# \#coordinates

**URL:** https://discourse.slicer.org/tag/coordinates/52.md

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

---

## [Aligning local coordinate system with RAS](https://discourse.slicer.org/t/aligning-local-coordinate-system-with-ras/43230)

<div class="topic-metadata">

**Author:** [@mariammtch](https://discourse.slicer.org/u/mariammtch)\
**Replies:** 1\
**Last updated:** [June 5, 2025, 2:29pm UTC](https://discourse.slicer.org/t/aligning-local-coordinate-system-with-ras/43230 "2025-06-05T14:29:58Z")

</div>

Hello everyone. I have several CT scans which are all positioned differently. It is not important to align them with each other but it is very important for me that I use the local coordinate system for the measurements.…

---

## [export coordinates of segmented plane .txt](https://discourse.slicer.org/t/export-coordinates-of-segmented-plane-txt/42358)

<div class="topic-metadata">

**Author:** [@Gabby](https://discourse.slicer.org/u/Gabby)\
**Replies:** 0\
**Last updated:** [March 29, 2025, 4:15am UTC](https://discourse.slicer.org/t/export-coordinates-of-segmented-plane-txt/42358 "2025-03-29T04:15:32Z")

</div>

Hi, I am very new to 3D Slicer. Someone told me that 3D Slicer can export the coordinates of a segmented plane. Can you please tell me, step by step, how to do that? I want to save the coordinates in a .txt file. Pleas…

---

## [Creating a new coordinate system](https://discourse.slicer.org/t/creating-a-new-coordinate-system/19446)

<div class="topic-metadata">

**Author:** [@matsuba8](https://discourse.slicer.org/u/matsuba8)\
**Replies:** 44\
**Last updated:** [October 26, 2024, 2:56pm UTC](https://discourse.slicer.org/t/creating-a-new-coordinate-system/19446 "2024-10-26T14:56:15Z")

</div>

Hello all, I am trying to create a local coordinate system within the global coordinate system in order to compute the displacement of a bone block between two different scans. The reason why the global coordinate syste…

---

## [Point on 2D CT slice image to RAS coordinate transformation](https://discourse.slicer.org/t/point-on-2d-ct-slice-image-to-ras-coordinate-transformation/35770)

<div class="topic-metadata">

**Author:** [@joanne40226](https://discourse.slicer.org/u/joanne40226)\
**Replies:** 0\
**Last updated:** [April 27, 2024, 12:57pm UTC](https://discourse.slicer.org/t/point-on-2d-ct-slice-image-to-ras-coordinate-transformation/35770 "2024-04-27T12:57:38Z")

</div>

Hi community, I encounter problems when doing point on 2D CT slice image to RAS coordinate. I have screen shot an 2D CT image as shown below. i check some imformation for example the actual size of the image in mm is :…

---

## [3D coordinate of input 3D matrix](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937)

<div class="topic-metadata">

**Author:** [@Cathy123](https://discourse.slicer.org/u/Cathy123)\
**Replies:** 5\
**Last updated:** [March 18, 2024, 7:09pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937 "2024-03-18T19:09:09Z")

</div>

Hi, I have some problems of 3D coordinates and segmentation. what’s the coordinate relationship between 3D slicer and my volume coordinate? When I load my 3D matrix( 512512512 object) in the software, how can i set the…

---

## [Python code controls the display of a certain layer of slices in the view](https://discourse.slicer.org/t/python-code-controls-the-display-of-a-certain-layer-of-slices-in-the-view/34781)

<div class="topic-metadata">

**Author:** [@petit223](https://discourse.slicer.org/u/petit223)\
**Replies:** 0\
**Last updated:** [March 8, 2024, 3:05pm UTC](https://discourse.slicer.org/t/python-code-controls-the-display-of-a-certain-layer-of-slices-in-the-view/34781 "2024-03-08T15:05:01Z")

</div>

In the development of the 3D Slicer plug-in, I want to automatically display the corresponding slice on the Green view based on the serial number of the magnetic resonance image entered by the user (I don’t care about th…

---

## [Create a new coordinate system for an MRI, based on a defined plane](https://discourse.slicer.org/t/create-a-new-coordinate-system-for-an-mri-based-on-a-defined-plane/32694)

<div class="topic-metadata">

**Author:** [@Marina](https://discourse.slicer.org/u/Marina)\
**Replies:** 0\
**Last updated:** [November 9, 2023, 4:38pm UTC](https://discourse.slicer.org/t/create-a-new-coordinate-system-for-an-mri-based-on-a-defined-plane/32694 "2023-11-09T16:38:27Z")

</div>

Hi! I have two MRIs of the lower jaw (“before” and “after” treatment), that I’ve successfully aligned and overlayed with the Registration and Transformation tools. I also added a common Plane on these MRIs. What I need…

---

## [Coordinate Systems and Transformations in 3D Object Manipulation](https://discourse.slicer.org/t/coordinate-systems-and-transformations-in-3d-object-manipulation/29618)

<div class="topic-metadata">

**Author:** [@Dwij\_Mistry](https://discourse.slicer.org/u/Dwij_Mistry)\
**Replies:** 1\
**Last updated:** [May 24, 2023, 5:50pm UTC](https://discourse.slicer.org/t/coordinate-systems-and-transformations-in-3d-object-manipulation/29618 "2023-05-24T17:50:06Z")

</div>

Is there any direct option to translate or rotate an object using local coordinates? By default, the translation and rotation actions in the 3D view operate in global coordinates. The camera’s target always remains in …

---

## [Trying to understand the different coordinate systems](https://discourse.slicer.org/t/trying-to-understand-the-different-coordinate-systems/27332)

<div class="topic-metadata">

**Author:** [@spodamon](https://discourse.slicer.org/u/spodamon)\
**Replies:** 0\
**Last updated:** [January 18, 2023, 7:04pm UTC](https://discourse.slicer.org/t/trying-to-understand-the-different-coordinate-systems/27332 "2023-01-18T19:04:41Z")

</div>

I am trying to make a bounding box based on a segmentation. I initially tried using SimpleITK and their LabelShapeStatisticsImageFilter class and their GetBoundingBox method to get some coordinates. When I tried doing th…

---

## [vtkMRMLCameraNode's coordinate system](https://discourse.slicer.org/t/vtkmrmlcameranodes-coordinate-system/27160)

<div class="topic-metadata">

**Author:** [@dsa934](https://discourse.slicer.org/u/dsa934)\
**Replies:** 1\
**Last updated:** [January 10, 2023, 6:30pm UTC](https://discourse.slicer.org/t/vtkmrmlcameranodes-coordinate-system/27160 "2023-01-10T18:30:23Z")

</div>

Operating system: window 11 Slicer version: 4.13.0 Hi, everyone I want to calculate the z-buffer of an object based on the camera position. As far as I know, the z buffer is calculated based on the camera coordinate …

---

## [qSlicerMarkupsPlaceWidget - Get control point coordinates](https://discourse.slicer.org/t/qslicermarkupsplacewidget-get-control-point-coordinates/26506)

<div class="topic-metadata">

**Author:** [@LuisaDantas](https://discourse.slicer.org/u/LuisaDantas)\
**Replies:** 5\
**Last updated:** [December 7, 2022, 10:20am UTC](https://discourse.slicer.org/t/qslicermarkupsplacewidget-get-control-point-coordinates/26506 "2022-12-07T10:20:15Z")

</div>

Hey! I’m building a module for Slicer and using qSlicerMarkupsPlaceWidget() to let the user place a control point on the image. The ideia is just to get the coordinates of this control point, but I’m not sure how to acc…

---

## [Defining a new coordinate system using markups plane node](https://discourse.slicer.org/t/defining-a-new-coordinate-system-using-markups-plane-node/19726)

<div class="topic-metadata">

**Author:** [@matsuba8](https://discourse.slicer.org/u/matsuba8)\
**Replies:** 6\
**Last updated:** [November 9, 2022, 6:17pm UTC](https://discourse.slicer.org/t/defining-a-new-coordinate-system-using-markups-plane-node/19726 "2022-11-09T18:17:48Z")

</div>

Continuing the discussion from Creating a new coordinate system: Hello all, I would like to continue this discussion on defining a coordinate system using the markups plane node, as suggested by Andras in the forum link…

---

## [Centroid Voxel/Coordinates Intensity Value Measurement - Is it possible?](https://discourse.slicer.org/t/centroid-voxel-coordinates-intensity-value-measurement-is-it-possible/25218)

<div class="topic-metadata">

**Author:** [@dokay1](https://discourse.slicer.org/u/dokay1)\
**Replies:** 1\
**Last updated:** [September 28, 2022, 2:43pm UTC](https://discourse.slicer.org/t/centroid-voxel-coordinates-intensity-value-measurement-is-it-possible/25218 "2022-09-28T14:43:26Z")

</div>

I bumped into an issue I can’t seem to find a solution for. I have a large number (\>400) of segments for each I want to measure the intensity (essentially the anatomical location off an atlas) from the centroid voxel. I …

---

## [Xyz coordinates](https://discourse.slicer.org/t/xyz-coordinates/25246)

<div class="topic-metadata">

**Author:** [@maria\_2000](https://discourse.slicer.org/u/maria_2000)\
**Replies:** 2\
**Last updated:** [September 14, 2022, 1:06pm UTC](https://discourse.slicer.org/t/xyz-coordinates/25246 "2022-09-14T13:06:31Z")

</div>

Hi ! I want to find the xyz coordinates of the centerline I created in the 3d slicer. How can I export coordinates as xyz?

---

## [How to get mouse IJK coordinates?](https://discourse.slicer.org/t/how-to-get-mouse-ijk-coordinates/24968)

<div class="topic-metadata">

**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 3:44am UTC](https://discourse.slicer.org/t/how-to-get-mouse-ijk-coordinates/24968 "2022-08-29T03:44:46Z")

</div>

Hi everyone, I am trying to write my first module using MarkUp PointList. And I would like to use a label in UI to show the real-time mouse position, both RAS and IJK, just like the screenshot below. I found the RAS…

---

## [mrmlScene is not available anymore in slicer module](https://discourse.slicer.org/t/mrmlscene-is-not-available-anymore-in-slicer-module/24811)

<div class="topic-metadata">

**Author:** [@spichardo](https://discourse.slicer.org/u/spichardo)\
**Replies:** 1\
**Last updated:** [August 17, 2022, 5:50pm UTC](https://discourse.slicer.org/t/mrmlscene-is-not-available-anymore-in-slicer-module/24811 "2022-08-17T17:50:22Z")

</div>

Hi, I updated my Slicer installation to 5.0.3 and my scripts stopped working because the attribute mrmlScene is not available in the slice module. I tried to reinstall slicer 5.3.0, install the pre-release 5.10 version,…

---

## [How to use linear transform to convert X,Y Coordinate to RAS coordinates](https://discourse.slicer.org/t/how-to-use-linear-transform-to-convert-x-y-coordinate-to-ras-coordinates/23735)

<div class="topic-metadata">

**Author:** [@minhtan16](https://discourse.slicer.org/u/minhtan16)\
**Replies:** 1\
**Last updated:** [June 7, 2022, 10:43am UTC](https://discourse.slicer.org/t/how-to-use-linear-transform-to-convert-x-y-coordinate-to-ras-coordinates/23735 "2022-06-07T10:43:22Z")

</div>

Hi everyone, I have multiples 2D coordinates (X,Y). These coordinates are all mapped by a linear transform in which I have access. I’m wondering if there’s a way to convert a 2D coordinates using the linear transform ma…

---

## [Coordinate system in brainstorm SCS to coordinate system in 3D Slicer](https://discourse.slicer.org/t/coordinate-system-in-brainstorm-scs-to-coordinate-system-in-3d-slicer/22615)

<div class="topic-metadata">

**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 1\
**Last updated:** [March 21, 2022, 1:54pm UTC](https://discourse.slicer.org/t/coordinate-system-in-brainstorm-scs-to-coordinate-system-in-3d-slicer/22615 "2022-03-21T13:54:40Z")

</div>

Dear Andras, I am running into problem of converting the coordinates from SCS to world coordinate system. I exported the mesh from brain storm and then importing it to 3D slicer. It looks as below. any idea on the tr…

---

## [How to change origin of dicom to 0,0,0 in RAS?](https://discourse.slicer.org/t/how-to-change-origin-of-dicom-to-0-0-0-in-ras/18567)

<div class="topic-metadata">

**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 4\
**Last updated:** [July 9, 2021, 5:51am UTC](https://discourse.slicer.org/t/how-to-change-origin-of-dicom-to-0-0-0-in-ras/18567 "2021-07-09T05:51:25Z")

</div>

Operating system: windows 10 I want to use a set of dicoms as input for image processing using deep learning models and in order for me to feed these images I want them all to have the same orientation. All my dicom fil…

---

## [Setting an MNI origo to a volume](https://discourse.slicer.org/t/setting-an-mni-origo-to-a-volume/16164)

<div class="topic-metadata">

**Author:** [@Kalman](https://discourse.slicer.org/u/Kalman)\
**Replies:** 6\
**Last updated:** [February 27, 2021, 6:12pm UTC](https://discourse.slicer.org/t/setting-an-mni-origo-to-a-volume/16164 "2021-02-27T18:12:43Z")

</div>

I would like to ask whether there is a possibility to set and/or visualize of the MNI-origo of a volume. A bit more detail about the question: I’m working with MRI images of different (mostly dog) brains. Looking at …

---

## [Change reference system](https://discourse.slicer.org/t/change-reference-system/15840)

<div class="topic-metadata">

**Author:** [@lorenzo\_bennati](https://discourse.slicer.org/u/lorenzo_bennati)\
**Replies:** 3\
**Last updated:** [February 4, 2021, 4:23pm UTC](https://discourse.slicer.org/t/change-reference-system/15840 "2021-02-04T16:23:38Z")

</div>

Hi everyone, I have a Dicom image that is represented in Slicer using the Anatomical coordinate system (RAS namely Right, Anterior and Superior). I was wondering if it is possible in Slicer to change the reference syst…

---

## [Coordinate system](https://discourse.slicer.org/t/coordinate-system/15404)

<div class="topic-metadata">

**Author:** [@danila](https://discourse.slicer.org/u/danila)\
**Replies:** 1\
**Last updated:** [January 8, 2021, 4:17pm UTC](https://discourse.slicer.org/t/coordinate-system/15404 "2021-01-08T16:17:12Z")

</div>

Hi, I have an STL file of a virtual surgical planning and I would like to compare it with the 3D model, obtained from a post-operative CBCT. The goal is to evaluate the accuracy of the VSP. When I load the two files (S…

---

## [ROI to IJK coordinates with MATLAB bridge](https://discourse.slicer.org/t/roi-to-ijk-coordinates-with-matlab-bridge/14764)

<div class="topic-metadata">

**Author:** [@OscarD](https://discourse.slicer.org/u/OscarD)\
**Replies:** 1\
**Last updated:** [December 4, 2020, 9:06am UTC](https://discourse.slicer.org/t/roi-to-ijk-coordinates-with-matlab-bridge/14764 "2020-12-04T09:06:04Z")

</div>

Operating system: Windows 10 Slicer version: 4.11.0 Expected behavior: Find IJK coordinates of ROI Actual behavior: I get negative or bigger than dimensions IJK coordinates Dear slicers, I am trying to get iMin, iMa…

---

## [How to map volume data to a slice viewer in a non-linear transformation using custom code?](https://discourse.slicer.org/t/how-to-map-volume-data-to-a-slice-viewer-in-a-non-linear-transformation-using-custom-code/12882)

<div class="topic-metadata">

**Author:** [@Tesla2687](https://discourse.slicer.org/u/Tesla2687)\
**Replies:** 2\
**Last updated:** [August 9, 2020, 12:52am UTC](https://discourse.slicer.org/t/how-to-map-volume-data-to-a-slice-viewer-in-a-non-linear-transformation-using-custom-code/12882 "2020-08-09T00:52:47Z")

</div>

Operating system:Windows 10 Slicer version: 4.11.0 Expected behavior: How to map volume data to a slice display viewer in a non-linear transformation using custom code? Actual behavior: I would like to display a cur…

---

## [User setting for coordinate system in v4.11?](https://discourse.slicer.org/t/user-setting-for-coordinate-system-in-v4-11/11567)

<div class="topic-metadata">

**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 3\
**Last updated:** [May 25, 2020, 4:16am UTC](https://discourse.slicer.org/t/user-setting-for-coordinate-system-in-v4-11/11567 "2020-05-25T04:16:31Z")

</div>

Hi, I am working with v4.11 and recently became aware that v4.11 has changed the default coordinate system (RAS -\> LPS). Wondering if there will be an option in settings for the user to select their preferred coordinate…

---

## [Converting fiducial coordinates from RAS to LPS](https://discourse.slicer.org/t/converting-fiducial-coordinates-from-ras-to-lps/9707)

<div class="topic-metadata">

**Author:** [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Replies:** 6\
**Last updated:** [January 4, 2020, 12:37am UTC](https://discourse.slicer.org/t/converting-fiducial-coordinates-from-ras-to-lps/9707 "2020-01-04T00:37:38Z")

</div>

Hi, I am working with some chest CT scans and I have some fiducials which denote the 3D centre of a tumour mass. I have saved/exported the fiducials from Slicer as .fcsv files. I have done some searching online but I a…

---

## [Convert Matlab coordinates to Slicer](https://discourse.slicer.org/t/convert-matlab-coordinates-to-slicer/7163)

<div class="topic-metadata">

**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 7\
**Last updated:** [June 18, 2019, 7:24pm UTC](https://discourse.slicer.org/t/convert-matlab-coordinates-to-slicer/7163 "2019-06-18T19:24:00Z")

</div>

Hello, I would like to convert Matlab coordinates to Slicer. I load Dicom images to Matlab and I get some coordinates. Then, I try to load them on Slicer, but both are in a completely different position. Could you pl…

---

## [X, Y, Z Coordinates and Updated 3-D MPR Capability](https://discourse.slicer.org/t/x-y-z-coordinates-and-updated-3-d-mpr-capability/715)

<div class="topic-metadata">

**Author:** [@krb01](https://discourse.slicer.org/u/krb01)\
**Replies:** 8\
**Last updated:** [January 16, 2019, 6:04pm UTC](https://discourse.slicer.org/t/x-y-z-coordinates-and-updated-3-d-mpr-capability/715 "2019-01-16T18:04:28Z")

</div>

I read through the wiki pages, but I still had a few unanswered questions. First, is there a way to indicate the x, y, z-axis coordinates when freely moving the cursor around the DICOM image. This feature is available i…

---

## [How to display and move the origin coordinates of the surface model (.STL)](https://discourse.slicer.org/t/how-to-display-and-move-the-origin-coordinates-of-the-surface-model-stl/3329)

<div class="topic-metadata">

**Author:** [@Yuta](https://discourse.slicer.org/u/Yuta)\
**Replies:** 1\
**Last updated:** [October 11, 2018, 7:54pm UTC](https://discourse.slicer.org/t/how-to-display-and-move-the-origin-coordinates-of-the-surface-model-stl/3329 "2018-10-11T19:54:05Z")

</div>

Operating system: WINDOWS Slicer version: 4.8.1 thank you for the outstanding work with 3DSlicer Expected behavior: I want to set the origin (0, 0, 0) of the coordinates to an arbitrary position of the segmented bone…

---

## [MINC2 Reader and RAS coordinate system](https://discourse.slicer.org/t/minc2-reader-and-ras-coordinate-system/2524)

<div class="topic-metadata">

**Author:** [@hgueziri](https://discourse.slicer.org/u/hgueziri)\
**Replies:** 7\
**Last updated:** [April 12, 2018, 8:16pm UTC](https://discourse.slicer.org/t/minc2-reader-and-ras-coordinate-system/2524 "2018-04-12T20:16:10Z")

</div>

Slicer 4.9.0-2017-11-29 r26666 Linux Mint 18.2 64-bit Hello all, It is a very helpful feature to be able to read/write MINC2 files directly in slicer. However, I noticed an unexpected behavior when loading MINC2 files…

[Next page](https://discourse.slicer.org/tag/coordinates/52.md?match_all_tags=true&page=1&tags%5B%5D=coordinates)