# \#file-import

**URL:** https://discourse.slicer.org/tag/file-import/158.md

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

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## [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)

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**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")

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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…

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## [Issues with scaling information added to .tiff volume- tried ImageStacks and saving as .nrrd?](https://discourse.slicer.org/t/issues-with-scaling-information-added-to-tiff-volume-tried-imagestacks-and-saving-as-nrrd/46084)

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**Author:** [@alsig](https://discourse.slicer.org/u/alsig)\
**Replies:** 10\
**Last updated:** [February 9, 2026, 12:10am UTC](https://discourse.slicer.org/t/issues-with-scaling-information-added-to-tiff-volume-tried-imagestacks-and-saving-as-nrrd/46084 "2026-02-09T00:10:01Z")

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Hi everyone, I am having a issue when trying to import/save TIFF data in a way that lets me add the scaling information. I have a single file ImageJ hyperstack .tiff that has my entire volume, with X-Y scale of 0.00128…

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## [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)

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**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")

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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-…

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## [Convert relative 3ddose to absolute dose in 3DSlicer](https://discourse.slicer.org/t/convert-relative-3ddose-to-absolute-dose-in-3dslicer/42852)

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**Author:** [@TaHamI](https://discourse.slicer.org/u/TaHamI)\
**Replies:** 1\
**Last updated:** [May 12, 2025, 1:56pm UTC](https://discourse.slicer.org/t/convert-relative-3ddose-to-absolute-dose-in-3dslicer/42852 "2025-05-12T13:56:13Z")

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Hello, I know, DOSXYZnrc like other monte-carlo simulations reports relative (normalized) dose (averaging on the number of histories, the number of histories just relates to dose uncertainty, no change the dose value). …

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## [How to prevent automatic renaming after patching and loading echcardiograms?](https://discourse.slicer.org/t/how-to-prevent-automatic-renaming-after-patching-and-loading-echcardiograms/42689)

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**Author:** [@Maeva](https://discourse.slicer.org/u/Maeva)\
**Replies:** 3\
**Last updated:** [April 30, 2025, 10:22pm UTC](https://discourse.slicer.org/t/how-to-prevent-automatic-renaming-after-patching-and-loading-echcardiograms/42689 "2025-04-30T22:22:46Z")

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Hello, I am doing a research in which I model 3D hearts of neonates. I have downloaded the images to DICOM cartesian maps, and all works. Then, using the cardiac drop down botton (provided by the HeartSlicer extension),…

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## [MorphoSource files not Opening](https://discourse.slicer.org/t/morphosource-files-not-opening/42290)

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**Author:** [@Vincent\_Girgenti](https://discourse.slicer.org/u/Vincent_Girgenti)\
**Replies:** 1\
**Last updated:** [March 25, 2025, 2:28pm UTC](https://discourse.slicer.org/t/morphosource-files-not-opening/42290 "2025-03-25T14:28:48Z")

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Hello! I’m new to 3d Slicer and am looking to use it for models from MorphoSource. I have downloaded the .zip folder and attempt to open it I’m not entirely sure what to do about it so if anyone has tips I’d apprecia…

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## [Issues loading Python script and .mrb file](https://discourse.slicer.org/t/issues-loading-python-script-and-mrb-file/41012)

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**Author:** [@Symon](https://discourse.slicer.org/u/Symon)\
**Replies:** 1\
**Last updated:** [January 9, 2025, 4:24pm UTC](https://discourse.slicer.org/t/issues-loading-python-script-and-mrb-file/41012 "2025-01-09T16:24:06Z")

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Hi, I’m new to 3D Slicer and I have somme issues with it. I have DICOM files that I load to 3D Slicer (no problem there). These are CT-Scan Dynamic with 247 images (7.8Go for the DICOM file). I saved my work in a “.mr…

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## [Failure to load RTSTRUCT dicom file](https://discourse.slicer.org/t/failure-to-load-rtstruct-dicom-file/33504)

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**Author:** [@Michele\_R](https://discourse.slicer.org/u/Michele_R)\
**Replies:** 7\
**Last updated:** [December 18, 2024, 10:39am UTC](https://discourse.slicer.org/t/failure-to-load-rtstruct-dicom-file/33504 "2024-12-18T10:39:14Z")

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Operating system: MacOS Ventura Slicer version: 5.7.0 Hello, I am trying to load an image set including a 3D MRI with RT files containing volumetric and dosimetric information that have been exported from a DICOM view…

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## [Combine Multiple Orientations / Volumes in Axial View](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073)

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**Author:** [@waterbottle](https://discourse.slicer.org/u/waterbottle)\
**Replies:** 1\
**Last updated:** [July 8, 2024, 4:33pm UTC](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073 "2024-07-08T16:33:50Z")

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Hi all, Still new to slicer. I am working on MRIs in Slicer. Some MRIs load in as one big volume which works for my needs, however others come split into “imageOrientationPatient X” where X = some number, typically from…

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## [Dicom import RTSTRUCT that were exported from slicer](https://discourse.slicer.org/t/dicom-import-rtstruct-that-were-exported-from-slicer/36986)

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**Author:** [@gleesoi](https://discourse.slicer.org/u/gleesoi)\
**Replies:** 2\
**Last updated:** [June 24, 2024, 8:15pm UTC](https://discourse.slicer.org/t/dicom-import-rtstruct-that-were-exported-from-slicer/36986 "2024-06-24T20:15:38Z")

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Hi, new to slicer and working on a dicom workflow. I notice that importing my dicom ct and segments look fine in dicom apart from a body rind and couch roi. I then export the ct and contours in dicom to file. I then lo…

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## [Problem loading MRI scan. Only one view, axial, is clear, the other two are blurry](https://discourse.slicer.org/t/problem-loading-mri-scan-only-one-view-axial-is-clear-the-other-two-are-blurry/1799)

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**Author:** [@olivya\_caballero](https://discourse.slicer.org/u/olivya_caballero)\
**Replies:** 7\
**Last updated:** [June 19, 2024, 11:39pm UTC](https://discourse.slicer.org/t/problem-loading-mri-scan-only-one-view-axial-is-clear-the-other-two-are-blurry/1799 "2024-06-19T23:39:28Z")

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Operating system: Windows 10 Slicer version: 4.8.0 Expected behavior: All three views are clear Actual behavior: Only axial is clear and the other views are a bit titled and blurry. Unable to get a good 3d model out o…

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## [Import dicom is not working while running the segmentation script from AWS ssm "tils.importDicom(skullfolder)"](https://discourse.slicer.org/t/import-dicom-is-not-working-while-running-the-segmentation-script-from-aws-ssm-tils-importdicom-skullfolder/35273)

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**Author:** [@Mani\_Barathi](https://discourse.slicer.org/u/Mani_Barathi)\
**Replies:** 0\
**Last updated:** [April 4, 2024, 5:13am UTC](https://discourse.slicer.org/t/import-dicom-is-not-working-while-running-the-segmentation-script-from-aws-ssm-tils-importdicom-skullfolder/35273 "2024-04-04T05:13:33Z")

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import dicom is not working while running the segmentation script from AWS ssm “utils.importDicom(skullfolder)” SQL failed Bad SQL: Error text: No query Unable to fetch row

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## [Not imported DICOM files](https://discourse.slicer.org/t/not-imported-dicom-files/32868)

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**Author:** [@luarpy](https://discourse.slicer.org/u/luarpy)\
**Replies:** 9\
**Last updated:** [December 1, 2023, 10:03pm UTC](https://discourse.slicer.org/t/not-imported-dicom-files/32868 "2023-12-01T22:03:03Z")

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Hello I could see that Slicer for Linux is not able to load all the DICOM files present in a folder. I have checked the following checks: Files exist: yes Slicer for Windows loads them: yes The files contain data: yes …

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## [How to import 3D Structured Data into 3D Slicer?](https://discourse.slicer.org/t/how-to-import-3d-structured-data-into-3d-slicer/31558)

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**Author:** [@iwangwangwang](https://discourse.slicer.org/u/iwangwangwang)\
**Replies:** 9\
**Last updated:** [September 8, 2023, 3:17am UTC](https://discourse.slicer.org/t/how-to-import-3d-structured-data-into-3d-slicer/31558 "2023-09-08T03:17:10Z")

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How to import 3D Structured Data File into 3D Slicer ? such as .xyz/.csv/.grd/.p3d etc.

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## [What would be the best way to let a user select scenes and channel colours in a microscopy oriented importer?](https://discourse.slicer.org/t/what-would-be-the-best-way-to-let-a-user-select-scenes-and-channel-colours-in-a-microscopy-oriented-importer/31595)

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**Author:** [@EgorZindy](https://discourse.slicer.org/u/EgorZindy)\
**Replies:** 5\
**Last updated:** [September 6, 2023, 9:01pm UTC](https://discourse.slicer.org/t/what-would-be-the-best-way-to-let-a-user-select-scenes-and-channel-colours-in-a-microscopy-oriented-importer/31595 "2023-09-06T21:01:47Z")

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Hello everyone. So for my CZI importer, there are two things I think need to be user-selectable at import time: A CZI file may contain multiple scenes, and a user may decide which scenes need importing. The channel co…

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## [MultiVolume Explorer and Segment Editor Error](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732)

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**Author:** [@aginn](https://discourse.slicer.org/u/aginn)\
**Replies:** 22\
**Last updated:** [August 31, 2023, 2:04am UTC](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732 "2023-08-31T02:04:23Z")

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Hi all - I am trying to load a cine-MRI (link to data is below). I was able to import it through the DICOM import, but the results look off. Furthermore, when I go to “volume rendering,” there is no volume generated, bu…

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## [Working on a CZI Zeiss microscopy image stack reader for 3D slicer, any help or advice welcome](https://discourse.slicer.org/t/working-on-a-czi-zeiss-microscopy-image-stack-reader-for-3d-slicer-any-help-or-advice-welcome/30769)

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**Author:** [@EgorZindy](https://discourse.slicer.org/u/EgorZindy)\
**Replies:** 11\
**Last updated:** [August 24, 2023, 10:15am UTC](https://discourse.slicer.org/t/working-on-a-czi-zeiss-microscopy-image-stack-reader-for-3d-slicer-any-help-or-advice-welcome/30769 "2023-08-24T10:15:54Z")

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Some general info: Operating system: Windows 10 Slicer version: 5.3.0 - 2023.06.17 Expected behavior: 3D stack(s) imported from a CZI scene with minimum hassle for the user… Actual behavior: Work in progress, 3D view …

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## [Repost in support (sorry) python function vs main / crash in function but not in main](https://discourse.slicer.org/t/repost-in-support-sorry-python-function-vs-main-crash-in-function-but-not-in-main/29915)

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**Author:** [@Nicolas\_Tempier](https://discourse.slicer.org/u/Nicolas_Tempier)\
**Replies:** 3\
**Last updated:** [June 9, 2023, 1:43pm UTC](https://discourse.slicer.org/t/repost-in-support-sorry-python-function-vs-main-crash-in-function-but-not-in-main/29915 "2023-06-09T13:43:12Z")

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Hello everyone, first of all, sorry for the repost, i posted this issue in development section instead of support … i have a little problem understanding why my code crashes when i use it as a function. i want to disp…

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## [Morita .vol file import](https://discourse.slicer.org/t/morita-vol-file-import/29544)

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**Author:** [@Tijl](https://discourse.slicer.org/u/Tijl)\
**Replies:** 1\
**Last updated:** [May 22, 2023, 9:20am UTC](https://discourse.slicer.org/t/morita-vol-file-import/29544 "2023-05-22T09:20:30Z")

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I have a .vol file from a cbct volume from a morita cbct machine This is the header from the file I dont know how to proceed or what to do to import. JmVolumeVersion=1Ú \<?xml version='1.0' encoding='Shift\_JIS' ?\>…

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## [Report a bug about import the fcsv file](https://discourse.slicer.org/t/report-a-bug-about-import-the-fcsv-file/28958)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 1\
**Last updated:** [April 17, 2023, 12:04pm UTC](https://discourse.slicer.org/t/report-a-bug-about-import-the-fcsv-file/28958 "2023-04-17T12:04:34Z")

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Hi, I would like to report a bug when I load the fcsv files. I export landmarks as fcsv files, but when I want to load them in a new slicer windows. I found the value was changed to the opposite value automatically. F…

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## [Import Numpy File in as image volume](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 5\
**Last updated:** [December 12, 2022, 10:47pm UTC](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653 "2022-12-12T22:47:35Z")

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I have been working with trying to compress files down to NPY and NPZ files to save binary labelmaps for some of my data. Is there a way to import them into slicer? Every time I try the load data option with it, it doesn…

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## [Import 3DUS Stradwin Files](https://discourse.slicer.org/t/import-3dus-stradwin-files/25480)

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**Author:** [@PaulT95](https://discourse.slicer.org/u/PaulT95)\
**Replies:** 15\
**Last updated:** [October 20, 2022, 4:53pm UTC](https://discourse.slicer.org/t/import-3dus-stradwin-files/25480 "2022-10-20T16:53:11Z")

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Hi everyone, I have been collecting freehand 3DUS data using StradWin (http://mi.eng.cam.ac.uk/Main/StradWin) but I would like to perform the segmentation in 3D slicer, however, the file format of the recorded data is .…

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## [Loading a .bmp sequence from directory as a LabelMap](https://discourse.slicer.org/t/loading-a-bmp-sequence-from-directory-as-a-labelmap/24802)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 8\
**Last updated:** [August 24, 2022, 2:53pm UTC](https://discourse.slicer.org/t/loading-a-bmp-sequence-from-directory-as-a-labelmap/24802 "2022-08-24T14:53:34Z")

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Operating system: Windows 10 Education Slicer version: 5.0.2 Expected behavior: I have a set of segmented slices in a directory. It has 2 classes (0 and 255). The image format is .bmp. I want to load them as a segment…

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## [Problem importing JPEG series ](https://discourse.slicer.org/t/problem-importing-jpeg-series/24233)

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**Author:** [@marco1](https://discourse.slicer.org/u/marco1)\
**Replies:** 6\
**Last updated:** [July 7, 2022, 10:13pm UTC](https://discourse.slicer.org/t/problem-importing-jpeg-series/24233 "2022-07-07T22:13:13Z")

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Hi, I’m currently importing JPEG series of brain MRIs for a volumetric tumor analysis. I’m having no problems importing axial sequences, but importing sagittal or coronal sequences always ends up with the sequences in t…

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## [openDialog does not load node into scene](https://discourse.slicer.org/t/opendialog-does-not-load-node-into-scene/23874)

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**Author:** [@mholden8](https://discourse.slicer.org/u/mholden8)\
**Replies:** 2\
**Last updated:** [June 14, 2022, 9:15pm UTC](https://discourse.slicer.org/t/opendialog-does-not-load-node-into-scene/23874 "2022-06-14T21:15:59Z")

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When using the openDialog function in the Slicer IO Manager, the selected node is not loaded into the scene. For example, when I run the code below (see Documentation/Nightly/Developers/IO - Slicer Wiki), nothing happen…

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## [Issue loading .nii files onto 3D slicer ](https://discourse.slicer.org/t/issue-loading-nii-files-onto-3d-slicer/4378)

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**Author:** [@rjortiz2](https://discourse.slicer.org/u/rjortiz2)\
**Replies:** 6\
**Last updated:** [February 27, 2019, 10:32pm UTC](https://discourse.slicer.org/t/issue-loading-nii-files-onto-3d-slicer/4378 "2019-02-27T22:32:26Z")

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I am having issue loading/viewing my .nii files onto my computer. \*I was able to view and view my .nii files on itk snap, so it doesn’t seem to be a data problem I loaded some example .nii files that I downloaded onli…

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## [DICOM import contrast problem](https://discourse.slicer.org/t/dicom-import-contrast-problem/22007)

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**Author:** [@AsliBeriL](https://discourse.slicer.org/u/AsliBeriL)\
**Replies:** 7\
**Last updated:** [February 19, 2022, 12:02pm UTC](https://discourse.slicer.org/t/dicom-import-contrast-problem/22007 "2022-02-19T12:02:58Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Dear 3D Slicer experts, I searched for the answer to my question but couldn’t find it. When I add a new patient (MRI stacks), the contrast of the slices looks…

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## [Issues with New Module for Numpy Files](https://discourse.slicer.org/t/issues-with-new-module-for-numpy-files/21840)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 4\
**Last updated:** [February 10, 2022, 9:57am UTC](https://discourse.slicer.org/t/issues-with-new-module-for-numpy-files/21840 "2022-02-10T09:57:44Z")

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Hi, I am trying to work out a new extension that is capable of going into a directory and pulling out all npy or npz files and importing them into 3D slicer as a volume. I am positive that the radio button logic on my co…

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## [Import displacement field from Matlab](https://discourse.slicer.org/t/import-displacement-field-from-matlab/21224)

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**Author:** [@Engineer90](https://discourse.slicer.org/u/Engineer90)\
**Replies:** 2\
**Last updated:** [December 28, 2021, 6:46pm UTC](https://discourse.slicer.org/t/import-displacement-field-from-matlab/21224 "2021-12-28T18:46:49Z")

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Hi everyone. I was wondering if on 3D Slicer it was possible to import a registration matrix that I obtained with Matlab (using an optical flow algorithm), so to apply it to a segment. In my case I have three 512x512x3…

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## [How read the .tag file for landmarks visualization](https://discourse.slicer.org/t/how-read-the-tag-file-for-landmarks-visualization/7487)

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**Author:** [@ljc19800331](https://discourse.slicer.org/u/ljc19800331)\
**Replies:** 3\
**Last updated:** [October 19, 2021, 2:11pm UTC](https://discourse.slicer.org/t/how-read-the-tag-file-for-landmarks-visualization/7487 "2021-10-19T14:11:05Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: Hello, I want to check the fiducial on the ultrasound and MRI data and all the fiducials are saved in a .tag file. Since it is not a common .fcsv …

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