# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=296

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

**Page:** 297

---

## [3D colored model to segmentations](https://discourse.slicer.org/t/3d-colored-model-to-segmentations/16139)

<div class="topic-metadata">

**Author:** [@inesdfelix](https://discourse.slicer.org/u/inesdfelix)\
**Replies:** 0\
**Last updated:** [February 22, 2021, 6:34pm UTC](https://discourse.slicer.org/t/3d-colored-model-to-segmentations/16139 "2021-02-22T18:34:46Z")

</div>

I have a 3D model with regions of interest (ROIs) identified with different vertex/face colors. I can see the colored model in Slicer by enabling “Visible” in the Scalars section in Models module. Screenshot bellow for r…

---

## [Extension for planning of orthopedic surgeries?](https://discourse.slicer.org/t/extension-for-planning-of-orthopedic-surgeries/16086)

<div class="topic-metadata">

**Author:** [@MCMF](https://discourse.slicer.org/u/MCMF)\
**Replies:** 5\
**Last updated:** [February 22, 2021, 1:25pm UTC](https://discourse.slicer.org/t/extension-for-planning-of-orthopedic-surgeries/16086 "2021-02-22T13:25:38Z")

</div>

Hello I may start to develop an extension for planning of orthopedic surgeries of the lower extremities. Focus will be on the hip an knee joint. One important feature will be the definition of bone coordinate systems b…

---

## [Remove markup lines on adjacent slices](https://discourse.slicer.org/t/remove-markup-lines-on-adjacent-slices/16136)

<div class="topic-metadata">

**Author:** [@kmalexander](https://discourse.slicer.org/u/kmalexander)\
**Replies:** 6\
**Last updated:** [February 22, 2021, 5:10pm UTC](https://discourse.slicer.org/t/remove-markup-lines-on-adjacent-slices/16136 "2021-02-22T17:10:14Z")

</div>

I’m drawing straight lines across a CT image (using the ruler markup tool). When scrolling between adjacent slices, the line still appears on slices adjacent (either blue or red). Is there any way to have the markup li…

---

## [Transforming a volume makes it disappear from views](https://discourse.slicer.org/t/transforming-a-volume-makes-it-disappear-from-views/16133)

<div class="topic-metadata">

**Author:** [@kanikayad15](https://discourse.slicer.org/u/kanikayad15)\
**Replies:** 3\
**Last updated:** [February 22, 2021, 5:02pm UTC](https://discourse.slicer.org/t/transforming-a-volume-makes-it-disappear-from-views/16133 "2021-02-22T17:02:30Z")

</div>

Currently trying to register two tiff files. Loaded them both in and set them at 50% opacity. Then I went into the transform module and tried rotating/moving one of the images, but when I move certain settings one of the…

---

## [My images don't appear in the General Registration Module (BRAINS)](https://discourse.slicer.org/t/my-images-dont-appear-in-the-general-registration-module-brains/16138)

<div class="topic-metadata">

**Author:** [@kanikayad15](https://discourse.slicer.org/u/kanikayad15)\
**Replies:** 1\
**Last updated:** [February 22, 2021, 4:50pm UTC](https://discourse.slicer.org/t/my-images-dont-appear-in-the-general-registration-module-brains/16138 "2021-02-22T16:50:43Z")

</div>

Title pretty much explains it all. But I am uploading two tiff files to register and was hoping to utilize the general registration module. When I go to choose fixed and moving image volumes, the options for my loaded fi…

---

## [Is there a way to segment heart valves from a CTA scan using 3D Slicer](https://discourse.slicer.org/t/is-there-a-way-to-segment-heart-valves-from-a-cta-scan-using-3d-slicer/16121)

<div class="topic-metadata">

**Author:** [@dayanjan](https://discourse.slicer.org/u/dayanjan)\
**Replies:** 4\
**Last updated:** [February 22, 2021, 1:39pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-segment-heart-valves-from-a-cta-scan-using-3d-slicer/16121 "2021-02-22T13:39:40Z")

</div>

Hello All, I’ve been tying to figure out a way to do this. Basically, I have a pretty high resolution CTA scan. I want to be able to segment out the heart valves. The only challenge is none of the 3 planes allow me to s…

---

## [toggle between segments ](https://discourse.slicer.org/t/toggle-between-segments/16124)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [February 21, 2021, 10:34pm UTC](https://discourse.slicer.org/t/toggle-between-segments/16124 "2021-02-21T22:34:17Z")

</div>

i wish there is a way I can toggle between segments selection instead of choosing from menu. i go back and from making segments and i wish i can do that faster thank you

---

## [The size of the segmentation image (DICOM-SEG) does not match the size of the main image (DICOM)](https://discourse.slicer.org/t/the-size-of-the-segmentation-image-dicom-seg-does-not-match-the-size-of-the-main-image-dicom/16114)

<div class="topic-metadata">

**Author:** [@cnhwl](https://discourse.slicer.org/u/cnhwl)\
**Replies:** 4\
**Last updated:** [February 21, 2021, 1:45pm UTC](https://discourse.slicer.org/t/the-size-of-the-segmentation-image-dicom-seg-does-not-match-the-size-of-the-main-image-dicom/16114 "2021-02-21T13:45:45Z")

</div>

hello everyone! As shown in the figure, I downloaded the LIDC-IDRC dataset (https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI#1966254f633413761b746ff9e49dd8f0d5b679d) and the corresponding annotation data (h…

---

## [The size of the segmentation image (DICOM-SEG) does not match the size of the main image (DICOM)](https://discourse.slicer.org/t/the-size-of-the-segmentation-image-dicom-seg-does-not-match-the-size-of-the-main-image-dicom/16115)

<div class="topic-metadata">

**Author:** [@cnhwl](https://discourse.slicer.org/u/cnhwl)\
**Replies:** 0\
**Last updated:** [February 21, 2021, 5:41am UTC](https://discourse.slicer.org/t/the-size-of-the-segmentation-image-dicom-seg-does-not-match-the-size-of-the-main-image-dicom/16115 "2021-02-21T05:41:14Z")

</div>

Operating system: win 10 Slicer version: Slicer 4.11 Hi Everyone, As shown in the figure, I downloaded the LIDC-IDRC dataset and standardized representation of the TCIA LIDC-IDRI annotations using from TICA , and the…

---

## [Query on exporting annotation](https://discourse.slicer.org/t/query-on-exporting-annotation/16032)

<div class="topic-metadata">

**Author:** [@Akash](https://discourse.slicer.org/u/Akash)\
**Replies:** 6\
**Last updated:** [February 20, 2021, 6:14am UTC](https://discourse.slicer.org/t/query-on-exporting-annotation/16032 "2021-02-20T06:14:36Z")

</div>

Operating system: Windows10 Slicer version:4.11.20200930 Expected behavior: NA Actual behavior:NA I would like to export the annotation co ordinates in a JSON/CSV/XML format containing the filename, label and co ordi…

---

## [Is it possible to enable interaction points for a specific control point with a Marksup node?](https://discourse.slicer.org/t/is-it-possible-to-enable-interaction-points-for-a-specific-control-point-with-a-marksup-node/16096)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [February 19, 2021, 10:44pm UTC](https://discourse.slicer.org/t/is-it-possible-to-enable-interaction-points-for-a-specific-control-point-with-a-marksup-node/16096 "2021-02-19T22:44:38Z")

</div>

As it is, interaction handles applies to all the control points within a node. Would be possible to enable for single points for better control over axis of movement in 3D viewer? (i.e., without exporting that point temp…

---

## [Hollow from inside surface but keep outlet open](https://discourse.slicer.org/t/hollow-from-inside-surface-but-keep-outlet-open/16095)

<div class="topic-metadata">

**Author:** [@szhang](https://discourse.slicer.org/u/szhang)\
**Replies:** 3\
**Last updated:** [February 20, 2021, 4:27am UTC](https://discourse.slicer.org/t/hollow-from-inside-surface-but-keep-outlet-open/16095 "2021-02-20T04:27:19Z")

</div>

Hello I have a inner model segment, which can be used as inside surface under “Segment Editor”-\>“Hollow”, but how can I keep these outlet still open rather than enclosed?

---

## [How to change the ball](https://discourse.slicer.org/t/how-to-change-the-ball/14740)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 2\
**Last updated:** [November 24, 2020, 6:39pm UTC](https://discourse.slicer.org/t/how-to-change-the-ball/14740 "2020-11-24T18:39:41Z")

</div>

I made a solid ball, then showed it in the" model "as a model, and showed the inside through plane cutting, and found that the whole ball became a hollow with very thin edges. How to get a solid ball, and the inside …

---

## [Cut a part of segmentation](https://discourse.slicer.org/t/cut-a-part-of-segmentation/16099)

<div class="topic-metadata">

**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 2\
**Last updated:** [February 19, 2021, 9:45pm UTC](https://discourse.slicer.org/t/cut-a-part-of-segmentation/16099 "2021-02-19T21:45:29Z")

</div>

Hello all, How can I cut a part of my segmentation that is inside a specific ROI?

---

## [High Slicer CPU usage while live streaming](https://discourse.slicer.org/t/high-slicer-cpu-usage-while-live-streaming/6078)

<div class="topic-metadata">

**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 12\
**Last updated:** [February 19, 2021, 3:50pm UTC](https://discourse.slicer.org/t/high-slicer-cpu-usage-while-live-streaming/6078 "2021-02-19T15:50:22Z")

</div>

I’ve been seeing high CPU usage by the Slicer process when viewing live stream images from PLUS. I’m not sure if the issue is the rendering changes between Slicer 4.8 and 4.10 or an issue with OpenIGTLinkIF. Environment…

---

## [Drawing circle in the 3D slicer](https://discourse.slicer.org/t/drawing-circle-in-the-3d-slicer/16082)

<div class="topic-metadata">

**Author:** [@ensieh](https://discourse.slicer.org/u/ensieh)\
**Replies:** 5\
**Last updated:** [February 19, 2021, 3:32pm UTC](https://discourse.slicer.org/t/drawing-circle-in-the-3d-slicer/16082 "2021-02-19T15:32:17Z")

</div>

Hi, I want to draw a circle in the 3D slicer, how can I draw circles with specific R? I suppose to draw circle in the MRI image of the Tibial of the knee in order to measure the tibial slope, would you please help me ho…

---

## [Change default delimiter for csv files](https://discourse.slicer.org/t/change-default-delimiter-for-csv-files/16087)

<div class="topic-metadata">

**Author:** [@elledriver](https://discourse.slicer.org/u/elledriver)\
**Replies:** 4\
**Last updated:** [February 19, 2021, 3:17pm UTC](https://discourse.slicer.org/t/change-default-delimiter-for-csv-files/16087 "2021-02-19T15:17:05Z")

</div>

Hello there, I want to use 3DSlicer to plot data from csv files that use semicolons as delimiter. However, it seems that this is not possible. I cannot use a comma as a delimiter for certain reasons. Is there really no…

---

## [FUSE PET and CT images](https://discourse.slicer.org/t/fuse-pet-and-ct-images/16081)

<div class="topic-metadata">

**Author:** [@Kalpa](https://discourse.slicer.org/u/Kalpa)\
**Replies:** 1\
**Last updated:** [February 19, 2021, 1:39pm UTC](https://discourse.slicer.org/t/fuse-pet-and-ct-images/16081 "2021-02-19T13:39:48Z")

</div>

Operating system: Windows 10 pro Slicer version:4.13.0-2021-01-11 r29598 / c1d3ac1 Expected behavior: Actual behavior:

---

## [Correctly reconstructed surface mesh from the DICOM-seg format](https://discourse.slicer.org/t/correctly-reconstructed-surface-mesh-from-the-dicom-seg-format/16075)

<div class="topic-metadata">

**Author:** [@hwkim0325](https://discourse.slicer.org/u/hwkim0325)\
**Replies:** 1\
**Last updated:** [February 19, 2021, 1:10pm UTC](https://discourse.slicer.org/t/correctly-reconstructed-surface-mesh-from-the-dicom-seg-format/16075 "2021-02-19T13:10:26Z")

</div>

Hello!, I am trying to use brain segmentations in the Finite Element Method. So far, I could develop codes successfully to convert contours of DICOM-RT structure set to surface mesh by myself. Now, I’m trying to use Di…

---

## [DICOM viewer - non-volumetric images](https://discourse.slicer.org/t/dicom-viewer-non-volumetric-images/16068)

<div class="topic-metadata">

**Author:** [@Shai](https://discourse.slicer.org/u/Shai)\
**Replies:** 4\
**Last updated:** [February 19, 2021, 8:08am UTC](https://discourse.slicer.org/t/dicom-viewer-non-volumetric-images/16068 "2021-02-19T08:08:04Z")

</div>

Operating system:Win 10 Slicer version:4.11.20200930 Hi, I want to upload non-volumetric DICOM images to the viewer for ROI marking. When I upload the images , Slicer by default upload them as volumetric. How can I upl…

---

## [Changing a segmented mask datatype from int16 to uint8](https://discourse.slicer.org/t/changing-a-segmented-mask-datatype-from-int16-to-uint8/16049)

<div class="topic-metadata">

**Author:** [@Abdulrahman](https://discourse.slicer.org/u/Abdulrahman)\
**Replies:** 3\
**Last updated:** [February 19, 2021, 4:30am UTC](https://discourse.slicer.org/t/changing-a-segmented-mask-datatype-from-int16-to-uint8/16049 "2021-02-19T04:30:16Z")

</div>

Hi, I’ve exporting a segmented mask of brain in nifti format, which is int16, for CNN segmentation using Matlab, however, pixel Label Datastore only supports pixel label image files with uint8 data. Is there anyway to …

---

## [NIFTI Problem with Reformatted Segmentations](https://discourse.slicer.org/t/nifti-problem-with-reformatted-segmentations/16035)

<div class="topic-metadata">

**Author:** [@e25](https://discourse.slicer.org/u/e25)\
**Replies:** 5\
**Last updated:** [February 18, 2021, 11:56pm UTC](https://discourse.slicer.org/t/nifti-problem-with-reformatted-segmentations/16035 "2021-02-18T23:56:41Z")

</div>

I am reformatting segmentations, and I am able to save them without issue as an NRRD fiel. However, when I attempt to save them as a NIFTI file (the utilized form for our research group) and reload the file, they are a f…

---

## [Please add last modified date for extensions](https://discourse.slicer.org/t/please-add-last-modified-date-for-extensions/16052)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [February 18, 2021, 6:24pm UTC](https://discourse.slicer.org/t/please-add-last-modified-date-for-extensions/16052 "2021-02-18T18:24:48Z")

</div>

While it is good that revision is listed, without an actual date it is not straightforward to tell when was that revision (one needs to go to the extension source repository and cross reference). It will be good to add …

---

## [3d reconstruction of implants in ct image](https://discourse.slicer.org/t/3d-reconstruction-of-implants-in-ct-image/16062)

<div class="topic-metadata">

**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 1\
**Last updated:** [February 18, 2021, 5:09pm UTC](https://discourse.slicer.org/t/3d-reconstruction-of-implants-in-ct-image/16062 "2021-02-18T17:09:55Z")

</div>

Hi all, I have an issue of reconstructing implants in CT image. The ultimate goal is to form a 3d convex hull which could encompass all the clips. My solution would be 1) reconstruct these clips, 2) choose some surface…

---

## [Why per-frame transforms stored in .seq.mhd files are not converted from LPS to RAS?](https://discourse.slicer.org/t/why-per-frame-transforms-stored-in-seq-mhd-files-are-not-converted-from-lps-to-ras/16045)

<div class="topic-metadata">

**Author:** [@nathanbmnt](https://discourse.slicer.org/u/nathanbmnt)\
**Replies:** 3\
**Last updated:** [February 18, 2021, 1:12pm UTC](https://discourse.slicer.org/t/why-per-frame-transforms-stored-in-seq-mhd-files-are-not-converted-from-lps-to-ras/16045 "2021-02-18T13:12:43Z")

</div>

When I load a .seq.mhd file, the IJKtoRAS matrix is unity: I would expect the IJKtoRAS matrix to have -1 and -1 as the first two diagonal values from the top, because .mhd volumes are always in LPS coordinates. This i…

---

## [VMTK centrelines - stl format in ascii mode](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16060)

<div class="topic-metadata">

**Author:** [@Dhaya](https://discourse.slicer.org/u/Dhaya)\
**Replies:** 0\
**Last updated:** [February 18, 2021, 12:11pm UTC](https://discourse.slicer.org/t/vmtk-centrelines-stl-format-in-ascii-mode/16060 "2021-02-18T12:11:05Z")

</div>

I want to create a centerline for my patient specific geometry. I have successfully created in .vtp format using VMTK sotware. code: vmtksurfacereader -ifile “E:/geometry/v3\_shortIliacExtendIMACAP\_V2\_vtmk.stl” --pipe v…

---

## [How to convert freesurfer results to DICOM-SEG or DICOM-RT?](https://discourse.slicer.org/t/how-to-convert-freesurfer-results-to-dicom-seg-or-dicom-rt/16026)

<div class="topic-metadata">

**Author:** [@hwkim0325](https://discourse.slicer.org/u/hwkim0325)\
**Replies:** 1\
**Last updated:** [February 17, 2021, 12:26pm UTC](https://discourse.slicer.org/t/how-to-convert-freesurfer-results-to-dicom-seg-or-dicom-rt/16026 "2021-02-17T12:26:44Z")

</div>

I would like to export the result (.mgz) of freesurfer to dicom-seg or dicom-RT. What I’ve done so far is (A) open mgz in the segmentation editor module, export it as the nifti format. But, all the segmentation labels …

---

## [Export DICOM to filesystem fails on UTF-8 characters](https://discourse.slicer.org/t/export-dicom-to-filesystem-fails-on-utf-8-characters/16030)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 5\
**Last updated:** [February 18, 2021, 9:39am UTC](https://discourse.slicer.org/t/export-dicom-to-filesystem-fails-on-utf-8-characters/16030 "2021-02-18T09:39:50Z")

</div>

Hi, My environment’s locale is fr\_FR.UTF-8, which does not always plays well with Slicer, rarely though. While exporting DICOM series that have accented characters to filesystem, it fails on non-ascii characters as suc…

---

## [GeneraeOverlayImages in CIP not working](https://discourse.slicer.org/t/generaeoverlayimages-in-cip-not-working/16044)

<div class="topic-metadata">

**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 1\
**Last updated:** [February 17, 2021, 11:39pm UTC](https://discourse.slicer.org/t/generaeoverlayimages-in-cip-not-working/16044 "2021-02-17T23:39:23Z")

</div>

Operating system: Windows Slicer version:4.11 Expected behavior: Actual behavior: I’m trying to use Generate Overlay Images cip script in my ubuntu terminal using the CLI command-line tools. Can anyone tell me how to…

---

## [Obtain Roi list of voxel with position and value](https://discourse.slicer.org/t/obtain-roi-list-of-voxel-with-position-and-value/16041)

<div class="topic-metadata">

**Author:** [@GMA](https://discourse.slicer.org/u/GMA)\
**Replies:** 2\
**Last updated:** [February 17, 2021, 8:01pm UTC](https://discourse.slicer.org/t/obtain-roi-list-of-voxel-with-position-and-value/16041 "2021-02-17T20:01:56Z")

</div>

Hello to all, I’d like to know if it is possible to obtain the list of voxel within a segmentation in osirix and the corrispective value. I’d like to have a list of each value of every voxel in a roi. Is there any imple…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=295)

[Next page](https://discourse.slicer.org/c/support/11.md?page=297)