# \#nrrd

**URL:** https://discourse.slicer.org/tag/nrrd/96.md

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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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## [Nrrd vs vtp model coordinate systems in Python](https://discourse.slicer.org/t/nrrd-vs-vtp-model-coordinate-systems-in-python/44323)

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**Author:** [@elisedl1](https://discourse.slicer.org/u/elisedl1)\
**Replies:** 1\
**Last updated:** [September 3, 2025, 4:07am UTC](https://discourse.slicer.org/t/nrrd-vs-vtp-model-coordinate-systems-in-python/44323 "2025-09-03T04:07:24Z")

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Hello, My model (.vtp) and image (.nrrd) align in slicer correctly. I am trying to use the model and image information in Python, but they do not visually align when plotted; they are in different coordinate systems (wo…

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## [\[DICOM to NRRD Converter\] A Python 3 - based script for converting DICOM to nrrd](https://discourse.slicer.org/t/dicom-to-nrrd-converter-a-python-3-based-script-for-converting-dicom-to-nrrd/44005)

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**Author:** [@Unicom](https://discourse.slicer.org/u/Unicom)\
**Replies:** 7\
**Last updated:** [August 13, 2025, 3:20am UTC](https://discourse.slicer.org/t/dicom-to-nrrd-converter-a-python-3-based-script-for-converting-dicom-to-nrrd/44005 "2025-08-13T03:20:12Z")

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\[DICOM to NRRD Converter\] A Python 3 - based script for converting DICOM to nrrd Currently, there are no very good methods or extensions available for efficient loading of large-size DICOM data. Spending some time conver…

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## [Error when saving .nrrd files](https://discourse.slicer.org/t/error-when-saving-nrrd-files/41119)

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**Author:** [@Willa\_Coultley](https://discourse.slicer.org/u/Willa_Coultley)\
**Replies:** 1\
**Last updated:** [January 16, 2025, 9:08pm UTC](https://discourse.slicer.org/t/error-when-saving-nrrd-files/41119 "2025-01-16T21:08:03Z")

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Os - Mac sequoia 15 Slicer version - most current File types - Dicom loaded Expected behavior - saving volume renders in the .nrrd file format Actual behavior - receiving error status only on the volume renders that …

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## [Incorrect volume information when loading .nrrd](https://discourse.slicer.org/t/incorrect-volume-information-when-loading-nrrd/33907)

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**Author:** [@mns.larsson](https://discourse.slicer.org/u/mns.larsson)\
**Replies:** 4\
**Last updated:** [January 23, 2024, 3:37pm UTC](https://discourse.slicer.org/t/incorrect-volume-information-when-loading-nrrd/33907 "2024-01-23T15:37:31Z")

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When I load a .nrrd file I believe the direction matrix under volume information might be incorrect. In my example, the space directions in the .nrrd file is: space directions: (1.99900970198094,0.0716907704748626,-1.35…

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## [Cannot save DICOM to NRRD files](https://discourse.slicer.org/t/cannot-save-dicom-to-nrrd-files/32609)

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**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")

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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…

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## [DICOM to NRRD conversion in command line (for PyRadiomics)](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306)

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**Author:** [@marcin.jakalski](https://discourse.slicer.org/u/marcin.jakalski)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 5:50pm UTC](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306 "2023-10-18T17:50:25Z")

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Hello! I would like to recreate some of the functionality of 3D Slicer in command line for batch analysis of several hundred of patients’ images. I have a set of DICOM images along with their segmentations. For these I w…

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## [Edit the IJK to RAS Matrix in 3D Slicer](https://discourse.slicer.org/t/edit-the-ijk-to-ras-matrix-in-3d-slicer/28129)

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**Author:** [@elrond11](https://discourse.slicer.org/u/elrond11)\
**Replies:** 3\
**Last updated:** [October 12, 2023, 2:47pm UTC](https://discourse.slicer.org/t/edit-the-ijk-to-ras-matrix-in-3d-slicer/28129 "2023-10-12T14:47:33Z")

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I am working on registering two nrrd files. I have noticed that one of the images appears flipped in the x and y direction resulting in inaccurate registration results. The two volumes have different IJK to RAS Matrix. O…

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## [Building the ijk to RAS transform from a nrrd file](https://discourse.slicer.org/t/building-the-ijk-to-ras-transform-from-a-nrrd-file/1513)

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**Author:** [@dcantor](https://discourse.slicer.org/u/dcantor)\
**Replies:** 5\
**Last updated:** [June 27, 2023, 7:17am UTC](https://discourse.slicer.org/t/building-the-ijk-to-ras-transform-from-a-nrrd-file/1513 "2023-06-27T07:17:46Z")

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Hi Slicers, I am working on a project with Slicer generated nrrd files and after looking at the nrrd header I notice there is no info about the ijk to RAS matrix yet when I load that nrrd file into Slicer I obtain the m…

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## [Removing "Closed Surface" from seg.nrrd image header Line: Segmentation\_ContainedRepresentationNames](https://discourse.slicer.org/t/removing-closed-surface-from-seg-nrrd-image-header-line-segmentation-containedrepresentationnames/28987)

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**Author:** [@Joshua\_Binswanger](https://discourse.slicer.org/u/Joshua_Binswanger)\
**Replies:** 1\
**Last updated:** [June 9, 2023, 10:51pm UTC](https://discourse.slicer.org/t/removing-closed-surface-from-seg-nrrd-image-header-line-segmentation-containedrepresentationnames/28987 "2023-06-09T22:51:13Z")

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Removing or giving the option to bypass “Closed Surface” Representation of Segmentations in the image header of seg.nrrd files on the line “Segmentation\_ContainedRepresentationNames” The Corresponding Line in the Header…

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## [Is there any difference between nrrd converted by plastimatch and slicer? What algorithm is used by slicer to convert to nrrd](https://discourse.slicer.org/t/is-there-any-difference-between-nrrd-converted-by-plastimatch-and-slicer-what-algorithm-is-used-by-slicer-to-convert-to-nrrd/29026)

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**Author:** [@b\_s\_umesh\_sherkhane](https://discourse.slicer.org/u/b_s_umesh_sherkhane)\
**Replies:** 6\
**Last updated:** [May 8, 2023, 2:26pm UTC](https://discourse.slicer.org/t/is-there-any-difference-between-nrrd-converted-by-plastimatch-and-slicer-what-algorithm-is-used-by-slicer-to-convert-to-nrrd/29026 "2023-05-08T14:26:14Z")

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Hi , I am trying to extract radiomics from PET dicom. I converted the dicom to nrrd using two methods. using slicer i saved the image and mask to nrrd Using plastimatch i converted the dicom to nrrd. When i run pyrad…

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## [Negative values in nrrd field 'Segmentation\_ReferenceImageExtentOffset' ](https://discourse.slicer.org/t/negative-values-in-nrrd-field-segmentation-referenceimageextentoffset/28931)

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**Author:** [@Megan](https://discourse.slicer.org/u/Megan)\
**Replies:** 1\
**Last updated:** [April 15, 2023, 4:10pm UTC](https://discourse.slicer.org/t/negative-values-in-nrrd-field-segmentation-referenceimageextentoffset/28931 "2023-04-15T16:10:32Z")

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When reading in a .seg.nrrd file in python using pynrrd, I get a negative value in the ‘Segmentation\_ReferenceImageExtentOffset’ field (‘35 86 -1’). Are negative values relative to the end of the volume e.g. work backwa…

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## [How to import markup control points as nodes?](https://discourse.slicer.org/t/how-to-import-markup-control-points-as-nodes/28806)

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**Author:** [@Vathsan](https://discourse.slicer.org/u/Vathsan)\
**Replies:** 3\
**Last updated:** [April 10, 2023, 8:33pm UTC](https://discourse.slicer.org/t/how-to-import-markup-control-points-as-nodes/28806 "2023-04-10T20:33:29Z")

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I’ve exported a set of markup control points as a table (.csv format). When I import the table, the control points do not appear under nodes section of the markup module. I need to apply a set of transformations to these…

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## [Image registration nrrd files appear to be scaled differently despite adjusting scaling](https://discourse.slicer.org/t/image-registration-nrrd-files-appear-to-be-scaled-differently-despite-adjusting-scaling/28512)

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**Author:** [@elrond11](https://discourse.slicer.org/u/elrond11)\
**Replies:** 6\
**Last updated:** [March 22, 2023, 2:59am UTC](https://discourse.slicer.org/t/image-registration-nrrd-files-appear-to-be-scaled-differently-despite-adjusting-scaling/28512 "2023-03-22T02:59:36Z")

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I have been using 3D Slicer for rigid registration of two nrrd volumes. The first is an STL file that I have rasterized into an nrrd file within Slicer, this is the fixed image. The second nrrd file, moving image, has be…

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## [Removing the 4th dimension from NRRD file](https://discourse.slicer.org/t/removing-the-4th-dimension-from-nrrd-file/27362)

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**Author:** [@Senn81](https://discourse.slicer.org/u/Senn81)\
**Replies:** 2\
**Last updated:** [January 19, 2023, 6:58pm UTC](https://discourse.slicer.org/t/removing-the-4th-dimension-from-nrrd-file/27362 "2023-01-19T18:58:14Z")

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Hi Slicer support In some of my segmentations my NRRD files have an extra dimension (4th dimension). This has caused issues with compatibility with certain software loading the file up. Would anyone know how to remove t…

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## [NRRD volume - Save a slice](https://discourse.slicer.org/t/nrrd-volume-save-a-slice/26489)

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**Author:** [@lucas\_sd](https://discourse.slicer.org/u/lucas_sd)\
**Replies:** 5\
**Last updated:** [December 6, 2022, 4:17pm UTC](https://discourse.slicer.org/t/nrrd-volume-save-a-slice/26489 "2022-12-06T16:17:16Z")

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Hi everybody, Im working in a new module and I have a volume NRRD. I need to save just one slice, like \[:,:,Zn\], in a new NRRD volume. Is there a specific command to do this? I need to get the node first? Thanks, Lucas…

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## [Black layers on z-axis](https://discourse.slicer.org/t/black-layers-on-z-axis/26264)

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**Author:** [@hpok](https://discourse.slicer.org/u/hpok)\
**Replies:** 2\
**Last updated:** [December 4, 2022, 11:31am UTC](https://discourse.slicer.org/t/black-layers-on-z-axis/26264 "2022-12-04T11:31:51Z")

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Hello everyone, I would like to ask about importing data into Slicer. I have a sequence of tiffs of cells. I have converted them to nrrd data to use within the Slicer. When I load them in, their almost correct measuremen…

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## [NRRD segmentation file header](https://discourse.slicer.org/t/nrrd-segmentation-file-header/26344)

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**Author:** [@Francesca\_Lo\_Iacono](https://discourse.slicer.org/u/Francesca_Lo_Iacono)\
**Replies:** 1\
**Last updated:** [November 21, 2022, 7:15pm UTC](https://discourse.slicer.org/t/nrrd-segmentation-file-header/26344 "2022-11-21T19:15:28Z")

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Hi! I’m developing an automatic segmentation algorithm on python and I am trying to export obtained segmentations in a .nrrd file. Looking at .nrrd file obtained from Slicer I can see some header I can’t understand how t…

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## [NRRD File Version](https://discourse.slicer.org/t/nrrd-file-version/25245)

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**Author:** [@Michael\_French](https://discourse.slicer.org/u/Michael_French)\
**Replies:** 4\
**Last updated:** [September 14, 2022, 5:42pm UTC](https://discourse.slicer.org/t/nrrd-file-version/25245 "2022-09-14T17:42:13Z")

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With the recent Slicer patch, nrrd files we are exporting are now being exported as NRRD0004, whereas previously they were being exported as NRRD0005. This is causing issues as our application supports NRRD0005 only. Is …

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## [Export transformed 4D image as nifti?](https://discourse.slicer.org/t/export-transformed-4d-image-as-nifti/25032)

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**Author:** [@ch-n](https://discourse.slicer.org/u/ch-n)\
**Replies:** 3\
**Last updated:** [September 1, 2022, 12:54pm UTC](https://discourse.slicer.org/t/export-transformed-4d-image-as-nifti/25032 "2022-09-01T12:54:46Z")

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Hi I would like to apply a bspline transformation I generated with the plastimatch plugin to a 4D image. That works all fine but afterwards I can no longer export the image in nifti format. I need the image for further…

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## [NaN or infinite value in the segment(.nrrd)](https://discourse.slicer.org/t/nan-or-infinite-value-in-the-segment-nrrd/25027)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 0\
**Last updated:** [August 31, 2022, 2:21pm UTC](https://discourse.slicer.org/t/nan-or-infinite-value-in-the-segment-nrrd/25027 "2022-08-31T14:21:59Z")

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Hello, I have been trying to train monailabel from scratch with 10 segmentations I created. I changed the label\_values in following 3 files and changed pretrained to false. Anaconda3\\Lib\\site-packages\\monai\\apps\\deep…

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## [Decomposing 4d nrrd](https://discourse.slicer.org/t/decomposing-4d-nrrd/24722)

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**Author:** [@Deepthy\_Rose\_Jose\_am](https://discourse.slicer.org/u/Deepthy_Rose_Jose_am)\
**Replies:** 0\
**Last updated:** [August 12, 2022, 5:30am UTC](https://discourse.slicer.org/t/decomposing-4d-nrrd/24722 "2022-08-12T05:30:27Z")

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Hello! I wanted to decompose a 4d nrrd file into a sequence of 3d nrrd files with timestamp. Please find the attached image for reference. Looking forward to your inputs

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## [Converting DICOM to NRRD on Docker via a Python script](https://discourse.slicer.org/t/converting-dicom-to-nrrd-on-docker-via-a-python-script/21096)

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**Author:** [@adouv](https://discourse.slicer.org/u/adouv)\
**Replies:** 7\
**Last updated:** [June 3, 2022, 12:18pm UTC](https://discourse.slicer.org/t/converting-dicom-to-nrrd-on-docker-via-a-python-script/21096 "2022-06-03T12:18:11Z")

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Hello, I would like to start off thanking all of you for the great work with 3D Slicer. It is truly a phenomenal piece of software! The issue we are having requires some description, so I will split this question into tw…

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## [The saved segmentation file size is different from the original volume nrrd file size](https://discourse.slicer.org/t/the-saved-segmentation-file-size-is-different-from-the-original-volume-nrrd-file-size/23644)

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**Author:** [@parijat\_patel](https://discourse.slicer.org/u/parijat_patel)\
**Replies:** 4\
**Last updated:** [May 31, 2022, 10:17am UTC](https://discourse.slicer.org/t/the-saved-segmentation-file-size-is-different-from-the-original-volume-nrrd-file-size/23644 "2022-05-31T10:17:12Z")

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Hello, I am using Slicer-4.11.20210226-linux-amd64 to create segmentations data to train a segmentation algorithm to automatically segment the fat depots in CT scan. The dimensions of the saved 3D segmentation file (rows…

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## [In NRDD file format, CBCT scan of any skull](https://discourse.slicer.org/t/in-nrdd-file-format-cbct-scan-of-any-skull/23332)

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**Author:** [@Fatih\_Hamircu](https://discourse.slicer.org/u/Fatih_Hamircu)\
**Replies:** 4\
**Last updated:** [May 10, 2022, 4:46am UTC](https://discourse.slicer.org/t/in-nrdd-file-format-cbct-scan-of-any-skull/23332 "2022-05-10T04:46:54Z")

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I want a clean cbct scan of a skull to do segmentation on it and find out more about the 3dslicer (I am beginner). Where can I find it?

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## [FSL transfer to nrrd have no output file](https://discourse.slicer.org/t/fsl-transfer-to-nrrd-have-no-output-file/22412)

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**Author:** [@talelee](https://discourse.slicer.org/u/talelee)\
**Replies:** 0\
**Last updated:** [March 9, 2022, 2:51pm UTC](https://discourse.slicer.org/t/fsl-transfer-to-nrrd-have-no-output-file/22412 "2022-03-09T14:51:01Z")

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The only hint in my dialog box Diffusion-weighted DICOM Import (DWIConvert) standard output: ======= DWI Convert Tool Program========= INPUT VOLUME: /home/lee/100417/data/data.nii.gz

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## [what thing do I miss to create volume sequence from tiff](https://discourse.slicer.org/t/what-thing-do-i-miss-to-create-volume-sequence-from-tiff/20039)

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**Author:** [@BingYen](https://discourse.slicer.org/u/BingYen)\
**Replies:** 5\
**Last updated:** [October 9, 2021, 7:49pm UTC](https://discourse.slicer.org/t/what-thing-do-i-miss-to-create-volume-sequence-from-tiff/20039 "2021-10-09T19:49:26Z")

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Hi, I’m new to Slicer and Python I want to load 512x512x619x9 uint16 data from microscopy into Slicer as volume sequence data. First, I save ome.tiff as nrrd (C2withmeta.nrrd) via Fiji after I checked the properties. …

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## [Read NRRD detached headers that omit blank line](https://discourse.slicer.org/t/read-nrrd-detached-headers-that-omit-blank-line/19393)

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**Author:** [@Chris\_Rorden](https://discourse.slicer.org/u/Chris_Rorden)\
**Replies:** 1\
**Last updated:** [August 31, 2021, 7:07pm UTC](https://discourse.slicer.org/t/read-nrrd-detached-headers-that-omit-blank-line/19393 "2021-08-31T19:07:34Z")

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I have a feature request to allow Slicer to detect NRRD detached headers where the user omits the trailing blank line. Tested on Slicer 4.13.0-2021-08-24 r30133 / 5af0a09 The NRRD format specification clearly states Aft…

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## [Hdf5 to NRRD to SEQ.NRRD](https://discourse.slicer.org/t/hdf5-to-nrrd-to-seq-nrrd/18277)

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**Author:** [@Jamal\_K](https://discourse.slicer.org/u/Jamal_K)\
**Replies:** 3\
**Last updated:** [June 25, 2021, 10:23pm UTC](https://discourse.slicer.org/t/hdf5-to-nrrd-to-seq-nrrd/18277 "2021-06-25T22:23:02Z")

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I have an hdf5 4D Volume rendering with 1 dimension begin time. I transformed this file using python into an NRRD for Slicer to read it. I then added the ‘seq’ label to the file as mentioned here (Documentation/4.10/Exte…

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## [Issue with Mesh to Label Map](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875)

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**Author:** [@quan](https://discourse.slicer.org/u/quan)\
**Replies:** 2\
**Last updated:** [June 1, 2021, 5:18am UTC](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875 "2021-06-01T05:18:30Z")

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I’m trying to generate a SPHARM-PDM mesh from a .stl file. I imported the .stl and used “Mesh to Label Map” to obtain the .nrrd. However, the .nrrd is inverted (the white space are supposed to be black and vice versa). T…

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