# \#file-export **URL:** https://discourse.slicer.org/tag/file-export/74.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [New extension: OMEZarr - open OME-Zarr images directly in Slicer](https://discourse.slicer.org/t/new-extension-omezarr-open-ome-zarr-images-directly-in-slicer/48238)
**Author:** [@vboussot](https://discourse.slicer.org/u/vboussot)\ **Replies:** 5\ **Last updated:** [September 23, 2026, 5:23pm UTC](https://discourse.slicer.org/t/new-extension-omezarr-open-ome-zarr-images-directly-in-slicer/48238 "2026-09-23T17:23:04Z")
Hi all, We’re happy to announce OMEZarr, a new extension from Fideus Labs that opens and saves OME-Zarr images. It is available in the Extensions Manager for Slicer 5.12.4 and the Preview release, on Linux, macOS and Wi… --- ## [Why won't my mrml file open in 3D slicer, or my stl file become visible?](https://discourse.slicer.org/t/why-wont-my-mrml-file-open-in-3d-slicer-or-my-stl-file-become-visible/47172)
**Author:** [@Emerson](https://discourse.slicer.org/u/Emerson)\ **Replies:** 1\ **Last updated:** [May 29, 2026, 2:34pm UTC](https://discourse.slicer.org/t/why-wont-my-mrml-file-open-in-3d-slicer-or-my-stl-file-become-visible/47172 "2026-05-29T14:34:17Z")
I was trying to open an mrml file I have saved, and while it opened the app it did not open the file or show up anywhere. I tried again with the stl file and while it showed up under ‘data’ (which is farther than I got w… --- ## [Process to Import an STL File and Convert/Export a Series of DICOM Files?](https://discourse.slicer.org/t/process-to-import-an-stl-file-and-convert-export-a-series-of-dicom-files/9906)
**Author:** [@aleesdesigner](https://discourse.slicer.org/u/aleesdesigner)\ **Replies:** 19\ **Last updated:** [December 19, 2025, 7:38pm UTC](https://discourse.slicer.org/t/process-to-import-an-stl-file-and-convert-export-a-series-of-dicom-files/9906 "2025-12-19T19:38:26Z")
Hi, I’m hoping someone can help with a workflow to import an STL file into Slicer, convert it to a series of DICOM files and export those DICOM files. I’ve checked other forums and can’t find anything that gives a step-… --- ## [Segmentation export to DICOM-RT](https://discourse.slicer.org/t/segmentation-export-to-dicom-rt/44099)
**Author:** [@CSalt](https://discourse.slicer.org/u/CSalt)\ **Replies:** 2\ **Last updated:** [August 18, 2025, 10:04am UTC](https://discourse.slicer.org/t/segmentation-export-to-dicom-rt/44099 "2025-08-18T10:04:00Z")
Hello, I have segmentations from PET dicom source images that I would like to export as DICOM-RT files. I have the extension SlicerRT. Is this possible? --- ## [How to export centerline generated by the VMTK?](https://discourse.slicer.org/t/how-to-export-centerline-generated-by-the-vmtk/22735)
**Author:** [@canadan](https://discourse.slicer.org/u/canadan)\ **Replies:** 6\ **Last updated:** [August 4, 2025, 12:48pm UTC](https://discourse.slicer.org/t/how-to-export-centerline-generated-by-the-vmtk/22735 "2025-08-04T12:48:54Z")
Operating system: Linux Slicer version:4.11.20210226 r29738 / 7a593c8 Expected behavior: Actual behavior: Following a recent online tutorial, I was able to generate a centerline of a segemented aorta. I would like to… --- ## [Dashes silently removed from filename in "export to file" operation](https://discourse.slicer.org/t/dashes-silently-removed-from-filename-in-export-to-file-operation/43923)
**Author:** [@flomei](https://discourse.slicer.org/u/flomei)\ **Replies:** 6\ **Last updated:** [August 1, 2025, 9:09pm UTC](https://discourse.slicer.org/t/dashes-silently-removed-from-filename-in-export-to-file-operation/43923 "2025-08-01T21:09:28Z")
Hi, I’m using Slicer (v5.8.1) for manual annotation of structural MRI nifti data (T1 + parcellations). I’m loading T1 volume and freesurfer parcellations (both .nii.gz) via a selfmade startup script, but use the GUI fo… --- ## [Can I export the data for multiple points at once?](https://discourse.slicer.org/t/can-i-export-the-data-for-multiple-points-at-once/42189)
**Author:** [@MIZ](https://discourse.slicer.org/u/MIZ)\ **Replies:** 8\ **Last updated:** [July 2, 2025, 1:13am UTC](https://discourse.slicer.org/t/can-i-export-the-data-for-multiple-points-at-once/42189 "2025-07-02T01:13:35Z")
I am landmarking approximately 44 points in a mesh. Exporting the x,y,z coordinates into an .fcsv file is extremely laborious. Is there any way to export the data for all 44 points simultaneously? Also, it would be great… --- ## [Portable 3D Slicer for macOS with Auto-Import DICOM Directory](https://discourse.slicer.org/t/portable-3d-slicer-for-macos-with-auto-import-dicom-directory/43276)
**Author:** [@Wyatt\_Gray](https://discourse.slicer.org/u/Wyatt_Gray)\ **Replies:** 2\ **Last updated:** [June 10, 2025, 2:01pm UTC](https://discourse.slicer.org/t/portable-3d-slicer-for-macos-with-auto-import-dicom-directory/43276 "2025-06-10T14:01:28Z")
Introduction: I’m an engineer and have been tasked with sharing a patient’s DICOM dataset with a macOS-based Dr. (expert). The imaging location provided a DICOM directory and an application but users report errors openi… --- ## [How to convert xml file to RT Struct](https://discourse.slicer.org/t/how-to-convert-xml-file-to-rt-struct/43225)
**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\ **Replies:** 0\ **Last updated:** [June 5, 2025, 3:26am UTC](https://discourse.slicer.org/t/how-to-convert-xml-file-to-rt-struct/43225 "2025-06-05T03:26:24Z")
Dear Expert, I have xml file (xml folder) that I done contouring on that file. The original file also I have as attached. Both file can get here: File XML and Original Anyone can help me to convert xml file to RT Stru… --- ## [export coordinates of segmented plane .txt](https://discourse.slicer.org/t/export-coordinates-of-segmented-plane-txt/42358)
**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")
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… --- ## [The exported label comes LAI while image is LAS](https://discourse.slicer.org/t/the-exported-label-comes-lai-while-image-is-las/42341)
**Author:** [@Berk\_Gezgin](https://discourse.slicer.org/u/Berk_Gezgin)\ **Replies:** 0\ **Last updated:** [March 28, 2025, 7:24am UTC](https://discourse.slicer.org/t/the-exported-label-comes-lai-while-image-is-las/42341 "2025-03-28T07:24:10Z")
I create a segmentation and then do a labeling on an images (.nii.gz). When I export by clicking on export at the bottom of the image, the label comes in LAI format. However, my image is LAS and I want the label to come … --- ## [4D Registration: How to output the coordinates of the meshing points?](https://discourse.slicer.org/t/4d-registration-how-to-output-the-coordinates-of-the-meshing-points/22586)
**Author:** [@Gening\_Dong](https://discourse.slicer.org/u/Gening_Dong)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 11:19am UTC](https://discourse.slicer.org/t/4d-registration-how-to-output-the-coordinates-of-the-meshing-points/22586 "2024-11-20T11:19:08Z")
Operating system: Windows 11 Slicer version: 4.11 Hi! I used the 4D Elastix plugin (Sequence Registration) to complete the image registration and the module Transform to transform a model generated by the module Segme… --- ## [Export 3d model to Hololens 2 device](https://discourse.slicer.org/t/export-3d-model-to-hololens-2-device/27259)
**Author:** [@Caterina](https://discourse.slicer.org/u/Caterina)\ **Replies:** 5\ **Last updated:** [August 3, 2024, 9:53pm UTC](https://discourse.slicer.org/t/export-3d-model-to-hololens-2-device/27259 "2024-08-03T21:53:41Z")
Good morning, I need to export a 3d model from Slicer to the Hololens 2 device (MRTK 2.8.3). I performed segmentation on 3d slicer (Segment Editor) and I used OpenAnatomy module to export the segmentation part as gltf. … --- ## [problem with exporting photos](https://discourse.slicer.org/t/problem-with-exporting-photos/35945)
**Author:** [@PLS](https://discourse.slicer.org/u/PLS)\ **Replies:** 4\ **Last updated:** [May 7, 2024, 8:04am UTC](https://discourse.slicer.org/t/problem-with-exporting-photos/35945 "2024-05-07T08:04:35Z")
Good afternoon, I have a problem when exporting images only with the 3D view, it doesn’t allow me to do it, and I don’t know what I’m doing wrong. I don’t know if you could help me, thank you very much --- ## [Open Anatomy Export in gltf format](https://discourse.slicer.org/t/open-anatomy-export-in-gltf-format/34819)
**Author:** [@Caterina](https://discourse.slicer.org/u/Caterina)\ **Replies:** 14\ **Last updated:** [April 2, 2024, 8:20am UTC](https://discourse.slicer.org/t/open-anatomy-export-in-gltf-format/34819 "2024-04-02T08:20:40Z")
Dear support, I used Lung CT Segmented and Analyzer extensions and I exported lung volume from segmentation and vessels from CT Analyzer in gltf format using Open Anatomy. The visualization in Slicer showed good detail… --- ## [File Save Behavior Query: TIFF Files Auto-Selecting on Second Save](https://discourse.slicer.org/t/file-save-behavior-query-tiff-files-auto-selecting-on-second-save/34665)
**Author:** [@Aram\_Harutyunyan](https://discourse.slicer.org/u/Aram_Harutyunyan)\ **Replies:** 2\ **Last updated:** [March 5, 2024, 8:15am UTC](https://discourse.slicer.org/t/file-save-behavior-query-tiff-files-auto-selecting-on-second-save/34665 "2024-03-05T08:15:29Z")
I’ve encountered a unexpected behavior in an application running on Ubuntu 22.04 , app version 5.7.0-2024-02-29 , and I’m trying to determine whether it’s a bug or an intended feature. The issue revolves around the proce… --- ## [Exporting to as GLTF changes names](https://discourse.slicer.org/t/exporting-to-as-gltf-changes-names/34623)
**Author:** [@MuckYu](https://discourse.slicer.org/u/MuckYu)\ **Replies:** 0\ **Last updated:** [February 29, 2024, 6:34pm UTC](https://discourse.slicer.org/t/exporting-to-as-gltf-changes-names/34623 "2024-02-29T18:34:22Z")
I am trying to export the centerline from a scene with a python script. OBJ/STL etc. don’t export the centerline at all. So I have to use GLTF - which works fine so far. The problem here is that it exports the whole s… --- ## [Preserve colors from segment editor node and export it as Nifti LabelMap](https://discourse.slicer.org/t/preserve-colors-from-segment-editor-node-and-export-it-as-nifti-labelmap/33100)
**Author:** [@Vishal\_P](https://discourse.slicer.org/u/Vishal_P)\ **Replies:** 8\ **Last updated:** [December 1, 2023, 2:11am UTC](https://discourse.slicer.org/t/preserve-colors-from-segment-editor-node-and-export-it-as-nifti-labelmap/33100 "2023-12-01T02:11:02Z")
Slicer 5.2.2 Hello, i am currently using segment editor and selected Generic Color Table and made following sample segments. and then i move the segments to segmentation module and export it as a new label map, once… --- ## [Cannot save DICOM to NRRD files](https://discourse.slicer.org/t/cannot-save-dicom-to-nrrd-files/32609)
**Author:** [@maiseld](https://discourse.slicer.org/u/maiseld)\ **Replies:** 3\ **Last updated:** [November 6, 2023, 5:45am UTC](https://discourse.slicer.org/t/cannot-save-dicom-to-nrrd-files/32609 "2023-11-06T05:45:00Z")
After loading in all of the DICOM files into Slicer, I click to save but do not have the option of saving into NRRD files. I was following this guide: I just downloaded Slicer as of today so I should have the current v… --- ## [How to export segments as one object with colors](https://discourse.slicer.org/t/how-to-export-segments-as-one-object-with-colors/31256)
**Author:** [@Mehdi\_Khamesi](https://discourse.slicer.org/u/Mehdi_Khamesi)\ **Replies:** 5\ **Last updated:** [August 22, 2023, 3:33pm UTC](https://discourse.slicer.org/t/how-to-export-segments-as-one-object-with-colors/31256 "2023-08-22T15:33:52Z")
Operating system: Windows 10 Slicer version: 5.2.2 Expected behavior: Creating volumetric mesh Actual behavior: exporting few segment as one object with their colors Hello everyone, I want to import part of brain in… --- ## [Error exporting Images and Structures in DICOM format](https://discourse.slicer.org/t/error-exporting-images-and-structures-in-dicom-format/31108)
**Author:** [@Sergio](https://discourse.slicer.org/u/Sergio)\ **Replies:** 1\ **Last updated:** [August 17, 2023, 5:14pm UTC](https://discourse.slicer.org/t/error-exporting-images-and-structures-in-dicom-format/31108 "2023-08-17T17:14:43Z")
Hi, this message error appears when I am trying to export the Images and Structures to DICOM format using DicomRtImportExportPlugin. What could be the problem? is there something I can do? Thanks in advance. --- ## [How to auto export Segmentation-Labels.tiff and Original images from .mrb file?](https://discourse.slicer.org/t/how-to-auto-export-segmentation-labels-tiff-and-original-images-from-mrb-file/30986)
**Author:** [@Jeff\_Boker](https://discourse.slicer.org/u/Jeff_Boker)\ **Replies:** 1\ **Last updated:** [August 5, 2023, 10:35am UTC](https://discourse.slicer.org/t/how-to-auto-export-segmentation-labels-tiff-and-original-images-from-mrb-file/30986 "2023-08-05T10:35:04Z")
I have several .mrb files which contain images and segmentation annotations. I currently manually open the .mrb file in 3D slicer and then go to “Data” → “Export visible segments to binary labelmap” → “Save” and then sel… --- ## [Exporting sequence annotation (2d + time)](https://discourse.slicer.org/t/exporting-sequence-annotation-2d-time/30163)
**Author:** [@cams2b](https://discourse.slicer.org/u/cams2b)\ **Replies:** 0\ **Last updated:** [June 20, 2023, 6:26pm UTC](https://discourse.slicer.org/t/exporting-sequence-annotation-2d-time/30163 "2023-06-20T18:26:58Z")
I am a new user of 3d slicer and I am working on segmenting 2d + time sequences. I have successfully annotated the sequences and I have saved the annotations as sequence files. I am now trying to export the annotations t… --- ## [exporting sequence of stl files from segmentation of 4D dicom images](https://discourse.slicer.org/t/exporting-sequence-of-stl-files-from-segmentation-of-4d-dicom-images/29759)
**Author:** [@Sanjib\_Gurung](https://discourse.slicer.org/u/Sanjib_Gurung)\ **Replies:** 1\ **Last updated:** [June 2, 2023, 11:38pm UTC](https://discourse.slicer.org/t/exporting-sequence-of-stl-files-from-segmentation-of-4d-dicom-images/29759 "2023-06-02T23:38:52Z")
Hi, I am new to 3D slicer. I segmented a volume sequence of 4D cardiac MRI images. I need to export the sequence of segmented geometries as a sequence of stl files. Currently, I can only export an stl file at a time poi… --- ## [Problems replicating an exported sequence](https://discourse.slicer.org/t/problems-replicating-an-exported-sequence/29727)
**Author:** [@abravo](https://discourse.slicer.org/u/abravo)\ **Replies:** 2\ **Last updated:** [June 2, 2023, 4:35pm UTC](https://discourse.slicer.org/t/problems-replicating-an-exported-sequence/29727 "2023-06-02T16:35:32Z")
Hello everyone, I have been trying to use the coordinates of some exported sequences from Slicer to replicate the movements in Blender for demonstration/learning purposes. These sequences have been recorded with slicer … --- ## [Export segmentation to PLY compatible with geomorph](https://discourse.slicer.org/t/export-segmentation-to-ply-compatible-with-geomorph/29251)
**Author:** [@thelobsternods](https://discourse.slicer.org/u/thelobsternods)\ **Replies:** 1\ **Last updated:** [May 2, 2023, 6:34pm UTC](https://discourse.slicer.org/t/export-segmentation-to-ply-compatible-with-geomorph/29251 "2023-05-02T18:34:21Z")
I have been using 3D Slicer to segment bones out of scans. So far we have been saving these as STL files for 3D printing. However we would like to begin 3D geometric morphometrics using geomorph in R. This requires PLY f… --- ## [Error while exporting a model node as stl file](https://discourse.slicer.org/t/error-while-exporting-a-model-node-as-stl-file/29047)
**Author:** [@Luca](https://discourse.slicer.org/u/Luca)\ **Replies:** 4\ **Last updated:** [April 25, 2023, 1:59pm UTC](https://discourse.slicer.org/t/error-while-exporting-a-model-node-as-stl-file/29047 "2023-04-25T13:59:05Z")
Hello everyone, every time I try to export a model node (simple or complex) as stl file by using the GUI, I get the following error: Error: ERROR: In D:\\D\\S\\S-0-build\\VTK\\IO\\Geometry\\vtkSTLWriter.cxx, line 248 vtkSTL… --- ## [Save IGTLink 3D coordinates](https://discourse.slicer.org/t/save-igtlink-3d-coordinates/27991)
**Author:** [@Hugo\_Angulo](https://discourse.slicer.org/u/Hugo_Angulo)\ **Replies:** 0\ **Last updated:** [February 22, 2023, 10:30pm UTC](https://discourse.slicer.org/t/save-igtlink-3d-coordinates/27991 "2023-02-22T22:30:25Z")
Hi there, I am currently simulating that I receive some coordinates through the usage of the TrackerSim binary file that I found in an old page in the website. Now, I was able to mimic that this is a remote machine that… --- ## [Saving RTSTRUCT Nodes as Nifti Files](https://discourse.slicer.org/t/saving-rtstruct-nodes-as-nifti-files/24843)
**Author:** [@enamdar](https://discourse.slicer.org/u/enamdar)\ **Replies:** 1\ **Last updated:** [August 24, 2022, 8:52pm UTC](https://discourse.slicer.org/t/saving-rtstruct-nodes-as-nifti-files/24843 "2022-08-24T20:52:48Z")
Hi everyone. I have loaded a patient volume, its segmentation, and the corresponding RTSTURCT. I need to save the components of the RTSTRUCT as separate nifti files using the python command line, but I have no idea how… --- ## [How to export segmentation to STEP or IGES format?](https://discourse.slicer.org/t/how-to-export-segmentation-to-step-or-iges-format/24717)
**Author:** [@mdear](https://discourse.slicer.org/u/mdear)\ **Replies:** 4\ **Last updated:** [August 19, 2022, 2:35am UTC](https://discourse.slicer.org/t/how-to-export-segmentation-to-step-or-iges-format/24717 "2022-08-19T02:35:14Z")
Hello, I have a DICOM-originated CAT scan segmentation of air in a patient’s trachea and a segmentation imported from an Informatics/Curve Maker model (proposed complex tracheostomy tube design) that I want to export tog… [Next page](https://discourse.slicer.org/tag/file-export/74.md?match_all_tags=true&page=1&tags%5B%5D=file-export)