# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=371

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

**Page:** 372

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## [Python debugger not working with pycharm64](https://discourse.slicer.org/t/python-debugger-not-working-with-pycharm64/8395)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 3\
**Last updated:** [September 12, 2019, 9:15pm UTC](https://discourse.slicer.org/t/python-debugger-not-working-with-pycharm64/8395 "2019-09-12T21:15:47Z")

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I’ve installed a new version of PyCharm, and tried to set up Python debugger in Slicer. But I got the error message below. I tried to find the missing registry entry, but noticed that I don’t have a pycharm.exe file, onl…

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## [Resampling Segmentation and Volume about a User-Defined Axis For Plotting](https://discourse.slicer.org/t/resampling-segmentation-and-volume-about-a-user-defined-axis-for-plotting/8392)

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**Author:** [@abniesen](https://discourse.slicer.org/u/abniesen)\
**Replies:** 3\
**Last updated:** [September 12, 2019, 7:19pm UTC](https://discourse.slicer.org/t/resampling-segmentation-and-volume-about-a-user-defined-axis-for-plotting/8392 "2019-09-12T19:19:06Z")

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Hi, I have segmented a CT scan of the proximal femur as shown below. I am looking to plot the cross-sectional area of this segmentation along the axis of the femoral neck using SliceAreaPlot.py ((Example module that …

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## [How to tell Slicer to save by default in whatever folder it is called from](https://discourse.slicer.org/t/how-to-tell-slicer-to-save-by-default-in-whatever-folder-it-is-called-from/8383)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [September 12, 2019, 6:30pm UTC](https://discourse.slicer.org/t/how-to-tell-slicer-to-save-by-default-in-whatever-folder-it-is-called-from/8383 "2019-09-12T18:30:45Z")

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I use Slicer on Linux a lot, and I usually invoke it from the terminal window and typically from the folder where the dataset I am going to work on is present. I would like to have the default save behavior to be in the …

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## [Filling up MRI missing voxels in cortical region](https://discourse.slicer.org/t/filling-up-mri-missing-voxels-in-cortical-region/8408)

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**Author:** [@banikr](https://discourse.slicer.org/u/banikr)\
**Replies:** 1\
**Last updated:** [September 12, 2019, 5:39pm UTC](https://discourse.slicer.org/t/filling-up-mri-missing-voxels-in-cortical-region/8408 "2019-09-12T17:39:04Z")

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Hello, I am using some MRI data that were used in Deep Brain Stimulation study. Now due to electrodes there are gaps in cortical section/skull in the images. Now for my purpose I would like to fill those missing skull se…

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## ["Cannot write data file... Do you want to continue Saving?"](https://discourse.slicer.org/t/cannot-write-data-file-do-you-want-to-continue-saving/8378)

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**Author:** [@NoahwithFish](https://discourse.slicer.org/u/NoahwithFish)\
**Replies:** 8\
**Last updated:** [September 12, 2019, 3:47pm UTC](https://discourse.slicer.org/t/cannot-write-data-file-do-you-want-to-continue-saving/8378 "2019-09-12T15:47:59Z")

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Hi All, I am having some issues saving my work in Slicer 4.10.2. After uploading a tiff stack, I adjust the image spacing in the Volume module according to the CT scanner settings, and then immediately try to save it as…

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## [How to import DICOM images and corresponding RT structure set for radiomic analysis](https://discourse.slicer.org/t/how-to-import-dicom-images-and-corresponding-rt-structure-set-for-radiomic-analysis/8391)

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**Author:** [@valebetx3ds](https://discourse.slicer.org/u/valebetx3ds)\
**Replies:** 1\
**Last updated:** [September 12, 2019, 1:13pm UTC](https://discourse.slicer.org/t/how-to-import-dicom-images-and-corresponding-rt-structure-set-for-radiomic-analysis/8391 "2019-09-12T13:13:05Z")

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Operating system: Windows and Linux Slicer version:4.10.2 Expected behavior: Actual behavior: On PET, CT or MRI images we manually draw, using in house and commercial software (e.g. PMOD) , VOIs on specific targets o…

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## [Unable to open segment editor without slicer closing](https://discourse.slicer.org/t/unable-to-open-segment-editor-without-slicer-closing/7755)

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**Author:** [@Andrew\_Kanawati](https://discourse.slicer.org/u/Andrew_Kanawati)\
**Replies:** 8\
**Last updated:** [September 12, 2019, 1:44am UTC](https://discourse.slicer.org/t/unable-to-open-segment-editor-without-slicer-closing/7755 "2019-09-12T01:44:36Z")

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Problem report for Slicer 4.10.2 win-amd64: Slicer keeps closing when I try to edit segment editor. \[DEBUG\]\[Qt\] 25.07.2019 10:17:00 \[\] (unknown:0) - Session start time …: 2019-07-25 10:17:00 \[DEBUG\]\[Qt\] 25.07.2019 10:…

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## [Is it possible to change a CBCT to 2D X-ray image?](https://discourse.slicer.org/t/is-it-possible-to-change-a-cbct-to-2d-x-ray-image/7617)

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**Author:** [@Jmarcs](https://discourse.slicer.org/u/Jmarcs)\
**Replies:** 6\
**Last updated:** [September 12, 2019, 12:46am UTC](https://discourse.slicer.org/t/is-it-possible-to-change-a-cbct-to-2d-x-ray-image/7617 "2019-09-12T00:46:28Z")

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Is it possible to change a cbct to a 2d Radiography sagital for orthodontics Thanks

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## [Slicer latest version not supporting install of modules](https://discourse.slicer.org/t/slicer-latest-version-not-supporting-install-of-modules/8393)

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**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 2\
**Last updated:** [September 12, 2019, 12:25am UTC](https://discourse.slicer.org/t/slicer-latest-version-not-supporting-install-of-modules/8393 "2019-09-12T00:25:58Z")

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Operating system:Windows 10 64 b Hi All, I just downloaded the recently preview version of slicer 4.11.0 but it’s not allowing to re-install extension. Pls see the attached picture. Thanks, Sarv

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## [Surface opacity jump](https://discourse.slicer.org/t/surface-opacity-jump/8384)

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**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 1\
**Last updated:** [September 11, 2019, 7:16pm UTC](https://discourse.slicer.org/t/surface-opacity-jump/8384 "2019-09-11T19:16:18Z")

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When changing the opacity of a surface, the first step from fully opaque to ‘just a little transparent’ (i.e. from 1.00 to 0.99) causes a relatively big visual difference, whereas the change from 0.99 to 0.98 causes no v…

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## [Non-rigid registration of meshes](https://discourse.slicer.org/t/non-rigid-registration-of-meshes/2247)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 12\
**Last updated:** [September 11, 2019, 1:09pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-meshes/2247 "2019-09-11T13:09:58Z")

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Hi, I was wondering if it is possible to perform non-rigid registrations of meshes between each other in slicer, or potentially in SPHARM-PDM? I know that SPHARM has Procrustes but I am looking for a deformation field to…

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## [SPHARM-PDM Shape Analysis Module Failing](https://discourse.slicer.org/t/spharm-pdm-shape-analysis-module-failing/8209)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 4\
**Last updated:** [September 11, 2019, 5:49am UTC](https://discourse.slicer.org/t/spharm-pdm-shape-analysis-module-failing/8209 "2019-09-11T05:49:14Z")

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Hi, I am having some major issues getting SPHARM-PDM’s Shape Analysis Module to work. I have tried it on the newest nightly build from today, and a nightly build from 2018. When I input a folder containing mandible VTK f…

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## [Single point placement for vtkMRMLMarkupsLineNode?](https://discourse.slicer.org/t/single-point-placement-for-vtkmrmlmarkupslinenode/8379)

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**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 1\
**Last updated:** [September 11, 2019, 4:12am UTC](https://discourse.slicer.org/t/single-point-placement-for-vtkmrmlmarkupslinenode/8379 "2019-09-11T04:12:55Z")

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Hello, I am wondering if it is possible to place one fiducial point at a time when using MarkupsLineNode. I would like the user to place one point, without having to place the second point to complete the line. I’d lik…

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## [What " Toggle selectable" can do?](https://discourse.slicer.org/t/what-toggle-selectable-can-do/8358)

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**Author:** [@mikecsu](https://discourse.slicer.org/u/mikecsu)\
**Replies:** 2\
**Last updated:** [September 11, 2019, 1:59am UTC](https://discourse.slicer.org/t/what-toggle-selectable-can-do/8358 "2019-09-11T01:59:37Z")

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Operating system:win10 Slicer version:slicer 4.10.1 Expected behavior: Actual behavior: Hi ,everyone . Can anyone tell me what this " Toggle selectable" can do ? I tried both ticking it or not ticking it, but it …

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## [qSlicerMarkupsPlaceWidget().deleteButton signal/slot?](https://discourse.slicer.org/t/qslicermarkupsplacewidget-deletebutton-signal-slot/8313)

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**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 2\
**Last updated:** [September 11, 2019, 1:58am UTC](https://discourse.slicer.org/t/qslicermarkupsplacewidget-deletebutton-signal-slot/8313 "2019-09-11T01:58:33Z")

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Hi! I am using slicer.qSlicerMarkupsPlaceWidget() in my scripted module. I give the user an option to delete the placed point by making the deleteButton active. I would like to emit a signal when the delete button is pr…

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## [SlicerIGT Extenstion](https://discourse.slicer.org/t/slicerigt-extenstion/8369)

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**Author:** [@burnhamd](https://discourse.slicer.org/u/burnhamd)\
**Replies:** 1\
**Last updated:** [September 10, 2019, 6:51pm UTC](https://discourse.slicer.org/t/slicerigt-extenstion/8369 "2019-09-10T18:51:01Z")

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When I updated to the latest build of slicer from the website build 9/8/19. I cannot find the SlicerIGT in the extensions library.

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## [Can we display oriented bounding boxes?](https://discourse.slicer.org/t/can-we-display-oriented-bounding-boxes/8367)

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**Author:** [@kab](https://discourse.slicer.org/u/kab)\
**Replies:** 1\
**Last updated:** [September 10, 2019, 5:04pm UTC](https://discourse.slicer.org/t/can-we-display-oriented-bounding-boxes/8367 "2019-09-10T17:04:18Z")

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I have several oriented bounding boxes I have generated. Is there a way to plot and/or edit these in Slicer? That is, I have a set of 8 vertices corresponding to an oriented box in the same image space as my volumes. Ca…

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## [DICOM to STL for 3D printing](https://discourse.slicer.org/t/dicom-to-stl-for-3d-printing/8356)

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**Author:** [@Angel\_Javier\_Gonzale](https://discourse.slicer.org/u/Angel_Javier_Gonzale)\
**Replies:** 1\
**Last updated:** [September 10, 2019, 1:00pm UTC](https://discourse.slicer.org/t/dicom-to-stl-for-3d-printing/8356 "2019-09-10T13:00:46Z")

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Operating system: Windows 10 64 bits Slicer version:4.10.2 What is the way to convert a DICOM file from Ultrasound to STL for 3D printing?

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## [Any publications related to colormap 'FreeSurferLabels' and algorithm of 'interpolate' checkbox?](https://discourse.slicer.org/t/any-publications-related-to-colormap-freesurferlabels-and-algorithm-of-interpolate-checkbox/7968)

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**Author:** [@jenaflex](https://discourse.slicer.org/u/jenaflex)\
**Replies:** 5\
**Last updated:** [September 10, 2019, 11:35am UTC](https://discourse.slicer.org/t/any-publications-related-to-colormap-freesurferlabels-and-algorithm-of-interpolate-checkbox/7968 "2019-09-10T11:35:12Z")

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Hi, I was wondering if any suggestion on finding publications related to colormap ‘FreeSurferLabels’? Also I was wondering: what is the algorithm behind the checkbox (and toggle) ‘interpolate’ for displaying image (n…

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## [Where to turn on and off color scale bar](https://discourse.slicer.org/t/where-to-turn-on-and-off-color-scale-bar/8347)

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**Author:** [@jenaflex](https://discourse.slicer.org/u/jenaflex)\
**Replies:** 3\
**Last updated:** [September 9, 2019, 10:19pm UTC](https://discourse.slicer.org/t/where-to-turn-on-and-off-color-scale-bar/8347 "2019-09-09T22:19:31Z")

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Hi, I am using 4.11 20190417. There used to a place to turn on and off color scale bar for foreground and background image. I followed the method in this topic and cannot find it. Thanks!

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## [Subtraction 2 RT Dose with Simple filters module](https://discourse.slicer.org/t/subtraction-2-rt-dose-with-simple-filters-module/8338)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [September 8, 2019, 10:44pm UTC](https://discourse.slicer.org/t/subtraction-2-rt-dose-with-simple-filters-module/8338 "2019-09-08T22:44:16Z")

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Slicer version:4.8.1 Hi 3D Slicer experts and all I have 2 RT Dose whit different Image Dimension and Image origin, which were exported from TPS. I want to subtract them with Subtract image filter in simple filters …

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## [Identifying which slice in DTI stack corresponds to b(not) value](https://discourse.slicer.org/t/identifying-which-slice-in-dti-stack-corresponds-to-b-not-value/8332)

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**Author:** [@mshah](https://discourse.slicer.org/u/mshah)\
**Replies:** 2\
**Last updated:** [September 7, 2019, 8:36pm UTC](https://discourse.slicer.org/t/identifying-which-slice-in-dti-stack-corresponds-to-b-not-value/8332 "2019-09-07T20:36:58Z")

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Hi everyone, I was wondering if there is a specific way in slicer to identify which image in a dti stack corresponds to the non weighted T2 image that corresponds to the b= 0 value? For example, the dimensions of my ima…

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## [Displaying heatmaps as contours](https://discourse.slicer.org/t/displaying-heatmaps-as-contours/8314)

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**Author:** [@ahmedhosny](https://discourse.slicer.org/u/ahmedhosny)\
**Replies:** 4\
**Last updated:** [September 6, 2019, 3:59pm UTC](https://discourse.slicer.org/t/displaying-heatmaps-as-contours/8314 "2019-09-06T15:59:37Z")

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Hello - I have 3 layers visualized in slicer as follows: L: a label map F: a heatmap of continousos values (think of it like an RT dosemap, but I am not using the SlicerRT extension) B: an image Currently, the heatm…

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## [CT image segmentation ankle cartilage](https://discourse.slicer.org/t/ct-image-segmentation-ankle-cartilage/8319)

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**Author:** [@chad](https://discourse.slicer.org/u/chad)\
**Replies:** 1\
**Last updated:** [September 6, 2019, 12:17pm UTC](https://discourse.slicer.org/t/ct-image-segmentation-ankle-cartilage/8319 "2019-09-06T12:17:23Z")

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I only have CT scan file.Can I segmentation cartilage from it? Thank you!

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## [After threshold-based bone segmentation in CT structure filled with holes](https://discourse.slicer.org/t/after-threshold-based-bone-segmentation-in-ct-structure-filled-with-holes/7983)

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**Author:** [@chad](https://discourse.slicer.org/u/chad)\
**Replies:** 6\
**Last updated:** [September 6, 2019, 6:00am UTC](https://discourse.slicer.org/t/after-threshold-based-bone-segmentation-in-ct-structure-filled-with-holes/7983 "2019-09-06T06:00:47Z")

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Hi all, I am segmenting the geometries of flatfoot skeleton from a CT scan using Threshold effect. What is the better way to fill the holes inside the segmented flatfoot skeleton (see picture below)? Thanks!

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## [2D View slice intensity doesn't correspond to python array value（Confusion）](https://discourse.slicer.org/t/2d-view-slice-intensity-doesnt-correspond-to-python-array-value-confusion/8318)

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**Author:** [@mikecsu](https://discourse.slicer.org/u/mikecsu)\
**Replies:** 1\
**Last updated:** [September 6, 2019, 3:42am UTC](https://discourse.slicer.org/t/2d-view-slice-intensity-doesnt-correspond-to-python-array-value-confusion/8318 "2019-09-06T03:42:27Z")

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Operating system:win10 Slicer version:slicer 4.10.0/4.10.1 Expected behavior: Actual behavior: Hi,everyone. I am trying to understand how slicer 2D images present in the form of an array in python. So i did some wo…

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## [RT struct contour interpolation](https://discourse.slicer.org/t/rt-struct-contour-interpolation/8287)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 4\
**Last updated:** [September 6, 2019, 1:07am UTC](https://discourse.slicer.org/t/rt-struct-contour-interpolation/8287 "2019-09-06T01:07:11Z")

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Hi all, What I have: original breast CT (0.703×0.703×5, 512×512×65); corresponding RT struct (planar contour, exist in 4 slices); cropped image (isotropic spacing 1.005, 173×104×111). Want to get: interpolated segment …

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## [Segmentation of muscles](https://discourse.slicer.org/t/segmentation-of-muscles/8315)

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**Author:** [@Nerea\_Lund](https://discourse.slicer.org/u/Nerea_Lund)\
**Replies:** 2\
**Last updated:** [September 5, 2019, 8:28pm UTC](https://discourse.slicer.org/t/segmentation-of-muscles/8315 "2019-09-05T20:28:55Z")

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Operating system: window 10 Slicer version: 4.10.2 Expected behavior: Segment muscles Actual behavior: Hi everyone! I want to check if it is possible to segment “muscles” or can only be segmented bones and organs?

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## [Volume rendering does not show when I click on the eye](https://discourse.slicer.org/t/volume-rendering-does-not-show-when-i-click-on-the-eye/8305)

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**Author:** [@Nerea\_Lund](https://discourse.slicer.org/u/Nerea_Lund)\
**Replies:** 3\
**Last updated:** [September 5, 2019, 8:11pm UTC](https://discourse.slicer.org/t/volume-rendering-does-not-show-when-i-click-on-the-eye/8305 "2019-09-05T20:11:15Z")

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Operating system: Windows 10 Slicer version: 3D slicer 4.10.2 Expected behavior: After loading dicom files, I cannot have a visualization with the rendering volume Actual behavior: Once the images are loaded, When I …

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## [Slicer NRRD support](https://discourse.slicer.org/t/slicer-nrrd-support/8136)

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**Author:** [@Chris\_Rorden](https://discourse.slicer.org/u/Chris_Rorden)\
**Replies:** 24\
**Last updated:** [September 5, 2019, 4:31pm UTC](https://discourse.slicer.org/t/slicer-nrrd-support/8136 "2019-09-05T16:31:56Z")

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I am having trouble loading some NRRD files into slicer. Here is a link to three images: ok.nhdr loads fine, ok2.nii.gz loads fine, bad.nhdr does not load in Slicer 4.10.2 on MacOS. All of these images load fine in MRIcr…

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