# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=78

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

**Page:** 79

---

## [Model ocular structure](https://discourse.slicer.org/t/model-ocular-structure/37981)

<div class="topic-metadata">

**Author:** [@David-Acurio](https://discourse.slicer.org/u/David-Acurio)\
**Replies:** 0\
**Last updated:** [August 21, 2024, 4:56pm UTC](https://discourse.slicer.org/t/model-ocular-structure/37981 "2024-08-21T16:56:12Z")

</div>

Hi, I am a biomedical student and I am doing an ocular study. I need information on how to segment ocular structure and where to find DICOM and MRI files. Can someone help me find this information? I would be very gratef…

---

## [Dental segmentator problem](https://discourse.slicer.org/t/dental-segmentator-problem/37982)

<div class="topic-metadata">

**Author:** [@DPDL](https://discourse.slicer.org/u/DPDL)\
**Replies:** 0\
**Last updated:** [August 21, 2024, 4:56pm UTC](https://discourse.slicer.org/t/dental-segmentator-problem/37982 "2024-08-21T16:56:42Z")

</div>

I tried the AI dental segmentator but it doesnt give any output. Dont know what I am doing wrong. Is there anyone who can assist me? BR Marc

---

## [Some SlicerRT tutorial links not working](https://discourse.slicer.org/t/some-slicerrt-tutorial-links-not-working/37979)

<div class="topic-metadata">

**Author:** [@achiravu](https://discourse.slicer.org/u/achiravu)\
**Replies:** 1\
**Last updated:** [August 21, 2024, 3:35pm UTC](https://discourse.slicer.org/t/some-slicerrt-tutorial-links-not-working/37979 "2024-08-21T15:35:45Z")

</div>

I am very new to 3D Slicer and want to learn a little more about Slicer RT. I have been trying to work through this tutorial: SlicerRtDoc/tutorials/SlicerRT\_Tutorial\_IGRT\_4.11.pptx at master · SlicerRt/SlicerRtDoc · GitH…

---

## [What are the required files for a 3d slicer](https://discourse.slicer.org/t/what-are-the-required-files-for-a-3d-slicer/37970)

<div class="topic-metadata">

**Author:** [@sleighmaster](https://discourse.slicer.org/u/sleighmaster)\
**Replies:** 0\
**Last updated:** [August 21, 2024, 12:31am UTC](https://discourse.slicer.org/t/what-are-the-required-files-for-a-3d-slicer/37970 "2024-08-21T00:31:55Z")

</div>

I want to import 3d slicer into Unreal project and use it. What are the essential files for using the functions of the 3d slicer? Or does anyone know how to do it?

---

## [PyTorch for TotalSegmentator](https://discourse.slicer.org/t/pytorch-for-totalsegmentator/37961)

<div class="topic-metadata">

**Author:** [@Shadi\_Tashakori](https://discourse.slicer.org/u/Shadi_Tashakori)\
**Replies:** 0\
**Last updated:** [August 20, 2024, 2:51pm UTC](https://discourse.slicer.org/t/pytorch-for-totalsegmentator/37961 "2024-08-20T14:51:33Z")

</div>

Hi Im trying to use totalSegmentator on my MRI images and I have installed the extension and also PyTorch extension, but I keep getting this error and IDK what is the problem. can anybody help me? raise RuntimeError(“…

---

## [How to implement CPR (curved planar reconstruction) from centerline?](https://discourse.slicer.org/t/how-to-implement-cpr-curved-planar-reconstruction-from-centerline/9456)

<div class="topic-metadata">

**Author:** [@RayCui](https://discourse.slicer.org/u/RayCui)\
**Replies:** 22\
**Last updated:** [August 20, 2024, 10:09am UTC](https://discourse.slicer.org/t/how-to-implement-cpr-curved-planar-reconstruction-from-centerline/9456 "2024-08-20T10:09:53Z")

</div>

I want to show the vessel in planar. Now I have a .csv file of centerline, that contains points of the veseel. How to reconstruction the vessel plannar from centerline file? How to import the csv file as a list of some…

---

## [Openslide-python not working when trying to use monailabel](https://discourse.slicer.org/t/openslide-python-not-working-when-trying-to-use-monailabel/33427)

<div class="topic-metadata">

**Author:** [@Vineet\_Saravanan](https://discourse.slicer.org/u/Vineet_Saravanan)\
**Replies:** 6\
**Last updated:** [August 20, 2024, 3:42am UTC](https://discourse.slicer.org/t/openslide-python-not-working-when-trying-to-use-monailabel/33427 "2024-08-20T03:42:31Z")

</div>

When I try to install monailabel with the command ‘pip install -U monailabel’, I get this issue: I pip installed openslide-python before, but I am still having an issue. I also tried installing it with a GitHub clone…

---

## [How to compare 2 time point volumes (STL) with color map](https://discourse.slicer.org/t/how-to-compare-2-time-point-volumes-stl-with-color-map/37951)

<div class="topic-metadata">

**Author:** [@Lamont](https://discourse.slicer.org/u/Lamont)\
**Replies:** 0\
**Last updated:** [August 20, 2024, 2:30am UTC](https://discourse.slicer.org/t/how-to-compare-2-time-point-volumes-stl-with-color-map/37951 "2024-08-20T02:30:53Z")

</div>

Hello. I studied compare 2 time volumes (with surface) I have dicom CBCT files. and I segmented mandible and export as STL format. I want to use color map on comparing 2 time point change. May be it’s too basic to as…

---

## [How can I draw normal vectors of a centerline in the 3D slicer?](https://discourse.slicer.org/t/how-can-i-draw-normal-vectors-of-a-centerline-in-the-3d-slicer/37933)

<div class="topic-metadata">

**Author:** [@mssm](https://discourse.slicer.org/u/mssm)\
**Replies:** 6\
**Last updated:** [August 19, 2024, 11:00pm UTC](https://discourse.slicer.org/t/how-can-i-draw-normal-vectors-of-a-centerline-in-the-3d-slicer/37933 "2024-08-19T23:00:54Z")

</div>

Dear respected experts, Please teach me how to draw normal vectors in the 3D slicer. I want to draw the normal vectors of the centerline of blood vessels obtained by VMTK’s “Extract centerline” module to visualize the …

---

## [Implement the mask adjustment function based on threshold in mimics in slicer](https://discourse.slicer.org/t/implement-the-mask-adjustment-function-based-on-threshold-in-mimics-in-slicer/37912)

<div class="topic-metadata">

**Author:** [@dream520nb](https://discourse.slicer.org/u/dream520nb)\
**Replies:** 4\
**Last updated:** [August 19, 2024, 8:00am UTC](https://discourse.slicer.org/t/implement-the-mask-adjustment-function-based-on-threshold-in-mimics-in-slicer/37912 "2024-08-19T08:00:28Z")

</div>

Operating system:Windows 10 Slicer version:4.11 Desired effect: The mask function in mimics is adjusted according to the threshold. In mimics, when stl is converted to mask, the edge pixels are automatically adju…

---

## [Subtraction of intersect area](https://discourse.slicer.org/t/subtraction-of-intersect-area/37923)

<div class="topic-metadata">

**Author:** [@khajta](https://discourse.slicer.org/u/khajta)\
**Replies:** 2\
**Last updated:** [August 19, 2024, 3:18am UTC](https://discourse.slicer.org/t/subtraction-of-intersect-area/37923 "2024-08-19T03:18:31Z")

</div>

Dear Experts, I have 2 segment dataset, organ and lesion. Some of these lesions are overlap or in the organ, such as liver. How can I erase organ area which overlap with tumor area (other than manual editing)? Sincerel…

---

## [Calling slicer module from a python file](https://discourse.slicer.org/t/calling-slicer-module-from-a-python-file/12720)

<div class="topic-metadata">

**Author:** [@Anand\_Mulay](https://discourse.slicer.org/u/Anand_Mulay)\
**Replies:** 7\
**Last updated:** [July 24, 2020, 9:36pm UTC](https://discourse.slicer.org/t/calling-slicer-module-from-a-python-file/12720 "2020-07-24T21:36:52Z")

</div>

i know we can call the slicer module with command line arguments or calling from a batch file, can i write a python file to call slicer with same same command?

---

## [Seeking Advice on Creating a 3D Mask with Colored Cell Annotations for Stardist 3D Training](https://discourse.slicer.org/t/seeking-advice-on-creating-a-3d-mask-with-colored-cell-annotations-for-stardist-3d-training/37911)

<div class="topic-metadata">

**Author:** [@mturin](https://discourse.slicer.org/u/mturin)\
**Replies:** 0\
**Last updated:** [August 16, 2024, 7:34am UTC](https://discourse.slicer.org/t/seeking-advice-on-creating-a-3d-mask-with-colored-cell-annotations-for-stardist-3d-training/37911 "2024-08-16T07:34:29Z")

</div>

Hello, I’m currently working on preparing a 3D mask from a volumetric dataset to train a Stardist 3D model. As part of this process, I need to annotate different cells within the volume, each with a unique color. Could…

---

## [Loading Robot into Slicer](https://discourse.slicer.org/t/loading-robot-into-slicer/36798)

<div class="topic-metadata">

**Author:** [@Jeff\_Boker](https://discourse.slicer.org/u/Jeff_Boker)\
**Replies:** 10\
**Last updated:** [August 15, 2024, 4:32pm UTC](https://discourse.slicer.org/t/loading-robot-into-slicer/36798 "2024-08-15T16:32:18Z")

</div>

I am trying to figure out how I load the Franka Robot into Slicer because I want to be able to send joint commands to it via OpenIGTLink and see it move in Slicer. It seems like I need to use Slicer\_ROS2, but I was wonde…

---

## [Reconstructing a 3D volume from 2D slices](https://discourse.slicer.org/t/reconstructing-a-3d-volume-from-2d-slices/37846)

<div class="topic-metadata">

**Author:** [@Trung\_L\_i\_Quang](https://discourse.slicer.org/u/Trung_L_i_Quang)\
**Replies:** 11\
**Last updated:** [August 15, 2024, 3:49pm UTC](https://discourse.slicer.org/t/reconstructing-a-3d-volume-from-2d-slices/37846 "2024-08-15T15:49:11Z")

</div>

Dear community, I am a newbie to 3D Slicer and I’m hoping to get some advice! I have a dataset consisting of 1700 2D image slices (60GB total) originally in 16-bit TIFF format. I converted these to 8-bit JPEGs (400MB t…

---

## [Calculation between two scalar volumes](https://discourse.slicer.org/t/calculation-between-two-scalar-volumes/36520)

<div class="topic-metadata">

**Author:** [@mssm](https://discourse.slicer.org/u/mssm)\
**Replies:** 3\
**Last updated:** [August 14, 2024, 4:39pm UTC](https://discourse.slicer.org/t/calculation-between-two-scalar-volumes/36520 "2024-08-14T16:39:43Z")

</div>

Dear respected experts, I have two Dicom volumes (Volume A, Volume B). The positions are exactly same. I would like to create a new volume by performing calculations on each voxel value. Specifically, I would like to…

---

## [Questions about CT Scan Analysis for Muscle and Fat Evaluation Using 3D Slicer](https://discourse.slicer.org/t/questions-about-ct-scan-analysis-for-muscle-and-fat-evaluation-using-3d-slicer/37906)

<div class="topic-metadata">

**Author:** [@marcelovoltani](https://discourse.slicer.org/u/marcelovoltani)\
**Replies:** 1\
**Last updated:** [August 15, 2024, 3:11pm UTC](https://discourse.slicer.org/t/questions-about-ct-scan-analysis-for-muscle-and-fat-evaluation-using-3d-slicer/37906 "2024-08-15T15:11:04Z")

</div>

Hello, I am starting CT scan analyses to evaluate muscle and fat in different slices. I have some questions regarding the data extracted from 3D Slicer and would like some help. When a new segment is added to be analyz…

---

## [Post-treatment of vascular segmentation](https://discourse.slicer.org/t/post-treatment-of-vascular-segmentation/37874)

<div class="topic-metadata">

**Author:** [@dream520nb](https://discourse.slicer.org/u/dream520nb)\
**Replies:** 1\
**Last updated:** [August 15, 2024, 1:53pm UTC](https://discourse.slicer.org/t/post-treatment-of-vascular-segmentation/37874 "2024-08-15T13:53:23Z")

</div>

Dear friends: I used machine learning methods to get a model of blood vessel segmentation, but it is not perfect. I would like to ask you if there is any way to complete the undivided blood vessels. Operating system: w…

---

## [MultivolumeExplorer for 4D NIFTI image](https://discourse.slicer.org/t/multivolumeexplorer-for-4d-nifti-image/37856)

<div class="topic-metadata">

**Author:** [@Aylin](https://discourse.slicer.org/u/Aylin)\
**Replies:** 1\
**Last updated:** [August 15, 2024, 1:44pm UTC](https://discourse.slicer.org/t/multivolumeexplorer-for-4d-nifti-image/37856 "2024-08-15T13:44:18Z")

</div>

Hello, I am trying to open Multivolume data (T2\*) using 3D Slicer. My 4D volume was .nii, and the slicer could not recognize it as 4D volume, so I transferred it to multiple 3D volumes and then uploaded it using the mul…

---

## [New feature: Interactive transformation + adjustable center of rotation](https://discourse.slicer.org/t/new-feature-interactive-transformation-adjustable-center-of-rotation/36974)

<div class="topic-metadata">

**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 18\
**Last updated:** [August 15, 2024, 1:29pm UTC](https://discourse.slicer.org/t/new-feature-interactive-transformation-adjustable-center-of-rotation/36974 "2024-08-15T13:29:59Z")

</div>

Any nodes can now be translated, rotated, or scaled by interactive handles. Editing operations can be constrained to specific axes and center of rotation can be freely chosen. The handles are available both in slice and…

---

## [How to display the OBB of a nrrd file in 3d slicer?](https://discourse.slicer.org/t/how-to-display-the-obb-of-a-nrrd-file-in-3d-slicer/37891)

<div class="topic-metadata">

**Author:** [@hk\_y](https://discourse.slicer.org/u/hk_y)\
**Replies:** 3\
**Last updated:** [August 15, 2024, 1:27pm UTC](https://discourse.slicer.org/t/how-to-display-the-obb-of-a-nrrd-file-in-3d-slicer/37891 "2024-08-15T13:27:15Z")

</div>

Operating system: mac Slicer version: 5.2.1 Expected behavior: I have an NRRD file and I can calculate its OBB and RAS diameter using Segment Statistics, but I want to display its bounding box. How can I do that?

---

## [Get axis-aligned bounding boxes for segments](https://discourse.slicer.org/t/get-axis-aligned-bounding-boxes-for-segments/27795)

<div class="topic-metadata">

**Author:** [@Caetox](https://discourse.slicer.org/u/Caetox)\
**Replies:** 7\
**Last updated:** [August 15, 2024, 1:26pm UTC](https://discourse.slicer.org/t/get-axis-aligned-bounding-boxes-for-segments/27795 "2024-08-15T13:26:34Z")

</div>

I created a segmentation with some segments and want to get an axis-aligned bounding box for each segment. As far as i know, with the segment statistics module we can compute oriented bounding boxes, but i couldn’t find …

---

## [Wrong order of slices when reading enhanced multi-frame MRI containing 3 image stacks](https://discourse.slicer.org/t/wrong-order-of-slices-when-reading-enhanced-multi-frame-mri-containing-3-image-stacks/37606)

<div class="topic-metadata">

**Author:** [@winter](https://discourse.slicer.org/u/winter)\
**Replies:** 16\
**Last updated:** [August 15, 2024, 12:48pm UTC](https://discourse.slicer.org/t/wrong-order-of-slices-when-reading-enhanced-multi-frame-mri-containing-3-image-stacks/37606 "2024-08-15T12:48:00Z")

</div>

Operating system: Windows Slicer version: 5.6.2. When loading slice packages (respiratory gated T2) to 3D Slicer, the slices get represented in a wrong order. When I open the DICOM file in ImageJ, the representation of…

---

## [How can I adjust window level of background volume?](https://discourse.slicer.org/t/how-can-i-adjust-window-level-of-background-volume/37880)

<div class="topic-metadata">

**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 4\
**Last updated:** [August 15, 2024, 12:38pm UTC](https://discourse.slicer.org/t/how-can-i-adjust-window-level-of-background-volume/37880 "2024-08-15T12:38:21Z")

</div>

When foreground volume and background volume are both set up and foreground opacity is not zero, only foreground volume’s window level can be changed when interaction node switched to AdjustWindowLevel mode. How can I …

---

## [Wich is the best version of 3D Slicer for Macbook Pro M1 (2021)](https://discourse.slicer.org/t/wich-is-the-best-version-of-3d-slicer-for-macbook-pro-m1-2021/37897)

<div class="topic-metadata">

**Author:** [@Borja](https://discourse.slicer.org/u/Borja)\
**Replies:** 1\
**Last updated:** [August 15, 2024, 5:47am UTC](https://discourse.slicer.org/t/wich-is-the-best-version-of-3d-slicer-for-macbook-pro-m1-2021/37897 "2024-08-15T05:47:09Z")

</div>

I have the Macbook Pro M1 and when I install 3D Slicer doesn’t open! What can I do? What’s the best version for my computer?

---

## [How to import STL as RAS coordinate system?](https://discourse.slicer.org/t/how-to-import-stl-as-ras-coordinate-system/37864)

<div class="topic-metadata">

**Author:** [@calvinsuzuki](https://discourse.slicer.org/u/calvinsuzuki)\
**Replies:** 2\
**Last updated:** [August 15, 2024, 1:52am UTC](https://discourse.slicer.org/t/how-to-import-stl-as-ras-coordinate-system/37864 "2024-08-15T01:52:04Z")

</div>

When I export a CT as STL and then re-import, the X and Y end up inverted. This issue is fixed when I select the coordinate system as RAS: But I’m looking to import this STL using a script. I want to prevent the use…

---

## [Registration of 4D Volume](https://discourse.slicer.org/t/registration-of-4d-volume/37854)

<div class="topic-metadata">

**Author:** [@Aylin](https://discourse.slicer.org/u/Aylin)\
**Replies:** 1\
**Last updated:** [August 14, 2024, 2:51pm UTC](https://discourse.slicer.org/t/registration-of-4d-volume/37854 "2024-08-14T14:51:55Z")

</div>

How can I register for the 4D volume that I have it is time-consuming to do for each and then recombine the volume again Are there any other possible ways (My volume is T2\* MGE)

---

## [Install error with dentalsegmentator (returned non-zero exit status 1)](https://discourse.slicer.org/t/install-error-with-dentalsegmentator-returned-non-zero-exit-status-1/37879)

<div class="topic-metadata">

**Author:** [@cedar0625](https://discourse.slicer.org/u/cedar0625)\
**Replies:** 0\
**Last updated:** [August 14, 2024, 8:01am UTC](https://discourse.slicer.org/t/install-error-with-dentalsegmentator-returned-non-zero-exit-status-1/37879 "2024-08-14T08:01:29Z")

</div>

I just installed the dentalsegmentator extension in Slicer 5.7.0-2024-08-08. When running the extension for the first time, this error appears. 2024/08/14 09:09:47.207 :: Start nnUNet install with requirements : nnunetv…

---

## [dcm file registration using segmentation as mask (vtk type changing)](https://discourse.slicer.org/t/dcm-file-registration-using-segmentation-as-mask-vtk-type-changing/37877)

<div class="topic-metadata">

**Author:** [@Lamont](https://discourse.slicer.org/u/Lamont)\
**Replies:** 0\
**Last updated:** [August 14, 2024, 7:54am UTC](https://discourse.slicer.org/t/dcm-file-registration-using-segmentation-as-mask-vtk-type-changing/37877 "2024-08-14T07:54:21Z")

</div>

Hello. I am doing a study comparing the changes in the two time points of 2 dcm files. A specific bone (from dcm file) was segmented and saved as a ‘stl’ file. After that, in order to compare the changes in the two …

---

## [Error when opening slicer - many instances trying to run](https://discourse.slicer.org/t/error-when-opening-slicer-many-instances-trying-to-run/8538)

<div class="topic-metadata">

**Author:** [@Georgian\_Ciobotaru](https://discourse.slicer.org/u/Georgian_Ciobotaru)\
**Replies:** 6\
**Last updated:** [August 14, 2024, 4:21am UTC](https://discourse.slicer.org/t/error-when-opening-slicer-many-instances-trying-to-run/8538 "2024-08-14T04:21:37Z")

</div>

Hello everyone, I’m using 4.10.2 version, but in the last 2 days it became unusable: it tries to open, there are many instances appearing to open, but it goes like this for as long as my patience goes. Did you happen to…

[Previous page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=77)

[Next page](https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=79)