# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=434

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

**Page:** 435

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## [Unable to load tiff sequence created by python3 tifffile module](https://discourse.slicer.org/t/unable-to-load-tiff-sequence-created-by-python3-tifffile-module/1792)

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**Author:** [@hclai](https://discourse.slicer.org/u/hclai)\
**Replies:** 6\
**Last updated:** [January 10, 2018, 5:26am UTC](https://discourse.slicer.org/t/unable-to-load-tiff-sequence-created-by-python3-tifffile-module/1792 "2018-01-10T05:26:08Z")

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Operating system: Windows 10 Slicer version: 4.8.1 Expected behavior: Load tiff sequence created by python3 tifffile module and render the volume Actual behavior: The loading bar shows up but the Active Volume is empt…

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## [NRRd to FSL bvecs values](https://discourse.slicer.org/t/nrrd-to-fsl-bvecs-values/814)

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**Author:** [@jfhartzell](https://discourse.slicer.org/u/jfhartzell)\
**Replies:** 4\
**Last updated:** [January 9, 2018, 10:20pm UTC](https://discourse.slicer.org/t/nrrd-to-fsl-bvecs-values/814 "2018-01-09T22:20:55Z")

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Operating system : Mac OS Sierra 10.12.6 Slicer version : 4.6.2 r25516 Expected behavior : correct bvecs output Actual behavior : values of x and z vectors flipped from negative to positive or vice versa Hi Afte…

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## [Calculate a scalp to scalp distance](https://discourse.slicer.org/t/calculate-a-scalp-to-scalp-distance/1141)

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**Author:** [@Frederic](https://discourse.slicer.org/u/Frederic)\
**Replies:** 49\
**Last updated:** [January 9, 2018, 3:06pm UTC](https://discourse.slicer.org/t/calculate-a-scalp-to-scalp-distance/1141 "2018-01-09T15:06:35Z")

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Dear Slicer experts, Quick mail to know if you know a way/a module to calculate a scalp to scalp distance (i.e. distance along the surface)? More than “CurveMaker”, I would like an automatic way to realize that (1/mesh…

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## [Cannot find SNRMeasurement Module in Slicer 4.8.0](https://discourse.slicer.org/t/cannot-find-snrmeasurement-module-in-slicer-4-8-0/1783)

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**Author:** [@xaggi](https://discourse.slicer.org/u/xaggi)\
**Replies:** 4\
**Last updated:** [January 9, 2018, 5:03am UTC](https://discourse.slicer.org/t/cannot-find-snrmeasurement-module-in-slicer-4-8-0/1783 "2018-01-09T05:03:04Z")

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I want to measure SNR in MRI images. I checked the documentation, one of the methods to measure SNR is using SNRMeasurement module. But I cannot find it in the modules list :frowning: Please guide. Also, if there is any …

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## [VMTK extension- Level Set Segmentation problem](https://discourse.slicer.org/t/vmtk-extension-level-set-segmentation-problem/1778)

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**Author:** [@Ella](https://discourse.slicer.org/u/Ella)\
**Replies:** 3\
**Last updated:** [January 9, 2018, 3:02am UTC](https://discourse.slicer.org/t/vmtk-extension-level-set-segmentation-problem/1778 "2018-01-09T03:02:49Z")

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I have downloaded the SlicerVMTK extension and followed this tutorial: https://www.youtube.com/watch?v=DJ2032yo5Co to extract a model of the Trachea and Bronchi from my DICOM images. However when I get up to the Level s…

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## [Calculating margin between two superimposed segments](https://discourse.slicer.org/t/calculating-margin-between-two-superimposed-segments/1788)

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**Author:** [@tnguyen](https://discourse.slicer.org/u/tnguyen)\
**Replies:** 1\
**Last updated:** [January 9, 2018, 1:47am UTC](https://discourse.slicer.org/t/calculating-margin-between-two-superimposed-segments/1788 "2018-01-09T01:47:39Z")

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Hi, I was wondering if there is a way to find the smallest margin between two superimposed 3D-segments, especially in an automatic fashion? Thank you!

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## [Sync “Volumes” color look-up table with “Volume Rendering”](https://discourse.slicer.org/t/sync-volumes-color-look-up-table-with-volume-rendering/1770)

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**Author:** [@Hamburgerfinger](https://discourse.slicer.org/u/Hamburgerfinger)\
**Replies:** 3\
**Last updated:** [January 8, 2018, 4:06am UTC](https://discourse.slicer.org/t/sync-volumes-color-look-up-table-with-volume-rendering/1770 "2018-01-08T04:06:05Z")

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In the Volume Rendering module there is an option to sync the scalar color mapping with the active color mapping in the Volumes module. Can I do the opposite, i.e. create a custom color mapping in the Volume Rendering mo…

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## [Function for surface registration](https://discourse.slicer.org/t/function-for-surface-registration/1776)

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**Author:** [@shellyverde](https://discourse.slicer.org/u/shellyverde)\
**Replies:** 3\
**Last updated:** [January 8, 2018, 2:48am UTC](https://discourse.slicer.org/t/function-for-surface-registration/1776 "2018-01-08T02:48:01Z")

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Operating system: Windows Slicer version: 4.8 Hi, I have patient data in CT Dicom space and I am capturing points in tracker space on patient. So I need to register the patient in tracker space (with captured points) …

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## [EMSegmenter with Atlas problem](https://discourse.slicer.org/t/emsegmenter-with-atlas-problem/1740)

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**Author:** [@NaglisR](https://discourse.slicer.org/u/NaglisR)\
**Replies:** 1\
**Last updated:** [January 7, 2018, 4:14pm UTC](https://discourse.slicer.org/t/emsegmenter-with-atlas-problem/1740 "2018-01-07T16:14:13Z")

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Hi, everyone, I am trying to use the EMSegmenter with Atlas module and run in to this screen: Don’t seem to be moving anywhere from this point as there are no options for input. Am I doing something wrong here?

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## [Cannot close contour in Segment editor drawing effect](https://discourse.slicer.org/t/cannot-close-contour-in-segment-editor-drawing-effect/1774)

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**Author:** [@MimiPoon](https://discourse.slicer.org/u/MimiPoon)\
**Replies:** 4\
**Last updated:** [January 6, 2018, 10:27pm UTC](https://discourse.slicer.org/t/cannot-close-contour-in-segment-editor-drawing-effect/1774 "2018-01-06T22:27:01Z")

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Problem report for Slicer 4.8.1 macosx-amd64: \[please describe expected and actual behavior\] Try to segment a tumor with draw but unable to do it with Enter key and ‘a’ key. log message as follows: \[DEBUG\]\[Qt\] 06.01.2…

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## [How to remove background right-angle slices from restored Scene Views of models from SPL Brain Atlas](https://discourse.slicer.org/t/how-to-remove-background-right-angle-slices-from-restored-scene-views-of-models-from-spl-brain-atlas/1769)

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**Author:** [@aNonprofessional](https://discourse.slicer.org/u/aNonprofessional)\
**Replies:** 2\
**Last updated:** [January 6, 2018, 9:24pm UTC](https://discourse.slicer.org/t/how-to-remove-background-right-angle-slices-from-restored-scene-views-of-models-from-spl-brain-atlas/1769 "2018-01-06T21:24:24Z")

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Note: my usage of Slicer is non-typical, just toward trying to learn brain anatomy. Operating system: Windows 8.1 win-amd64 Intel Core i7 Slicer version: 4.8.0 r26489 Expected behavior: restored SPL scene view minus b…

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## [Cannot load multiple images but not the single one](https://discourse.slicer.org/t/cannot-load-multiple-images-but-not-the-single-one/1773)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 2\
**Last updated:** [January 6, 2018, 3:29pm UTC](https://discourse.slicer.org/t/cannot-load-multiple-images-but-not-the-single-one/1773 "2018-01-06T15:29:30Z")

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

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## [How to convert .png images to DICOM files in a batch](https://discourse.slicer.org/t/how-to-convert-png-images-to-dicom-files-in-a-batch/1768)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 4\
**Last updated:** [January 6, 2018, 3:11pm UTC](https://discourse.slicer.org/t/how-to-convert-png-images-to-dicom-files-in-a-batch/1768 "2018-01-06T15:11:14Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: I have a CTA with png format. Can we convert png images to DICOM files in a batch? Thanks

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## [Converting MRtrix connectome model to .stl for 3D printing](https://discourse.slicer.org/t/converting-mrtrix-connectome-model-to-stl-for-3d-printing/1764)

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**Author:** [@Lena13](https://discourse.slicer.org/u/Lena13)\
**Replies:** 1\
**Last updated:** [January 5, 2018, 1:49pm UTC](https://discourse.slicer.org/t/converting-mrtrix-connectome-model-to-stl-for-3d-printing/1764 "2018-01-05T13:49:02Z")

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Hi, I created a whole brain connectome in MRtrix, which I converted to a .vtk file. I can open the file in Slicer, but when I save it as an .stl file, that file seems to be corrupted as I can’t open it with any software…

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## [New video tutorial for Segment editor - whole-heart segmentation from CT](https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-whole-heart-segmentation-from-ct/1731)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 3\
**Last updated:** [January 5, 2018, 10:09am UTC](https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-whole-heart-segmentation-from-ct/1731 "2018-01-05T10:09:59Z")

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This is the second part of a video tutorial series that teaches how to use Segment editor. This tutorial explains how to segment whole heart (heart ventricles, atria, and great vessels) from cardiac CT volumes. Used effe…

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## [2D Views in Slicer extremely slow on Windows](https://discourse.slicer.org/t/2d-views-in-slicer-extremely-slow-on-windows/782)

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**Author:** [@mschwier](https://discourse.slicer.org/u/mschwier)\
**Replies:** 16\
**Last updated:** [August 15, 2017, 5:35am UTC](https://discourse.slicer.org/t/2d-views-in-slicer-extremely-slow-on-windows/782 "2017-08-15T05:35:18Z")

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Dear all, I have my own Win 10 64 bit release build of Slicer (4.7.0-2017-07-27) running and I notice some extreme lags when interacting with the 2D views. This is particularly noticeable when I load a multi-volume (but…

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## [DWI loading from DICOM](https://discourse.slicer.org/t/dwi-loading-from-dicom/1746)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 9\
**Last updated:** [January 4, 2018, 4:44pm UTC](https://discourse.slicer.org/t/dwi-loading-from-dicom/1746 "2018-01-04T16:44:10Z")

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I’ve tried to load an MRI study from DICOM that contained DWI series (Slicer 4.8.1 on Windows). Although I’ve installed SlierDMRI extension, the series was still loaded using scalar volume importer and appeared garbled. …

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## [SlicerIGT pathexplorer](https://discourse.slicer.org/t/slicerigt-pathexplorer/1754)

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**Author:** [@shellyverde](https://discourse.slicer.org/u/shellyverde)\
**Replies:** 5\
**Last updated:** [January 2, 2018, 4:37am UTC](https://discourse.slicer.org/t/slicerigt-pathexplorer/1754 "2018-01-02T04:37:15Z")

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Hi， I am new to Slicer and SlicerIGT. Trying to use the SlicerIGT pathexplorer function. When pressing the ‘+’ in the Plan section, I couldn’t add a point. I think there is something missing. Could you please help? Tha…

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## [Model created from skull CT looks lacy with many bony holes](https://discourse.slicer.org/t/model-created-from-skull-ct-looks-lacy-with-many-bony-holes/1744)

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**Author:** [@lambrosone](https://discourse.slicer.org/u/lambrosone)\
**Replies:** 6\
**Last updated:** [January 1, 2018, 11:32pm UTC](https://discourse.slicer.org/t/model-created-from-skull-ct-looks-lacy-with-many-bony-holes/1744 "2018-01-01T23:32:37Z")

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Operating system: WIN 10 Slicer version: 4.6.2 Expected behavior: Actual behavior: Newbie to slicer. My skull ct model frequently come out lacy with many holes. Is this because of my processing inSlicer? How do I cor…

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## [How to measure the Orbit-Volume?](https://discourse.slicer.org/t/how-to-measure-the-orbit-volume/1742)

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**Author:** [@Eva-Maria](https://discourse.slicer.org/u/Eva-Maria)\
**Replies:** 3\
**Last updated:** [January 1, 2018, 11:13pm UTC](https://discourse.slicer.org/t/how-to-measure-the-orbit-volume/1742 "2018-01-01T23:13:16Z")

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Hi, I’m new in using slicer 4.8.0. I’ve tried to use the slicer in order to calculate the orbit volume but I was not able to find the tool/path. Can somebody please help me? Thanks in advance!

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## [Comparing the differences between two slices quantitatively ](https://discourse.slicer.org/t/comparing-the-differences-between-two-slices-quantitatively/1748)

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**Author:** [@Ishan\_Perera](https://discourse.slicer.org/u/Ishan_Perera)\
**Replies:** 4\
**Last updated:** [January 1, 2018, 2:28am UTC](https://discourse.slicer.org/t/comparing-the-differences-between-two-slices-quantitatively/1748 "2018-01-01T02:28:15Z")

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Operating system: MacOS High Sierra 10.13.1 Slicer version: 4.7.0-2017-09-21 r26391 (I can upgrade/downgrade if need be) Expected behavior: Quantitative comparison of slices Actual behavior: N/A I have been tasked wi…

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## [Hardware Configuration advice](https://discourse.slicer.org/t/hardware-configuration-advice/1738)

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**Author:** [@gsfoco](https://discourse.slicer.org/u/gsfoco)\
**Replies:** 1\
**Last updated:** [December 28, 2017, 8:42pm UTC](https://discourse.slicer.org/t/hardware-configuration-advice/1738 "2017-12-28T20:42:13Z")

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Operating system: Windows 10 pro Slicer version: 4.8 Expected behavior: Actual behavior: Would you be able to help recommend a configuration? I will be doping volume regeneration from 3 dicom images, each ~0.8GB lar…

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## [Why HeterogeneityCAD cannot produce the true number of % injected dose value and gray levels in a normalized PET image?](https://discourse.slicer.org/t/why-heterogeneitycad-cannot-produce-the-true-number-of-injected-dose-value-and-gray-levels-in-a-normalized-pet-image/1703)

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**Author:** [@MimiPoon](https://discourse.slicer.org/u/MimiPoon)\
**Replies:** 9\
**Last updated:** [December 28, 2017, 4:27am UTC](https://discourse.slicer.org/t/why-heterogeneitycad-cannot-produce-the-true-number-of-injected-dose-value-and-gray-levels-in-a-normalized-pet-image/1703 "2017-12-28T04:27:34Z")

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Dear professors, I have a set of PET images with intensity value normalized to % injected dose. The intensity range of the segmented tumor is around 0.450275 to 1.482173. I applied the heterogeneityCAD module to extract…

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## [Rescaling the DICOM images using the RescaleIntercept and RescaleSlope](https://discourse.slicer.org/t/rescaling-the-dicom-images-using-the-rescaleintercept-and-rescaleslope/1733)

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**Author:** [@fukiracs](https://discourse.slicer.org/u/fukiracs)\
**Replies:** 1\
**Last updated:** [December 27, 2017, 5:18pm UTC](https://discourse.slicer.org/t/rescaling-the-dicom-images-using-the-rescaleintercept-and-rescaleslope/1733 "2017-12-27T17:18:19Z")

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Hello Everyone, I am new to the 3D Slicer software and I wanted to know if there is an option to rescale the DICOM images (For example from a Cone Beam CT) using the RescaleSlope and RescaleIntercept. To convert from th…

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## [New extension does not show in Slicer 4.8 ExtensonManager](https://discourse.slicer.org/t/new-extension-does-not-show-in-slicer-4-8-extensonmanager/1729)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 7\
**Last updated:** [December 27, 2017, 3:59pm UTC](https://discourse.slicer.org/t/new-extension-does-not-show-in-slicer-4-8-extensonmanager/1729 "2017-12-27T15:59:20Z")

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A new extension (TOMAAT) was recently added to the ExtensionsIndex 4.8 branch (see https://github.com/Slicer/ExtensionsIndex/pull/1502). The extension was built and packaged without problems, based on CDash content here,…

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## [How to creat a plane by 3 fiducials and then used in "modelclip"?](https://discourse.slicer.org/t/how-to-creat-a-plane-by-3-fiducials-and-then-used-in-modelclip/1722)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 1\
**Last updated:** [December 26, 2017, 3:41pm UTC](https://discourse.slicer.org/t/how-to-creat-a-plane-by-3-fiducials-and-then-used-in-modelclip/1722 "2017-12-26T15:41:54Z")

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Operating system: Slicer version:12-24 Expected behavior: Actual behavior: I am going to creat a plane by 3 fiducials，and then cut a model like the module “modelclip”?

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## [In 'Restore Saved Scene', when is 'add & restore' important to do?](https://discourse.slicer.org/t/in-restore-saved-scene-when-is-add-restore-important-to-do/1723)

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**Author:** [@aNonprofessional](https://discourse.slicer.org/u/aNonprofessional)\
**Replies:** 1\
**Last updated:** [December 26, 2017, 3:00pm UTC](https://discourse.slicer.org/t/in-restore-saved-scene-when-is-add-restore-important-to-do/1723 "2017-12-26T15:00:59Z")

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After loading the SPL Brain Atlas, when I click on ‘Restore or delete saved scene views’, and then click on Restore a named scene, I get an error/warning message about ‘add & restore’, and I wonder: what it means, and i…

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## [In Documentation Wiki, refering to undocking/docking, what is the 'panel chrome'?](https://discourse.slicer.org/t/in-documentation-wiki-refering-to-undocking-docking-what-is-the-panel-chrome/1720)

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**Author:** [@aNonprofessional](https://discourse.slicer.org/u/aNonprofessional)\
**Replies:** 1\
**Last updated:** [December 26, 2017, 2:37pm UTC](https://discourse.slicer.org/t/in-documentation-wiki-refering-to-undocking-docking-what-is-the-panel-chrome/1720 "2017-12-26T14:37:41Z")

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In a Slicer Documentation Wiki I find the term ‘panel chrome’ in relation to re-docking the Welcome window after undocking it, when I am trying to see about expanding the 3D view to fill the screen. I experimentally cli…

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## [How to display the PolyData independently?](https://discourse.slicer.org/t/how-to-display-the-polydata-independently/1700)

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**Author:** [@spring](https://discourse.slicer.org/u/spring)\
**Replies:** 5\
**Last updated:** [December 25, 2017, 1:22am UTC](https://discourse.slicer.org/t/how-to-display-the-polydata-independently/1700 "2017-12-25T01:22:09Z")

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Operating system: Windows 10 64bit Slicer version:4.9.0 2017-10-23 Expected behavior: display the polydata independently Actual behavior: displayed one polydata in all of scenes. Hi SlicerExperts, I have setted the…

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## [how to open slicer in linux ubuntu command line](https://discourse.slicer.org/t/how-to-open-slicer-in-linux-ubuntu-command-line/1707)

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**Author:** [@meina](https://discourse.slicer.org/u/meina)\
**Replies:** 1\
**Last updated:** [December 22, 2017, 2:03pm UTC](https://discourse.slicer.org/t/how-to-open-slicer-in-linux-ubuntu-command-line/1707 "2017-12-22T14:03:17Z")

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I downloaded Slicer-4.8.0-linux-amd64 on my linux ubuntu system, when I tried to open slicer, I first cd to Slicer-4.8.0-linux-amd64 folder, and typed ./Slicer in terminal. It said “error: Failed to obtain launcher execu…

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