# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=286

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

**Page:** 287

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## [A problem with SegmentEditor](https://discourse.slicer.org/t/a-problem-with-segmenteditor/17156)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [April 18, 2021, 7:21pm UTC](https://discourse.slicer.org/t/a-problem-with-segmenteditor/17156 "2021-04-18T19:21:17Z")

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Slicer 4.11 20210226 win7 64 When I use Threshold,as you see in this video ,After I click apply, the dyeing disappears, but it actually exists. When I click show 3D, a preview of the model appears.

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## [Fill in between different contoures](https://discourse.slicer.org/t/fill-in-between-different-contoures/17137)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [April 18, 2021, 5:42am UTC](https://discourse.slicer.org/t/fill-in-between-different-contoures/17137 "2021-04-18T05:42:17Z")

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Slicer version: 4.10.1 Hi 3D slicer experts and all I have a number of contours that are in separate segments(like Fig A). I want to make a model of all of them (like Fig B). How can I fill in between them to finally h…

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## [Retain Image Color in Volume Rendering](https://discourse.slicer.org/t/retain-image-color-in-volume-rendering/12294)

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**Author:** [@David\_Brouwer](https://discourse.slicer.org/u/David_Brouwer)\
**Replies:** 26\
**Last updated:** [April 18, 2021, 4:49am UTC](https://discourse.slicer.org/t/retain-image-color-in-volume-rendering/12294 "2021-04-18T04:49:33Z")

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I am looking to create a 3D model of a stack of images, retaining the original image color. See the screenshot as a reference. By creating a segmentation with a threshold of 22 - 255 I am able to select the desired part…

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## [How do I use GetLogBiasFieldAsImage in c#?](https://discourse.slicer.org/t/how-do-i-use-getlogbiasfieldasimage-in-c/17043)

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**Author:** [@Tami](https://discourse.slicer.org/u/Tami)\
**Replies:** 5\
**Last updated:** [April 18, 2021, 3:56am UTC](https://discourse.slicer.org/t/how-do-i-use-getlogbiasfieldasimage-in-c/17043 "2021-04-18T03:56:45Z")

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Operating system:window10 Slicer version:4.10.2 I have the N4BiasFieldCorrectionImageFilter implemented in c# (visual studio) and it is working correctly and improving images. However, I need to use a ShrinkFactor hig…

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## [Download.slicer.org server is down!](https://discourse.slicer.org/t/download-slicer-org-server-is-down/353)

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**Author:** [@Andres\_Pineda](https://discourse.slicer.org/u/Andres_Pineda)\
**Replies:** 43\
**Last updated:** [April 17, 2021, 1:15pm UTC](https://discourse.slicer.org/t/download-slicer-org-server-is-down/353 "2021-04-17T13:15:27Z")

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Have been trying for 2 days to download slicer and the download server is down. This is the link on the web site: http://download.slicer.org/ Please let me know when it is back up.

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## [Trouble loading Open Sound Control Module](https://discourse.slicer.org/t/trouble-loading-open-sound-control-module/17138)

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**Author:** [@smallvalthoss](https://discourse.slicer.org/u/smallvalthoss)\
**Replies:** 0\
**Last updated:** [April 16, 2021, 7:13pm UTC](https://discourse.slicer.org/t/trouble-loading-open-sound-control-module/17138 "2021-04-16T19:13:55Z")

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Here is the error I get whenever loading the open sound control module. Any help is appreciated. Traceback (most recent call last): File "C:/Users/Madhavi/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29…

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## [ctkPathLineEdit can't find setCurrentFileExtension function?](https://discourse.slicer.org/t/ctkpathlineedit-cant-find-setcurrentfileextension-function/17118)

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**Author:** [@Teresa\_Gadda](https://discourse.slicer.org/u/Teresa_Gadda)\
**Replies:** 2\
**Last updated:** [April 16, 2021, 4:43pm UTC](https://discourse.slicer.org/t/ctkpathlineedit-cant-find-setcurrentfileextension-function/17118 "2021-04-16T16:43:51Z")

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I’m trying to set up my own slicer extension and one of the things I want to do is to be able to load a file but restrict the allowed extensions (or at least make it easier to select the correct one). Other posts here h…

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## [prostatic manual segmentation and mask extraction](https://discourse.slicer.org/t/prostatic-manual-segmentation-and-mask-extraction/17131)

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**Author:** [@Marco\_Catinozzi](https://discourse.slicer.org/u/Marco_Catinozzi)\
**Replies:** 0\
**Last updated:** [April 16, 2021, 1:26pm UTC](https://discourse.slicer.org/t/prostatic-manual-segmentation-and-mask-extraction/17131 "2021-04-16T13:26:20Z")

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Operating system: macOS Big Sur 11.2.3 Slicer version: 4.11.20200930 Hallo folks! Need your help! I am working with a prostatic MRI data set, my boss is suggesting to extract a binary mask and to manually segment the…

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## [Export Hounsfield Unit values from segmentation](https://discourse.slicer.org/t/export-hounsfield-unit-values-from-segmentation/17127)

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**Author:** [@Dave](https://discourse.slicer.org/u/Dave)\
**Replies:** 1\
**Last updated:** [April 16, 2021, 1:00pm UTC](https://discourse.slicer.org/t/export-hounsfield-unit-values-from-segmentation/17127 "2021-04-16T13:00:52Z")

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Hi everyone, Is it possible to extract/export the whole set of Hounsfield Unit values from a segmentation performed via threshold tool? I want to use them for statistical purposes. Thanks in advance, Best, Dave.

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## [AMD zen3 CPU Support](https://discourse.slicer.org/t/amd-zen3-cpu-support/17120)

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**Author:** [@zyy](https://discourse.slicer.org/u/zyy)\
**Replies:** 1\
**Last updated:** [April 16, 2021, 8:21am UTC](https://discourse.slicer.org/t/amd-zen3-cpu-support/17120 "2021-04-16T08:21:32Z")

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I use amd zen3 cpu to do segement test,the film is CTChest. It takes a long time to render the image or cut the image,about 30s,too slow,another laptop only use 7s,(Intel 9750h,16GB,RTX 2060) And I has been set VTK GP…

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## [3Dslicer Difussion Tractogoraphy](https://discourse.slicer.org/t/3dslicer-difussion-tractogoraphy/17029)

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**Author:** [@xinnosige](https://discourse.slicer.org/u/xinnosige)\
**Replies:** 2\
**Last updated:** [April 16, 2021, 6:43am UTC](https://discourse.slicer.org/t/3dslicer-difussion-tractogoraphy/17029 "2021-04-16T06:43:04Z")

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At present, I have a batch of DSI data, and the scanning data of each subject is divided into AP and PA directions. I have fitted the data of each subject in two directions through FSL, and finally obtained the files of …

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## [Creating a basic Paint Foreground and Paint Background Tool](https://discourse.slicer.org/t/creating-a-basic-paint-foreground-and-paint-background-tool/17050)

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**Author:** [@masadcv](https://discourse.slicer.org/u/masadcv)\
**Replies:** 7\
**Last updated:** [April 16, 2021, 3:54am UTC](https://discourse.slicer.org/t/creating-a-basic-paint-foreground-and-paint-background-tool/17050 "2021-04-16T03:54:07Z")

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Hi, I am new to 3D Slicer. I am trying to implement an interactive segmentation tool for correcting issues in existing segmentation labels. The expected behaviour of this tool is to have “background” and “foreground” p…

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## [In Pivot Callbration, how to convert a transform file to a Python script file?](https://discourse.slicer.org/t/in-pivot-callbration-how-to-convert-a-transform-file-to-a-python-script-file/17119)

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**Author:** [@WangZhen1175701153](https://discourse.slicer.org/u/WangZhen1175701153)\
**Replies:** 0\
**Last updated:** [April 16, 2021, 2:28am UTC](https://discourse.slicer.org/t/in-pivot-callbration-how-to-convert-a-transform-file-to-a-python-script-file/17119 "2021-04-16T02:28:29Z")

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For example, Stylustoreference.h5 is the file generated by the Pivot Calibration example. Can I convert this file to the Python script file?

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## [Resample Scalar Volume](https://discourse.slicer.org/t/resample-scalar-volume/17097)

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**Author:** [@Yasuhiro\_TAKEDA](https://discourse.slicer.org/u/Yasuhiro_TAKEDA)\
**Replies:** 2\
**Last updated:** [April 16, 2021, 2:00am UTC](https://discourse.slicer.org/t/resample-scalar-volume/17097 "2021-04-16T02:00:22Z")

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Hi I often use “Resample Scalar Volume”, and think it is very useful because “Resample Image” seems not to be able to set Spacing, but “Resample Scalar Volume” can. Why was Resample Scalar Volume put into Legacy? Does…

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## [Neighborhood Size in median filter](https://discourse.slicer.org/t/neighborhood-size-in-median-filter/17110)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 1\
**Last updated:** [April 15, 2021, 9:45pm UTC](https://discourse.slicer.org/t/neighborhood-size-in-median-filter/17110 "2021-04-15T21:45:08Z")

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Hi: The Neighborhood Size in the Median Filter parameters section is in voxels or mm? Sincerely, Gonzalo Rojas Costa

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## [Update model appearance based on real-time parameter change](https://discourse.slicer.org/t/update-model-appearance-based-on-real-time-parameter-change/17102)

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**Author:** [@szhang](https://discourse.slicer.org/u/szhang)\
**Replies:** 3\
**Last updated:** [April 15, 2021, 4:21pm UTC](https://discourse.slicer.org/t/update-model-appearance-based-on-real-time-parameter-change/17102 "2021-04-15T16:21:01Z")

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Hello, in order to have appearance changes (e.g. color, transparency etc) on a model, in accordance to parameter changes in real-time, do I have to create a new vtkMRMLDynamicModelerNode which copies the model I meant to…

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## [MRI image quality getting worse after registration](https://discourse.slicer.org/t/mri-image-quality-getting-worse-after-registration/17104)

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**Author:** [@peter\_adidharma](https://discourse.slicer.org/u/peter_adidharma)\
**Replies:** 1\
**Last updated:** [April 15, 2021, 2:01pm UTC](https://discourse.slicer.org/t/mri-image-quality-getting-worse-after-registration/17104 "2021-04-15T14:01:15Z")

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Hello everyone, I was having as issue where everytime a registration was performed, the image quality of the MRI seems to get worse. Is there any way to avoid such condition? Many thanks, Peter

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## [Save segmentation directly to STL or OBJ files](https://discourse.slicer.org/t/save-segmentation-directly-to-stl-or-obj-files/2428)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 7\
**Last updated:** [April 15, 2021, 12:33pm UTC](https://discourse.slicer.org/t/save-segmentation-directly-to-stl-or-obj-files/2428 "2021-04-15T12:33:09Z")

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We often received questions about how to export segmentation to STL file for 3D printing. We’ve added a simplified, dedicated tool to make this step easier. 1-minute demo video: Main features: Export ST…

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## [Segmenting skull base, cranial nerves & posterior circulation](https://discourse.slicer.org/t/segmenting-skull-base-cranial-nerves-posterior-circulation/16736)

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**Author:** [@peter\_adidharma](https://discourse.slicer.org/u/peter_adidharma)\
**Replies:** 5\
**Last updated:** [April 15, 2021, 1:20am UTC](https://discourse.slicer.org/t/segmenting-skull-base-cranial-nerves-posterior-circulation/16736 "2021-04-15T01:20:53Z")

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Hello everyone, I am planning to segment skull base from CT, and cranial nerves with posterior circulation arteries from MRI. Is there any way to fuse segmentation results from these two modalities (CT & MRI) so that th…

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## [Osteotomy Planner](https://discourse.slicer.org/t/osteotomy-planner/17084)

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**Author:** [@Marta\_Fernandez](https://discourse.slicer.org/u/Marta_Fernandez)\
**Replies:** 1\
**Last updated:** [April 14, 2021, 8:29pm UTC](https://discourse.slicer.org/t/osteotomy-planner/17084 "2021-04-14T20:29:39Z")

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The osteotomy tool is not working. I install it but the tool doesn´t appear. Someone can help me to install it properly or see the problem

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## [MeshLab and Slicer problem when Importing 3D Volume](https://discourse.slicer.org/t/meshlab-and-slicer-problem-when-importing-3d-volume/17093)

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**Author:** [@will\_kim](https://discourse.slicer.org/u/will_kim)\
**Replies:** 3\
**Last updated:** [April 14, 2021, 4:58pm UTC](https://discourse.slicer.org/t/meshlab-and-slicer-problem-when-importing-3d-volume/17093 "2021-04-14T16:58:08Z")

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Hi, when I import the same file on Slicer and MeshLab the STL volumes are either inverted or rotated differently. Firstly, I do not understand why this only occurs for few STL files I have and what I could do to fix it, …

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## [Elastix registration toolbox is now available in Slicer](https://discourse.slicer.org/t/elastix-registration-toolbox-is-now-available-in-slicer/165)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 6\
**Last updated:** [April 14, 2021, 4:26pm UTC](https://discourse.slicer.org/t/elastix-registration-toolbox-is-now-available-in-slicer/165 "2021-04-14T16:26:23Z")

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Elastix is a very powerful registration toolbox with lots of advantages over stock ITK registration tools - it has many more metrics, transformation methods, constraints, optimizers, and it comes with a large registratio…

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## [How to load script in HelloPython tutorial?](https://discourse.slicer.org/t/how-to-load-script-in-hellopython-tutorial/17072)

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**Author:** [@spycolyf](https://discourse.slicer.org/u/spycolyf)\
**Replies:** 5\
**Last updated:** [April 14, 2021, 3:40am UTC](https://discourse.slicer.org/t/how-to-load-script-in-hellopython-tutorial/17072 "2021-04-14T03:40:52Z")

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@lassoan @pieper, The HelloPython tutorial say to load HelloPython.py. Do I load it into Python Interactor? Or do I use a text editor? Which tool shall I use to make changes to the python code on a Windows system? Shall…

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## [I've got a vtk error when debug the project of Slicer](https://discourse.slicer.org/t/ive-got-a-vtk-error-when-debug-the-project-of-slicer/17017)

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**Author:** [@qin](https://discourse.slicer.org/u/qin)\
**Replies:** 4\
**Last updated:** [April 14, 2021, 3:03pm UTC](https://discourse.slicer.org/t/ive-got-a-vtk-error-when-debug-the-project-of-slicer/17017 "2021-04-14T15:03:00Z")

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Operating system:win10 x64 Slicer version:4.11 Expected behavior: Actual behavior:

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## [Add directories to PATH env when launching SlicerCAT](https://discourse.slicer.org/t/add-directories-to-path-env-when-launching-slicercat/16849)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 2\
**Last updated:** [April 14, 2021, 12:12pm UTC](https://discourse.slicer.org/t/add-directories-to-path-env-when-launching-slicercat/16849 "2021-04-14T12:12:33Z")

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Hi, My custom app have .dll dependency. To launch app I need to set PATH env to these .dll (on windows). Where can I see how this is done in slicer?

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## [Ignore nodes when placing fiducial?](https://discourse.slicer.org/t/ignore-nodes-when-placing-fiducial/17014)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 2\
**Last updated:** [April 14, 2021, 11:04am UTC](https://discourse.slicer.org/t/ignore-nodes-when-placing-fiducial/17014 "2021-04-14T11:04:48Z")

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Normally when you interactively place a fiducial in the 3D view, the cursor/placement fiducial jumps to the intersection point closest to the camera of whatever is visible. For example, let’s say I have a body with a ske…

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## [Segment visibility toggle 4.10 vs 4.11](https://discourse.slicer.org/t/segment-visibility-toggle-4-10-vs-4-11/16982)

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**Author:** [@ottensmeyer](https://discourse.slicer.org/u/ottensmeyer)\
**Replies:** 2\
**Last updated:** [April 14, 2021, 10:30am UTC](https://discourse.slicer.org/t/segment-visibility-toggle-4-10-vs-4-11/16982 "2021-04-14T10:30:56Z")

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Hello, Just installed 4.11.20210226, up from 4.10.2, running on Win10 Pro v20H2, build 19042.867 In the Segment Editor, in 4.10.2, when one segment is selected, one can toggle visibility (change open/closed eye icon st…

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## [4D volume import-modification-export](https://discourse.slicer.org/t/4d-volume-import-modification-export/16909)

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**Author:** [@Kalman](https://discourse.slicer.org/u/Kalman)\
**Replies:** 2\
**Last updated:** [April 14, 2021, 6:43am UTC](https://discourse.slicer.org/t/4d-volume-import-modification-export/16909 "2021-04-14T06:43:09Z")

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Hi, I’m interested in whether there is a possibility to import and modify 4D fMRI nifti files in the Slicer? A bit more explanation about the question: we are working with multivolume datasets, where one file contains s…

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## [Tips for semi-automatic segmentation of fetal brain MRI](https://discourse.slicer.org/t/tips-for-semi-automatic-segmentation-of-fetal-brain-mri/17020)

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**Author:** [@GMA](https://discourse.slicer.org/u/GMA)\
**Replies:** 1\
**Last updated:** [April 14, 2021, 5:20am UTC](https://discourse.slicer.org/t/tips-for-semi-automatic-segmentation-of-fetal-brain-mri/17020 "2021-04-14T05:20:30Z")

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Hello to all. I’m trying to segment fetal MRI brains acquired with multiplanar T2-HASTE sequences (see an example below taken from Radiopaedia). I’m currently having a harsh time with manual segmentation which is re…

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## [Display texture in 3D PLY models](https://discourse.slicer.org/t/display-texture-in-3d-ply-models/17039)

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**Author:** [@laiasevi](https://discourse.slicer.org/u/laiasevi)\
**Replies:** 1\
**Last updated:** [April 14, 2021, 5:17am UTC](https://discourse.slicer.org/t/display-texture-in-3d-ply-models/17039 "2021-04-14T05:17:19Z")

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I use photogrammetry to make 3D models. I have tried to export the meshes in PLY format, either exporting texture (JPEG file) or exporting the mesh with vertex colors. In other platforms (Meshlab) the colors/texture of t…

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