# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=403

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

**Page:** 404

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## ["other DICOM listeners running" on startup](https://discourse.slicer.org/t/other-dicom-listeners-running-on-startup/4980)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 7\
**Last updated:** [December 6, 2018, 1:36am UTC](https://discourse.slicer.org/t/other-dicom-listeners-running-on-startup/4980 "2018-12-06T01:36:42Z")

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I recently started seeing the message below every time on startup. I don’t start any listeners knowingly. Is this message expected?

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## [I can't install extensions](https://discourse.slicer.org/t/i-cant-install-extensions/4969)

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**Author:** [@rojer](https://discourse.slicer.org/u/rojer)\
**Replies:** 1\
**Last updated:** [December 5, 2018, 1:32pm UTC](https://discourse.slicer.org/t/i-cant-install-extensions/4969 "2018-12-05T13:32:23Z")

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Problem report for Slicer 4.8.1 win-amd64: \[The extension lib and share folds were downloaded successfully, but a warning “Failed to remove directory C:/Users/dell/AppData/Roaming/NA-MIC/Extensions-26813/SlicerDMRI/26813…

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## [Customization VR enviornment](https://discourse.slicer.org/t/customization-vr-enviornment/4962)

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**Author:** [@M\_pavi](https://discourse.slicer.org/u/M_pavi)\
**Replies:** 1\
**Last updated:** [December 5, 2018, 6:33am UTC](https://discourse.slicer.org/t/customization-vr-enviornment/4962 "2018-12-05T06:33:06Z")

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My problem is to customize Virtual reality space. In specifically I did render 3D and 4D data in the same VR environment at the same time. Where I did change the background color by using python interactor ( the proble…

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## [One DICOM study loading as multiple](https://discourse.slicer.org/t/one-dicom-study-loading-as-multiple/4958)

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**Author:** [@geodeltax](https://discourse.slicer.org/u/geodeltax)\
**Replies:** 3\
**Last updated:** [December 5, 2018, 4:09am UTC](https://discourse.slicer.org/t/one-dicom-study-loading-as-multiple/4958 "2018-12-05T04:09:30Z")

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Hi, I’m trying to import a CT scan using the DICOM Browser on Slicer 4.10.0. The directory I imported with one study loaded as several studies, each with one series containing one slice. It’s currently loading one i…

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## [3DSlicer for measuring pectoralis area on axial CT slice](https://discourse.slicer.org/t/3dslicer-for-measuring-pectoralis-area-on-axial-ct-slice/4948)

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**Author:** [@Benjamin\_Fortson](https://discourse.slicer.org/u/Benjamin_Fortson)\
**Replies:** 2\
**Last updated:** [December 5, 2018, 1:37am UTC](https://discourse.slicer.org/t/3dslicer-for-measuring-pectoralis-area-on-axial-ct-slice/4948 "2018-12-05T01:37:05Z")

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Hi, I’m completely new to 3DSlicer. Can it be used to measure the area and average density of the pectoralis muscle on an axial CT slice? Is this process called segmentation, or is that something else? Thanks, Ben

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## [Re-sampling vs Harden Transform for a dose volume](https://discourse.slicer.org/t/re-sampling-vs-harden-transform-for-a-dose-volume/4963)

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**Author:** [@Lowey](https://discourse.slicer.org/u/Lowey)\
**Replies:** 2\
**Last updated:** [December 4, 2018, 11:52pm UTC](https://discourse.slicer.org/t/re-sampling-vs-harden-transform-for-a-dose-volume/4963 "2018-12-04T23:52:49Z")

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Operating system: Windows 10 Slicer version: 4.8.1 Stable Hi there, I have a general question about how Slicer handles and applies deformable registration files that are exported from TPS software with respect to grid…

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## [Heart segmentation](https://discourse.slicer.org/t/heart-segmentation/4957)

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**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 4\
**Last updated:** [December 4, 2018, 9:28pm UTC](https://discourse.slicer.org/t/heart-segmentation/4957 "2018-12-04T21:28:48Z")

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Operating system: windows 10 Slicer version: 4.1.10 Expected behavior: Actual behavior: how can i prevent merging of hollow shells (F1) like in the image. Also is there away i can reduce size of brush tool below 1% a…

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## [How to run Scripted or loadable Modules from Shell Scrpt (batch mode?)](https://discourse.slicer.org/t/how-to-run-scripted-or-loadable-modules-from-shell-scrpt-batch-mode/4940)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 2\
**Last updated:** [December 4, 2018, 6:32pm UTC](https://discourse.slicer.org/t/how-to-run-scripted-or-loadable-modules-from-shell-scrpt-batch-mode/4940 "2018-12-04T18:32:09Z")

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Operating system: Linux Mint 17 Slicer version: 4.9 Expected behavior: Actual behavior: Hi everyone! I would like to know if it is possible to call a scripted or loadable Slicer module in a shell script giving its s…

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## [How to apply different kernels to different areas of an image using deconvolution process?](https://discourse.slicer.org/t/how-to-apply-different-kernels-to-different-areas-of-an-image-using-deconvolution-process/4922)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 4\
**Last updated:** [December 4, 2018, 1:34pm UTC](https://discourse.slicer.org/t/how-to-apply-different-kernels-to-different-areas-of-an-image-using-deconvolution-process/4922 "2018-12-04T13:34:58Z")

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Hi Dear developers and users I have a image that has degraded its quality due to blurring. The blurring process can be modelled as degradation function. The amount of blurring (degradation function) varies in different …

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## [Can I label a 3D segmentation of a hippocampus?](https://discourse.slicer.org/t/can-i-label-a-3d-segmentation-of-a-hippocampus/4893)

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**Author:** [@abiorac](https://discourse.slicer.org/u/abiorac)\
**Replies:** 5\
**Last updated:** [December 3, 2018, 11:04pm UTC](https://discourse.slicer.org/t/can-i-label-a-3d-segmentation-of-a-hippocampus/4893 "2018-12-03T23:04:39Z")

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Operating system: Mac OS Mojave Slicer version: 4.10 Expected behavior: I want to be able to place a label on certain structures on a 3D view of the hippocampus (using the editor module) and have the label appear when …

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## [Error with DSCMRIanalysis extension](https://discourse.slicer.org/t/error-with-dscmrianalysis-extension/4786)

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**Author:** [@happyle](https://discourse.slicer.org/u/happyle)\
**Replies:** 1\
**Last updated:** [December 1, 2018, 11:29pm UTC](https://discourse.slicer.org/t/error-with-dscmrianalysis-extension/4786 "2018-12-01T23:29:19Z")

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Dear Dr. Fedorov, @fedorov Thank you for your awesome work on DSCMRIAnalysis module. I am trying to use the DSCMRIanalysis extension to analyze DSC-MRI images and I am receiving the error below: DSCMRIAnalysis stand…

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## [Registration error using MMI with an ROI moving mask](https://discourse.slicer.org/t/registration-error-using-mmi-with-an-roi-moving-mask/4886)

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**Author:** [@Eloise](https://discourse.slicer.org/u/Eloise)\
**Replies:** 6\
**Last updated:** [December 1, 2018, 3:45pm UTC](https://discourse.slicer.org/t/registration-error-using-mmi-with-an-roi-moving-mask/4886 "2018-12-01T15:45:32Z")

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Hi, I am using the BRAINS registration module to register two MRI exams using an affine transform. I want to provide an ROI Masking image for the moving image, but I get the following error when using the MMI metric : t…

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## [Edges in 3d volume](https://discourse.slicer.org/t/edges-in-3d-volume/4921)

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**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 2\
**Last updated:** [December 1, 2018, 2:33pm UTC](https://discourse.slicer.org/t/edges-in-3d-volume/4921 "2018-12-01T14:33:22Z")

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Operating system: windows 10 Slicer version:4.10 Expected behavior: Actual behavior: Hi, Would appreciate thoughts on how to deal with edges in 3d volume after segmentation. I have seen these on few cases of mine no…

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## [Issues with downloading slicer heart on 3D slicer](https://discourse.slicer.org/t/issues-with-downloading-slicer-heart-on-3d-slicer/4918)

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**Author:** [@helenawill95](https://discourse.slicer.org/u/helenawill95)\
**Replies:** 3\
**Last updated:** [November 30, 2018, 4:55pm UTC](https://discourse.slicer.org/t/issues-with-downloading-slicer-heart-on-3d-slicer/4918 "2018-11-30T16:55:33Z")

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Operating system: Windows 7 Slicer version: 4.11.0 Expected behavior: To download Actual behavior: 100% loads on the download bar and two pop ups saying extensions downloading pop up but then the screen freezes and th…

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## [Saved Transformed Registration for Calculating Model To Model Distance](https://discourse.slicer.org/t/saved-transformed-registration-for-calculating-model-to-model-distance/4739)

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**Author:** [@Olivia\_Yeuhsin\_Chou](https://discourse.slicer.org/u/Olivia_Yeuhsin_Chou)\
**Replies:** 7\
**Last updated:** [November 30, 2018, 1:51pm UTC](https://discourse.slicer.org/t/saved-transformed-registration-for-calculating-model-to-model-distance/4739 "2018-11-30T13:51:05Z")

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Operating system: windows Slicer version: 4.8.1 Hello, I have a question regarding how I can save registration (done under transform module) to a file form that could be used for calculating model to model distance. T…

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## [Volume Rendering with Python](https://discourse.slicer.org/t/volume-rendering-with-python/3431)

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**Author:** [@trnhx001](https://discourse.slicer.org/u/trnhx001)\
**Replies:** 2\
**Last updated:** [July 11, 2018, 2:48pm UTC](https://discourse.slicer.org/t/volume-rendering-with-python/3431 "2018-07-11T14:48:20Z")

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Operating system: Windows 7 Slicer version: 4.9.0 Hi All, I am trying to use python to do volume rendering and set parameters for it. These are few lines of attempt. However, I run into the problem when trying to get…

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## [Rpy2 pip installation fails](https://discourse.slicer.org/t/rpy2-pip-installation-fails/4883)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 15\
**Last updated:** [November 29, 2018, 6:16pm UTC](https://discourse.slicer.org/t/rpy2-pip-installation-fails/4883 "2018-11-29T18:16:44Z")

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Following the thread, https://discourse.slicer.org/t/pip-in-nightly-build-not-working/3325, I got pip working as demonstrated. But this fails: \>\>\> pipmain(\[‘install’, ‘Rpy2’\]) Collecting Rpy2 Using cached https://fil…

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## [Interacting with external python](https://discourse.slicer.org/t/interacting-with-external-python/4897)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 5\
**Last updated:** [November 28, 2018, 8:14am UTC](https://discourse.slicer.org/t/interacting-with-external-python/4897 "2018-11-28T08:14:57Z")

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I am trying to build on this example in: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python\_scripting#How\_to\_run\_Python\_script\_using\_a\_non-Slicer\_Python\_environment This python\_path = "C:/Users/amaga/…

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## [Is pip documentation up to date](https://discourse.slicer.org/t/is-pip-documentation-up-to-date/4882)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [November 28, 2018, 7:00am UTC](https://discourse.slicer.org/t/is-pip-documentation-up-to-date/4882 "2018-11-28T07:00:51Z")

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On windows instructions at https://www.slicer.org/wiki/Documentation/Labs/Pip work for 4.8.1, but not for the latest stable 4.10.0. I get this \>\>\> import pip \>\>\> pip.main(\[‘install’, ‘pygments’\]) Traceback (most rece…

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## [Elastix extension not creating a transform](https://discourse.slicer.org/t/elastix-extension-not-creating-a-transform/4896)

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**Author:** [@stephan](https://discourse.slicer.org/u/stephan)\
**Replies:** 4\
**Last updated:** [November 28, 2018, 5:20am UTC](https://discourse.slicer.org/t/elastix-extension-not-creating-a-transform/4896 "2018-11-28T05:20:38Z")

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System: Win 7 64 bit, Slicer 4.10.0, SlicerElastix extension Expected behavior: Save Elastix results in transformation Actual behavior: Transformation is still identity (Linear transform, diag (1,1,1,1)) after running …

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## [Difference between two or more models](https://discourse.slicer.org/t/difference-between-two-or-more-models/4876)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 3\
**Last updated:** [November 27, 2018, 5:02pm UTC](https://discourse.slicer.org/t/difference-between-two-or-more-models/4876 "2018-11-27T17:02:05Z")

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Operating system: Windows Slicer version: 4.10.0 Expected behavior: How can I get a new 3D model showing the difference between both models? Actual behavior: I have two 3D models of MS lesions of the same patient. Si…

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## [Activate scissors effect](https://discourse.slicer.org/t/activate-scissors-effect/4890)

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**Author:** [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Replies:** 1\
**Last updated:** [November 27, 2018, 3:51pm UTC](https://discourse.slicer.org/t/activate-scissors-effect/4890 "2018-11-27T15:51:07Z")

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Problem report for Slicer 4.10.0 macosx-amd64: \[please describe expected and actual behavior\] Hi I am trying to use scissors effect but how can I apply it the covered part does not go?

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## [Use a centerline model and a segmentation to extract vessels from an image set](https://discourse.slicer.org/t/use-a-centerline-model-and-a-segmentation-to-extract-vessels-from-an-image-set/4880)

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**Author:** [@kantzoul](https://discourse.slicer.org/u/kantzoul)\
**Replies:** 0\
**Last updated:** [November 26, 2018, 11:19pm UTC](https://discourse.slicer.org/t/use-a-centerline-model-and-a-segmentation-to-extract-vessels-from-an-image-set/4880 "2018-11-26T23:19:18Z")

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Hi all, So I have been trying to extract the vessels from a partial MRA brain scan. I wanted to try using the centerline model I got from the VMTK extension and a manual segmentation I did to isolate the vessels. Using …

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## [How to test a scripted module](https://discourse.slicer.org/t/how-to-test-a-scripted-module/4578)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 1\
**Last updated:** [November 26, 2018, 6:58pm UTC](https://discourse.slicer.org/t/how-to-test-a-scripted-module/4578 "2018-11-26T18:58:37Z")

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I modified the SlicerCaseIterator module, but I don’t actually know how to test/debug it. the command i use is ~/tools/Slicer-4.10.0-linux-amd64/Slicer --additional-module-paths ~/build/slicer/SlicerCaseIterator/Slicer…

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## [Fail to load a big tiff stack ](https://discourse.slicer.org/t/fail-to-load-a-big-tiff-stack/4832)

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**Author:** [@cduque](https://discourse.slicer.org/u/cduque)\
**Replies:** 13\
**Last updated:** [November 26, 2018, 2:56pm UTC](https://discourse.slicer.org/t/fail-to-load-a-big-tiff-stack/4832 "2018-11-26T14:56:53Z")

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Hi There! I wanted to load a stack of images stored in a single tiff file of microscopic data, but only the first image is loaded. The dataset is approximatly 5Gb and its dimensions are 2159x2560x548, the bit depth is …

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## [How to export number of voxels for different colors in CT images after segmentation?](https://discourse.slicer.org/t/how-to-export-number-of-voxels-for-different-colors-in-ct-images-after-segmentation/4813)

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**Author:** [@sali](https://discourse.slicer.org/u/sali)\
**Replies:** 7\
**Last updated:** [November 26, 2018, 2:30pm UTC](https://discourse.slicer.org/t/how-to-export-number-of-voxels-for-different-colors-in-ct-images-after-segmentation/4813 "2018-11-26T14:30:54Z")

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Dear experts I segmented the human Brain with the editor modules for 100 slices of CT images, manually, now, I need to extract the number of voxels for each color with python or …, how can I do that? Thanks

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## [How to import a .mvl file format (3D Ultrasound image)](https://discourse.slicer.org/t/how-to-import-a-mvl-file-format-3d-ultrasound-image/3294)

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**Author:** [@Sherif\_Galal1](https://discourse.slicer.org/u/Sherif_Galal1)\
**Replies:** 3\
**Last updated:** [November 26, 2018, 2:28pm UTC](https://discourse.slicer.org/t/how-to-import-a-mvl-file-format-3d-ultrasound-image/3294 "2018-11-26T14:28:18Z")

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Operating system: windows 10 64 bit Slicer version: 4.9 nightly Expected behavior: import .mvl file Actual behavior: doesn’t import

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## [Data probe auto-resize issue](https://discourse.slicer.org/t/data-probe-auto-resize-issue/4671)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 1\
**Last updated:** [November 25, 2018, 8:43pm UTC](https://discourse.slicer.org/t/data-probe-auto-resize-issue/4671 "2018-11-25T20:43:11Z")

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Data probe seems to have an issue automatically resizing itself to fit its contents.The issue seems to be the default behavior after installing Slicer. I think this has been going on for a few weeks now, I tested today w…

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## [How to change the different flip angle volume into multivolume?](https://discourse.slicer.org/t/how-to-change-the-different-flip-angle-volume-into-multivolume/4589)

<div class="topic-metadata">

**Author:** [@Jin](https://discourse.slicer.org/u/Jin)\
**Replies:** 6\
**Last updated:** [November 25, 2018, 4:26pm UTC](https://discourse.slicer.org/t/how-to-change-the-different-flip-angle-volume-into-multivolume/4589 "2018-11-25T16:26:16Z")

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Operating system:windows 10 Slicer version: 4.7.0 Expected behavior: output multivolume Actual behavior: don’t know how to fill the settings, where can I get those informations? Thanks a lot!

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## [Can't download V 4.4.0](https://discourse.slicer.org/t/cant-download-v-4-4-0/4863)

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**Author:** [@aab](https://discourse.slicer.org/u/aab)\
**Replies:** 1\
**Last updated:** [November 24, 2018, 2:12pm UTC](https://discourse.slicer.org/t/cant-download-v-4-4-0/4863 "2018-11-24T14:12:47Z")

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Operating system: Windows 64 bit Slicer version: 4.8.1 Expected behavior: Download V 4.4.0 off http://slicer.kitware.com/midas3/folder/274 Actual behavior: : I have V 4.8.1 installed but I would like to download 4.4.0…

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