# Support **URL:** https://discourse.slicer.org/c/support/11.md?page=430 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 431 --- ## [use slicer in system's python, not in slicers python interpreter](https://discourse.slicer.org/t/use-slicer-in-systems-python-not-in-slicers-python-interpreter/2251)
**Author:** [@b\_s\_umesh\_sherkhane](https://discourse.slicer.org/u/b_s_umesh_sherkhane)\ **Replies:** 1\ **Last updated:** [March 6, 2018, 3:53pm UTC](https://discourse.slicer.org/t/use-slicer-in-systems-python-not-in-slicers-python-interpreter/2251 "2018-03-06T15:53:59Z")
Operating system: windows 64 bit Slicer version: 4.9 Expected behavior: Actual behavior: i am unable to import slicer in system’s python. I am using python 2.7. Please help ? --- ## [Slicer mrml scene not loading](https://discourse.slicer.org/t/slicer-mrml-scene-not-loading/2090)
**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\ **Replies:** 10\ **Last updated:** [March 6, 2018, 2:44pm UTC](https://discourse.slicer.org/t/slicer-mrml-scene-not-loading/2090 "2018-03-06T14:44:08Z")
Operating system: Windows 7 Slicer version: 4.8.1 Expected behavior: Stored studies should load Actual behavior: Nothing loads and screen remains blank Hi, I save a mrml scene with 2x2 view, 1 view containing a PET … --- ## [ROI movement points](https://discourse.slicer.org/t/roi-movement-points/2223)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 5\ **Last updated:** [March 6, 2018, 3:53am UTC](https://discourse.slicer.org/t/roi-movement-points/2223 "2018-03-06T03:53:01Z")
Is there any way that the future Slicer download could have either larger ROI control dots or at least the option for them. It is exceptionally challenging to be able to move them with the current settings when the user … --- ## [Importing models for segmentation to fix](https://discourse.slicer.org/t/importing-models-for-segmentation-to-fix/2229)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 4\ **Last updated:** [March 6, 2018, 3:42am UTC](https://discourse.slicer.org/t/importing-models-for-segmentation-to-fix/2229 "2018-03-06T03:42:04Z")
I have these scalp models that have big gaps on top and a knot (before).I imported as segmentations into the segment editor, and used the scissors to trim the knot. Segment editor automatically stitched the gap at the to… --- ## [GPU Volume rendering not working](https://discourse.slicer.org/t/gpu-volume-rendering-not-working/2246)
**Author:** [@MHB](https://discourse.slicer.org/u/MHB)\ **Replies:** 6\ **Last updated:** [March 6, 2018, 1:38am UTC](https://discourse.slicer.org/t/gpu-volume-rendering-not-working/2246 "2018-03-06T01:38:58Z")
Operating system: win64 Slicer version: 4.8.1 Having trouble volume rendering using the GPU raycasting option? (Dell XPS, intel i7, GTX 1050 GPU). When GPU volume rendering is enabled, it does not display anything, but… --- ## [How can I convert an rtstruct to an nrrd](https://discourse.slicer.org/t/how-can-i-convert-an-rtstruct-to-an-nrrd/539)
**Author:** [@Josiah\_McAllister](https://discourse.slicer.org/u/Josiah_McAllister)\ **Replies:** 8\ **Last updated:** [March 5, 2018, 11:06pm UTC](https://discourse.slicer.org/t/how-can-i-convert-an-rtstruct-to-an-nrrd/539 "2018-03-05T23:06:09Z")
Operating system: Windows Slicer version:4.6.2 Expected behavior: Actual behavior: --- ## [DICOM loading, patcher, general problems. ](https://discourse.slicer.org/t/dicom-loading-patcher-general-problems/1921)
**Author:** [@MSilent](https://discourse.slicer.org/u/MSilent)\ **Replies:** 10\ **Last updated:** [March 5, 2018, 5:20pm UTC](https://discourse.slicer.org/t/dicom-loading-patcher-general-problems/1921 "2018-03-05T17:20:42Z")
I have previously successfully patched DICOM data into slicer. Currently, after deleting and reinstalling the data I can now no longer successfully patch it. It doesn’t write to a DICOM folder, it writes it to a pa000 … --- ## [Controlling Slicer using hand gestures](https://discourse.slicer.org/t/controlling-slicer-using-hand-gestures/2237)
**Author:** [@Ahmed\_Soufane](https://discourse.slicer.org/u/Ahmed_Soufane)\ **Replies:** 4\ **Last updated:** [March 4, 2018, 11:38pm UTC](https://discourse.slicer.org/t/controlling-slicer-using-hand-gestures/2237 "2018-03-04T23:38:26Z")
For the SendMessage command, the handler parameter needs to be connected to the Python interactor process. In order to get c# to send Python code to the 3d slicer, how do you get 3d slicer to act as the process and set u… --- ## [Loading transformation from Matlab .mat file](https://discourse.slicer.org/t/loading-transformation-from-matlab-mat-file/2226)
**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\ **Replies:** 6\ **Last updated:** [March 3, 2018, 11:40pm UTC](https://discourse.slicer.org/t/loading-transformation-from-matlab-mat-file/2226 "2018-03-03T23:40:15Z")
Hi, I tried to load a FSL generated .mat transformation matrix as a transform but the system crashed. The simple goal is to use the .mat matrix to transform vtk objects into a different imaging space; using 3d Slicer, … --- ## [Ndi polaris failed to connect with plus](https://discourse.slicer.org/t/ndi-polaris-failed-to-connect-with-plus/2210)
**Author:** [@emetss](https://discourse.slicer.org/u/emetss)\ **Replies:** 4\ **Last updated:** [March 2, 2018, 8:45pm UTC](https://discourse.slicer.org/t/ndi-polaris-failed-to-connect-with-plus/2210 "2018-03-02T20:45:50Z")
Operating system: windows 10, or ubuntu 16.04 Plus version:2.6 or 2.7 I have an ndi polaris camera. It has a com port and is connected with the pc through com-usb adapter. The pc recognize it. But still cannot connect … --- ## [Panoramic image/view](https://discourse.slicer.org/t/panoramic-image-view/2203)
**Author:** [@bernard](https://discourse.slicer.org/u/bernard)\ **Replies:** 4\ **Last updated:** [March 2, 2018, 12:53pm UTC](https://discourse.slicer.org/t/panoramic-image-view/2203 "2018-03-02T12:53:28Z")
Is it possible to reconstruct a panoramic view as is often used in dentistry and if not, are there any plans to add that capability? Thank you. Operating system: MAC 10.13 (High Sierra) Slicer version: 4.6.2 Expected … --- ## [Tumor segmentation](https://discourse.slicer.org/t/tumor-segmentation/2211)
**Author:** [@nodi](https://discourse.slicer.org/u/nodi)\ **Replies:** 7\ **Last updated:** [March 1, 2018, 11:38pm UTC](https://discourse.slicer.org/t/tumor-segmentation/2211 "2018-03-01T23:38:28Z")
I tried to segment the tumor but when I save it as .nrrd, I got the whole volume with other tissues. I want to save and use JUST the tumor volume. how can I do that? Do I have to use the Editor to segment the tumor or I… --- ## [DWIConvert NIFTI to NRRD issue](https://discourse.slicer.org/t/dwiconvert-nifti-to-nrrd-issue/2201)
**Author:** [@ryanhucla](https://discourse.slicer.org/u/ryanhucla)\ **Replies:** 3\ **Last updated:** [March 1, 2018, 8:00pm UTC](https://discourse.slicer.org/t/dwiconvert-nifti-to-nrrd-issue/2201 "2018-03-01T20:00:16Z")
Hi all, I am using DWIConvert to convert NIFTIs to NRRDs so that I can use DTIPrep’s artifact detection and denoising tools. I then plan to convert these NRRDs back to NIFTI so that I can use FSL’s eddy and then FSL’s T… --- ## [Problem installing extension on windows](https://discourse.slicer.org/t/problem-installing-extension-on-windows/2221)
**Author:** [@Stephen\_Gwilym](https://discourse.slicer.org/u/Stephen_Gwilym)\ **Replies:** 2\ **Last updated:** [March 1, 2018, 3:49pm UTC](https://discourse.slicer.org/t/problem-installing-extension-on-windows/2221 "2018-03-01T15:49:48Z")
Operating system: Windows Slicer version:4.1.1 Expected behavior: download occurs Actual behavior: Error GUI pops up, informing me that " error opening files for writing" C:\\programfiles\\slicer 4.8.1\\slicer.exe If … --- ## [Plot 3d points onto scan and measuring 3d distances](https://discourse.slicer.org/t/plot-3d-points-onto-scan-and-measuring-3d-distances/2215)
**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\ **Replies:** 3\ **Last updated:** [March 1, 2018, 2:31am UTC](https://discourse.slicer.org/t/plot-3d-points-onto-scan-and-measuring-3d-distances/2215 "2018-03-01T02:31:14Z")
Hi, I’d like to plot a series of 3d contact points onto a diffusion-weighted image (DWI); these points are in the same coordinate system as the DWI and are stored as an Excel file. Is there a module that can be used to… --- ## [Python command line execution of Slicer functions](https://discourse.slicer.org/t/python-command-line-execution-of-slicer-functions/2213)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 1\ **Last updated:** [February 28, 2018, 11:29pm UTC](https://discourse.slicer.org/t/python-command-line-execution-of-slicer-functions/2213 "2018-02-28T23:29:41Z")
I am trying to use slicer to take in a batch of meshes and discretize those meshes into labelmaps for pyradiomics analysis. To do this I am working with using an anaconda command line and python to access each file, then… --- ## [How to read and process a '.seg' or '.seg.vtm' files in a CLI 3DSlicer module](https://discourse.slicer.org/t/how-to-read-and-process-a-seg-or-seg-vtm-files-in-a-cli-3dslicer-module/2190)
**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\ **Replies:** 9\ **Last updated:** [February 28, 2018, 6:05pm UTC](https://discourse.slicer.org/t/how-to-read-and-process-a-seg-or-seg-vtm-files-in-a-cli-3dslicer-module/2190 "2018-02-28T18:05:42Z")
Hello Friends!!! i need to load and process image files generated for a RT planning. Among those files, there is this ‘.seg’ or ‘.seg.vtm’ files which I would like to read and treat like a label map. Can anyone here g… --- ## [calculating distance map and getting text file](https://discourse.slicer.org/t/calculating-distance-map-and-getting-text-file/2157)
**Author:** [@nodi](https://discourse.slicer.org/u/nodi)\ **Replies:** 11\ **Last updated:** [February 28, 2018, 5:23pm UTC](https://discourse.slicer.org/t/calculating-distance-map-and-getting-text-file/2157 "2018-02-28T17:23:39Z")
hello. I’m new to Slicer. I want to use this filter: ApproximateSignedDistanceMapImageFilter. to calculate the distance of each point to the boundary after doing segmentation. How can I get the distance map as a text f… --- ## [Batch processing with SPHARM-PDM](https://discourse.slicer.org/t/batch-processing-with-spharm-pdm/2119)
**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\ **Replies:** 4\ **Last updated:** [February 28, 2018, 4:28pm UTC](https://discourse.slicer.org/t/batch-processing-with-spharm-pdm/2119 "2018-02-28T16:28:31Z")
Hi, I am very new to coding in Python, so hopefully there might be an easy, straightforward tutorial, or possibly a way to circumvent the use of python coding altogether, but is there anything like this on how to perform… --- ## [No slice viewers with nightly on Linux](https://discourse.slicer.org/t/no-slice-viewers-with-nightly-on-linux/2204)
**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\ **Replies:** 0\ **Last updated:** [February 28, 2018, 3:50am UTC](https://discourse.slicer.org/t/no-slice-viewers-with-nightly-on-linux/2204 "2018-02-28T03:50:04Z")
I’ve just tried running nightly on Ubuntu Linux (within Parallels on Mac), and all slice viewers are blank. In the log, I see the following messages: SystemError: /home/kitware/Dashboards/Nightly/Slicer-0-build/Python-… --- ## [Clip volume in Segment editor](https://discourse.slicer.org/t/clip-volume-in-segment-editor/1558)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 9\ **Last updated:** [February 27, 2018, 8:59am UTC](https://discourse.slicer.org/t/clip-volume-in-segment-editor/1558 "2018-02-27T08:59:25Z")
Hi, Is there a way to clip (but not segment) the 3D rendering of a segment in segment editor? I want to use scissors to crop cervical vertebrae in skull CTs, and at some point I need a view of them looking through the … --- ## [How to send python code from an external application?](https://discourse.slicer.org/t/how-to-send-python-code-from-an-external-application/2161)
**Author:** [@Ahmed\_Soufane](https://discourse.slicer.org/u/Ahmed_Soufane)\ **Replies:** 3\ **Last updated:** [February 25, 2018, 11:19pm UTC](https://discourse.slicer.org/t/how-to-send-python-code-from-an-external-application/2161 "2018-02-25T23:19:31Z")
Hi, I was wondering how to send python code from an external application ? --- ## [Slicer Debugging](https://discourse.slicer.org/t/slicer-debugging/2169)
**Author:** [@AhmadHossam10](https://discourse.slicer.org/u/AhmadHossam10)\ **Replies:** 1\ **Last updated:** [February 25, 2018, 9:26pm UTC](https://discourse.slicer.org/t/slicer-debugging/2169 "2018-02-25T21:26:23Z")
How can I debug Slicer line by line ? which IDE that is preferred to be used ? --- ## [2D segmentation](https://discourse.slicer.org/t/2d-segmentation/2171)
**Author:** [@jruiz](https://discourse.slicer.org/u/jruiz)\ **Replies:** 2\ **Last updated:** [February 25, 2018, 9:08pm UTC](https://discourse.slicer.org/t/2d-segmentation/2171 "2018-02-25T21:08:07Z")
Hi, I’ve tried to use the Segment Editor on 2D images. I’m aware it’s designed for 3D volumes, but, anyway, sometimes we have to deal with 2D images and I’m just wondering whether it’s a suitable tool for it. It seems t… --- ## [No load loadable modules of an extension after they have been installed from slicer extension catalog (Compiled Slicer 4.8.1 )](https://discourse.slicer.org/t/no-load-loadable-modules-of-an-extension-after-they-have-been-installed-from-slicer-extension-catalog-compiled-slicer-4-8-1/2165)
**Author:** [@carlos-luque](https://discourse.slicer.org/u/carlos-luque)\ **Replies:** 4\ **Last updated:** [February 25, 2018, 10:41am UTC](https://discourse.slicer.org/t/no-load-loadable-modules-of-an-extension-after-they-have-been-installed-from-slicer-extension-catalog-compiled-slicer-4-8-1/2165 "2018-02-25T10:41:27Z")
Operating system: Windows 10 64 bits Slicer version: 4.8.1 (svn r26813) Compiler: Microsoft Visual Studio Community 2015 Qt: 5.9.1 I’ve compiled the Slicer version 4.8.1 (svn 26813) without any errors and Slicer appl… --- ## [Performance degradation with large number of fiducials](https://discourse.slicer.org/t/performance-degradation-with-large-number-of-fiducials/2162)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 1\ **Last updated:** [February 23, 2018, 10:47pm UTC](https://discourse.slicer.org/t/performance-degradation-with-large-number-of-fiducials/2162 "2018-02-23T22:47:19Z")
I loaded a dataset with ~2K fiducials. Operating system: Linux (Centos 7) Slicer version: 4.8.1 Expected behavior: Actual behavior: Overall slow operations (zoom in/out in slices, 3d rotation etc). Settings in markup… --- ## [Endoscopy - camera not moving along path?](https://discourse.slicer.org/t/endoscopy-camera-not-moving-along-path/2146)
**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\ **Replies:** 9\ **Last updated:** [February 23, 2018, 9:02pm UTC](https://discourse.slicer.org/t/endoscopy-camera-not-moving-along-path/2146 "2018-02-23T21:02:20Z")
OK, I’m pretty sure this is pilot error, but I’ve tried to do a fly through on a couple of datasets and I’m not sure what I’m doing wrong. To make a fly though, I am: Load example dataset (CTACardio) Volume render Pick… --- ## [Generate a voxel-based mesh](https://discourse.slicer.org/t/generate-a-voxel-based-mesh/2159)
**Author:** [@Guido\_Buezas](https://discourse.slicer.org/u/Guido_Buezas)\ **Replies:** 1\ **Last updated:** [February 23, 2018, 5:34pm UTC](https://discourse.slicer.org/t/generate-a-voxel-based-mesh/2159 "2018-02-23T17:34:53Z")
Hi everyone Is there a way to generate a 3D mesh to use it in FEA analysis using the voxel-based method? I didn’t found the way. It’s simpler than using STL surfaces though less precise, but is for training purposes. T… --- ## [UKF\_tractography\_vtkExtractSelectedPolyData error](https://discourse.slicer.org/t/ukf-tractography-vtkextractselectedpolydata-error/2124)
**Author:** [@ssousa](https://discourse.slicer.org/u/ssousa)\ **Replies:** 4\ **Last updated:** [February 23, 2018, 3:13pm UTC](https://discourse.slicer.org/t/ukf-tractography-vtkextractselectedpolydata-error/2124 "2018-02-23T15:13:24Z")
When running UKF tractography the following error popup: ERROR: import port 0 of algorithm vtkExtractSelectedPolyDatalds (0x88e0fa0) has 0 connections but is not optional Can you help me on this? Thank you in advan… --- ## [Trouble opening .bin files](https://discourse.slicer.org/t/trouble-opening-bin-files/2150)
**Author:** [@aturner](https://discourse.slicer.org/u/aturner)\ **Replies:** 3\ **Last updated:** [February 23, 2018, 12:58pm UTC](https://discourse.slicer.org/t/trouble-opening-bin-files/2150 "2018-02-23T12:58:30Z")
Hi, I have a number of bin files from a micro ct scan which i am having trouble opening in 3d slicer, does anyone know how i can open them, as following the procedure for dicom files is not working? thanks alex [Previous page](https://discourse.slicer.org/c/support/11.md?page=429) [Next page](https://discourse.slicer.org/c/support/11.md?page=431)