discourse.slicer.org/t/segment-translated-after-load-segmentation/7745 "2019-07-26T19:41:24Z")

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Hello, For some reason, after I load a segmentation in my module, I see the segment move by itself from its correct place in the image to a lower position. This happens immediately, every time I load this segmentation. …

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## [CT is cropped atfer Elastix deformable registraton](https://discourse.slicer.org/t/ct-is-cropped-atfer-elastix-deformable-registraton/7766)

<div class="topic-metadata">

**Author:** [@kuba\_grepl](https://discourse.slicer.org/u/kuba_grepl)\
**Replies:** 1\
**Last updated:** [July 26, 2019, 7:03pm UTC](https://discourse.slicer.org/t/ct-is-cropped-atfer-elastix-deformable-registraton/7766 "2019-07-26T19:03:35Z")

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Dear community, I need your help :slight\_smile: I used Elastix module to register MR and CT of radiotherapy head and neck patient. MR is fixed volume and CT is moving volume. MR scan does not contain shoulders and uppe…

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## [Transform Model-rotate and translate remove box](https://discourse.slicer.org/t/transform-model-rotate-and-translate-remove-box/7744)

<div class="topic-metadata">

**Author:** [@Christina](https://discourse.slicer.org/u/Christina)\
**Replies:** 3\
**Last updated:** [July 26, 2019, 12:23pm UTC](https://discourse.slicer.org/t/transform-model-rotate-and-translate-remove-box/7744 "2019-07-26T12:23:41Z")

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Hello Slicer expert, In Slicer, how do you get rid of the white box around the model when you are rotating and translating a model in the Transform module? Thank you, Christina

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## [Is it possible to calculate airway length and number of airway tree generation with the help of slicer](https://discourse.slicer.org/t/is-it-possible-to-calculate-airway-length-and-number-of-airway-tree-generation-with-the-help-of-slicer/5075)

<div class="topic-metadata">

**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 25\
**Last updated:** [July 26, 2019, 12:01pm UTC](https://discourse.slicer.org/t/is-it-possible-to-calculate-airway-length-and-number-of-airway-tree-generation-with-the-help-of-slicer/5075 "2019-07-26T12:01:49Z")

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

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## [How to calibrate and track the movement of a non-stylus model in IGT](https://discourse.slicer.org/t/how-to-calibrate-and-track-the-movement-of-a-non-stylus-model-in-igt/7517)

<div class="topic-metadata">

**Author:** [@Christopher\_Ji](https://discourse.slicer.org/u/Christopher_Ji)\
**Replies:** 1\
**Last updated:** [July 26, 2019, 3:27am UTC](https://discourse.slicer.org/t/how-to-calibrate-and-track-the-movement-of-a-non-stylus-model-in-igt/7517 "2019-07-26T03:27:33Z")

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Hello, I’ve tried attaching the model of i.e. a human’s head with a NDI rigid body, from which I could track the movement, or the wobble of the model on 3D Slicer. However, this is not quite accurate, is there any furth…

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## [Converting .stl files into segments for editing](https://discourse.slicer.org/t/converting-stl-files-into-segments-for-editing/7764)

<div class="topic-metadata">

**Author:** [@stl](https://discourse.slicer.org/u/stl)\
**Replies:** 5\
**Last updated:** [July 26, 2019, 2:18am UTC](https://discourse.slicer.org/t/converting-stl-files-into-segments-for-editing/7764 "2019-07-26T02:18:23Z")

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Operating system:Windows Slicer version: 4.10 Hi, I have a group of .stl files that I have downloaded for a region of the body. I would like to convert them into segments that I can edit to further refine the model. I…

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## [Exporting multiple seg.nrrd files to obj all at once](https://discourse.slicer.org/t/exporting-multiple-seg-nrrd-files-to-obj-all-at-once/7747)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 2\
**Last updated:** [July 25, 2019, 7:52pm UTC](https://discourse.slicer.org/t/exporting-multiple-seg-nrrd-files-to-obj-all-at-once/7747 "2019-07-25T19:52:10Z")

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I have finally segmented some files I was planing now I want to \>\> export them all to obj. They are all in different seg.nrrd files. Is there some way to export them all at once instead of clicking on each seg.nrrd file…

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## [3D Slicer View Window Python Names](https://discourse.slicer.org/t/3d-slicer-view-window-python-names/1935)

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**Author:** [@Ahmed\_Soufane](https://discourse.slicer.org/u/Ahmed_Soufane)\
**Replies:** 3\
**Last updated:** [January 26, 2018, 1:31pm UTC](https://discourse.slicer.org/t/3d-slicer-view-window-python-names/1935 "2018-01-26T13:31:34Z")

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What would the python node names be for the red, yellow, and green views? I am getting a error in which the: markupsNode =slicer.mrmlScene.GetFirstNodeByName("CTChest") command does not grab the individual views caus…

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## [Obtain voxels coordinate of an image](https://discourse.slicer.org/t/obtain-voxels-coordinate-of-an-image/7739)

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**Author:** [@Mohsen\_Taheri](https://discourse.slicer.org/u/Mohsen_Taheri)\
**Replies:** 6\
**Last updated:** [July 24, 2019, 8:27pm UTC](https://discourse.slicer.org/t/obtain-voxels-coordinate-of-an-image/7739 "2019-07-24T20:27:05Z")

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Hi, I used 3d slicer to segment a part of a brain image (from a \*.nrrd file) and I need to obtain the the voxel coordinates of the segmentation. Actually I need the coordinates of all the inner and boundary voxels as a …

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## [About SwissSkullStripper](https://discourse.slicer.org/t/about-swissskullstripper/7544)

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**Author:** [@otanit](https://discourse.slicer.org/u/otanit)\
**Replies:** 8\
**Last updated:** [July 24, 2019, 1:09am UTC](https://discourse.slicer.org/t/about-swissskullstripper/7544 "2019-07-24T01:09:13Z")

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Operating system: Windows 10 Slicer version: Slicer 4.10.1 Expected behavior: Install SwissSkullStripper and calculate intracranial content volume with it. Actual behavior: Cannot install SwissSkullStripper and use th…

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## [Get slicer version within Python Interactor](https://discourse.slicer.org/t/get-slicer-version-within-python-interactor/7733)

<div class="topic-metadata">

**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 1\
**Last updated:** [July 23, 2019, 8:44pm UTC](https://discourse.slicer.org/t/get-slicer-version-within-python-interactor/7733 "2019-07-23T20:44:00Z")

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Is there a way to get my slicer version within the Python Interactor? For example: import sys print(sys.version) gives us Python version. I was wondering if there is a way to get slicer version from the Python console…

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## [Surface models types and voxelization](https://discourse.slicer.org/t/surface-models-types-and-voxelization/7728)

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**Author:** [@Alessandro\_Piol](https://discourse.slicer.org/u/Alessandro_Piol)\
**Replies:** 1\
**Last updated:** [July 23, 2019, 5:50pm UTC](https://discourse.slicer.org/t/surface-models-types-and-voxelization/7728 "2019-07-23T17:50:42Z")

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Hi all! I have to convert a surface model stl into a voxelized mask, with 1s inside and 0s outside. It is important that the mask has the same dimensions and voxel size as another volume I want to register with. In Matl…

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## [Choose one region to isolate it and change it in one segment](https://discourse.slicer.org/t/choose-one-region-to-isolate-it-and-change-it-in-one-segment/7729)

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**Author:** [@Jmarcs](https://discourse.slicer.org/u/Jmarcs)\
**Replies:** 1\
**Last updated:** [July 23, 2019, 5:41pm UTC](https://discourse.slicer.org/t/choose-one-region-to-isolate-it-and-change-it-in-one-segment/7729 "2019-07-23T17:41:36Z")

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Is there a fonction to change quickly A1 in 1 segment best regards You are really a great team

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## [Nifti file sform and Slicer image origin seem to disagree](https://discourse.slicer.org/t/nifti-file-sform-and-slicer-image-origin-seem-to-disagree/7711)

<div class="topic-metadata">

**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 2\
**Last updated:** [July 23, 2019, 3:04pm UTC](https://discourse.slicer.org/t/nifti-file-sform-and-slicer-image-origin-seem-to-disagree/7711 "2019-07-23T15:04:28Z")

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Hello, I have a nifti file (.nii.gz), and when I load it in Slicer, the Volumes module reports IJK to RAS direction matrix is diagonal with -1,1,1 on the diagonal, and an origin of approx 124,78,-142 mm. However, when I…

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## [Define pyramid with cross-section of polygon](https://discourse.slicer.org/t/define-pyramid-with-cross-section-of-polygon/7600)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 6\
**Last updated:** [July 23, 2019, 12:32pm UTC](https://discourse.slicer.org/t/define-pyramid-with-cross-section-of-polygon/7600 "2019-07-23T12:32:16Z")

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Hi Dear 3DSlicer developers I want to define one pyramid with cross-section of polygon (for example polygon with 160 vertices) using VTK. I think that I must use vtkFrustumSource. Is it ok? How can I do it? Please g…

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## [Error when run 3DSlicer in singularity container](https://discourse.slicer.org/t/error-when-run-3dslicer-in-singularity-container/7599)

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**Author:** [@lxwgcool](https://discourse.slicer.org/u/lxwgcool)\
**Replies:** 9\
**Last updated:** [July 23, 2019, 12:20pm UTC](https://discourse.slicer.org/t/error-when-run-3dslicer-in-singularity-container/7599 "2019-07-23T12:20:11Z")

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The following errors is reported when i run 3DSlicer in singularity container: X Error: BadValue (integer parameter out of range for operation) 2 Extension: 155 (Uknown extension) Minor opcode: 3 (Unknown request) …

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## [VR headset for Slicer](https://discourse.slicer.org/t/vr-headset-for-slicer/7572)

<div class="topic-metadata">

**Author:** [@Christina](https://discourse.slicer.org/u/Christina)\
**Replies:** 3\
**Last updated:** [July 23, 2019, 12:00am UTC](https://discourse.slicer.org/t/vr-headset-for-slicer/7572 "2019-07-23T00:00:19Z")

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Hello, what is the best VR headset you recommend for Slicer, that uses outside-in tracking? Thank you! Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Error message: Could not load as Scalar Volume](https://discourse.slicer.org/t/error-message-could-not-load-as-scalar-volume/7577)

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**Author:** [@J\_C](https://discourse.slicer.org/u/J_C)\
**Replies:** 4\
**Last updated:** [July 22, 2019, 9:58pm UTC](https://discourse.slicer.org/t/error-message-could-not-load-as-scalar-volume/7577 "2019-07-22T21:58:06Z")

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Hi, Recently I started using Slicer (4.10.2) to extract some radiomics features from MRI images using the radiomics module, but every time I try to import some DICOMs through the DICOM manager, I get a lot of warnings; …

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## [How to measure cartilage volume and thickness](https://discourse.slicer.org/t/how-to-measure-cartilage-volume-and-thickness/7696)

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**Author:** [@saf](https://discourse.slicer.org/u/saf)\
**Replies:** 4\
**Last updated:** [July 21, 2019, 6:25pm UTC](https://discourse.slicer.org/t/how-to-measure-cartilage-volume-and-thickness/7696 "2019-07-21T18:25:01Z")

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Can i use Slicer for measure cartilage volume and thickness with ? if yes, how can I do please!

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## [How many seg.nrrd files can be loaded at once in Slicer?](https://discourse.slicer.org/t/how-many-seg-nrrd-files-can-be-loaded-at-once-in-slicer/7699)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 2\
**Last updated:** [July 21, 2019, 9:42am UTC](https://discourse.slicer.org/t/how-many-seg-nrrd-files-can-be-loaded-at-once-in-slicer/7699 "2019-07-21T09:42:57Z")

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How many seg.nrrd files can be loaded at once in Slicer? Is there some kind of limit? Is it just a question of memory or maybe some other things? I will have to load around 50 segmentations for one project, so far I ma…

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## [How to show thickness distribution of a thin layer](https://discourse.slicer.org/t/how-to-show-thickness-distribution-of-a-thin-layer/7518)

<div class="topic-metadata">

**Author:** [@11125](https://discourse.slicer.org/u/11125)\
**Replies:** 2\
**Last updated:** [July 21, 2019, 3:17am UTC](https://discourse.slicer.org/t/how-to-show-thickness-distribution-of-a-thin-layer/7518 "2019-07-21T03:17:03Z")

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I have a micro-CT file of a coating. I want to demonstrate the coating thickness distribution as a color contour image. Can 3d slicer do so? Or is there a function I can get the thickness data matrix registered to the co…

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## [SEEG segmentation](https://discourse.slicer.org/t/seeg-segmentation/7683)

<div class="topic-metadata">

**Author:** [@Ann](https://discourse.slicer.org/u/Ann)\
**Replies:** 1\
**Last updated:** [July 21, 2019, 3:14am UTC](https://discourse.slicer.org/t/seeg-segmentation/7683 "2019-07-21T03:14:00Z")

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Hello, I’m new here and in need of some assistance with exporting SEEG segmentation in SEEG Assistant module. Do you know the meaning of the electrode parameters here？ For example, D08-05AM. Thank you.

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## [PET SUV factor and rescale slope](https://discourse.slicer.org/t/pet-suv-factor-and-rescale-slope/7355)

<div class="topic-metadata">

**Author:** [@pocolya](https://discourse.slicer.org/u/pocolya)\
**Replies:** 14\
**Last updated:** [July 20, 2019, 9:09am UTC](https://discourse.slicer.org/t/pet-suv-factor-and-rescale-slope/7355 "2019-07-20T09:09:11Z")

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I am working on PET images and I’d like to convert DICOM PET images into SUV factorised images on the data that took into account rescale slope and intercept. I can’t find any sure evidence that the SUV calculated with P…

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