# \#nifti

**URL:** https://discourse.slicer.org/tag/nifti/36.md

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

---

## [Multiple organs segmentation in a MRI sequence?](https://discourse.slicer.org/t/multiple-organs-segmentation-in-a-mri-sequence/46699)

<div class="topic-metadata">

**Author:** [@koperkill](https://discourse.slicer.org/u/koperkill)\
**Replies:** 0\
**Last updated:** [April 9, 2026, 1:36pm UTC](https://discourse.slicer.org/t/multiple-organs-segmentation-in-a-mri-sequence/46699 "2026-04-09T13:36:47Z")

</div>

Hello, For a DCE-MRI study, I would like to extract the signal intensity, through time, for a dozen organs and regions of the upper body. I have successfully built a time sequence using my 40 volumes in time, drawn a s…

---

## [Reproducing Nifti metadata](https://discourse.slicer.org/t/reproducing-nifti-metadata/46105)

<div class="topic-metadata">

**Author:** [@Yaroslav\_Plutenko](https://discourse.slicer.org/u/Yaroslav_Plutenko)\
**Replies:** 10\
**Last updated:** [February 20, 2026, 11:12am UTC](https://discourse.slicer.org/t/reproducing-nifti-metadata/46105 "2026-02-20T11:12:07Z")

</div>

Greetings! I have a question regarding Nifti format circulation. I’m developing a plugin that interacts with a remote repository and can upload/download images and whole datasets (viewing and fixing labels on the way if…

---

## [2D cine not playing when converted to nifti from dicom](https://discourse.slicer.org/t/2d-cine-not-playing-when-converted-to-nifti-from-dicom/45555)

<div class="topic-metadata">

**Author:** [@Nshehata](https://discourse.slicer.org/u/Nshehata)\
**Replies:** 0\
**Last updated:** [December 19, 2025, 12:48pm UTC](https://discourse.slicer.org/t/2d-cine-not-playing-when-converted-to-nifti-from-dicom/45555 "2025-12-19T12:48:40Z")

</div>

Operating system: Linux also MacOS Slicer version: 5.8.1 Expected behavior: Play button to be enabled when importing as DICOM Actual behavior: Play button disabled and fixed on one slice only I thought maybe the prob…

---

## [How to align NIfTI files with original DICOM files?](https://discourse.slicer.org/t/how-to-align-nifti-files-with-original-dicom-files/41107)

<div class="topic-metadata">

**Author:** [@oi\_o](https://discourse.slicer.org/u/oi_o)\
**Replies:** 4\
**Last updated:** [January 20, 2025, 4:49am UTC](https://discourse.slicer.org/t/how-to-align-nifti-files-with-original-dicom-files/41107 "2025-01-20T04:49:35Z")

</div>

I encountered an issue while trying to align NIfTI files (segmentation results from TotalSegmentator) with the original DICOM files in Jupyter Notebook. Despite my efforts to construct an appropriate affine matrix for th…

---

## [how to open a Dataset of 2D xrays in PNG format ? ](https://discourse.slicer.org/t/how-to-open-a-dataset-of-2d-xrays-in-png-format/41066)

<div class="topic-metadata">

**Author:** [@rihabu](https://discourse.slicer.org/u/rihabu)\
**Replies:** 0\
**Last updated:** [January 14, 2025, 12:56am UTC](https://discourse.slicer.org/t/how-to-open-a-dataset-of-2d-xrays-in-png-format/41066 "2025-01-14T00:56:02Z")

</div>

hello , i have a dataset of spine xrays (2D) in PNG format , i want to annotate them using 3d slicer and monai label , but i cant load the image in i found that converting tthe dataset to nifti .nii might be a solution …

---

## [Smoothen NIFTI file](https://discourse.slicer.org/t/smoothen-nifti-file/40281)

<div class="topic-metadata">

**Author:** [@Amine\_MK](https://discourse.slicer.org/u/Amine_MK)\
**Replies:** 1\
**Last updated:** [November 20, 2024, 9:52pm UTC](https://discourse.slicer.org/t/smoothen-nifti-file/40281 "2024-11-20T21:52:22Z")

</div>

Hello I noticed that when we open a NIFTI file in Slicer, it automatically applies a transformation to the mesh and make it smooth. I would like to know if we can access this feature through Python code? And what is the…

---

## [How to export data from Slicer to LifeX?](https://discourse.slicer.org/t/how-to-export-data-from-slicer-to-lifex/40210)

<div class="topic-metadata">

**Author:** [@Ann\_Jacob](https://discourse.slicer.org/u/Ann_Jacob)\
**Replies:** 3\
**Last updated:** [November 18, 2024, 3:19pm UTC](https://discourse.slicer.org/t/how-to-export-data-from-slicer-to-lifex/40210 "2024-11-18T15:19:19Z")

</div>

Hello, I need to export brain ROIs from Slicer and then use them in LifeX. However, something goes wrong and LifeX doesn’t display the ROIs, on top of flashing the “Inconsistent ROI size” warning. Both images (patient …

---

## [Instensity Reduction on Obtured Dental CT](https://discourse.slicer.org/t/instensity-reduction-on-obtured-dental-ct/39749)

<div class="topic-metadata">

**Author:** [@Marcellofabrizio](https://discourse.slicer.org/u/Marcellofabrizio)\
**Replies:** 0\
**Last updated:** [October 17, 2024, 11:14pm UTC](https://discourse.slicer.org/t/instensity-reduction-on-obtured-dental-ct/39749 "2024-10-17T23:14:41Z")

</div>

Hello all! I’m researching the segmentation and canal-type classification for the second mesial-buccal canal. My dataset consists of NIfTI files containing the teeth I want to classify. Some of these canals are obturate…

---

## [TI1 module for T1 map](https://discourse.slicer.org/t/ti1-module-for-t1-map/35756)

<div class="topic-metadata">

**Author:** [@abarat21](https://discourse.slicer.org/u/abarat21)\
**Replies:** 0\
**Last updated:** [April 26, 2024, 5:56pm UTC](https://discourse.slicer.org/t/ti1-module-for-t1-map/35756 "2024-04-26T17:56:35Z")

</div>

I have a T1 map file that I have loaded into Slicer. I want to create a simple module that has a TI1 slider that the user slides to change the TI value of the T1 map using the equation 1 - 2 exp(-TI / Tone), and that ou…

---

## [Module for manual segmentation (MONAI Label-like)](https://discourse.slicer.org/t/module-for-manual-segmentation-monai-label-like/35420)

<div class="topic-metadata">

**Author:** [@nicola-dallosto](https://discourse.slicer.org/u/nicola-dallosto)\
**Replies:** 2\
**Last updated:** [April 11, 2024, 4:30pm UTC](https://discourse.slicer.org/t/module-for-manual-segmentation-monai-label-like/35420 "2024-04-11T16:30:33Z")

</div>

I need to create a module to segment nifti images. My idea was to recreate the settings panel of MONAI Label (see screenshot) because it consent to connect to a server and there is a button to save the annotation and a b…

---

## [DICOM metadata transfer](https://discourse.slicer.org/t/dicom-metadata-transfer/35207)

<div class="topic-metadata">

**Author:** [@Bahram\_Zargar](https://discourse.slicer.org/u/Bahram_Zargar)\
**Replies:** 3\
**Last updated:** [April 1, 2024, 9:05pm UTC](https://discourse.slicer.org/t/dicom-metadata-transfer/35207 "2024-04-01T21:05:04Z")

</div>

Hi Slicer team! I wish to export the Dicom mri as a new file after segmenting it, however the new series of DICOMs lacks many of the original DICOm files’ tags. Is it possible to move the metadata from one series of the…

---

## [Merging masks of nifti format and assigning conductivities to each](https://discourse.slicer.org/t/merging-masks-of-nifti-format-and-assigning-conductivities-to-each/34401)

<div class="topic-metadata">

**Author:** [@savvy73](https://discourse.slicer.org/u/savvy73)\
**Replies:** 3\
**Last updated:** [February 21, 2024, 3:17am UTC](https://discourse.slicer.org/t/merging-masks-of-nifti-format-and-assigning-conductivities-to-each/34401 "2024-02-21T03:17:44Z")

</div>

Hi, I have masks of different regions of brain in niftii format. I want to combine all the masks and assign conductivities to the same after which I need to mesh the output. I wanted to know if it can be done using 3D sl…

---

## [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)

<div class="topic-metadata">

**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")

</div>

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…

---

## [The dark slice problem in the Nifti formant?](https://discourse.slicer.org/t/the-dark-slice-problem-in-the-nifti-formant/32688)

<div class="topic-metadata">

**Author:** [@Berk\_Gezgin](https://discourse.slicer.org/u/Berk_Gezgin)\
**Replies:** 0\
**Last updated:** [November 9, 2023, 6:10am UTC](https://discourse.slicer.org/t/the-dark-slice-problem-in-the-nifti-formant/32688 "2023-11-09T06:10:07Z")

</div>

Hello everyone, first of all. I am dealing with a cbct image in nii.gz format. This image has a filling in one tooth. When I save these slices in png format, I get a dark image. However, other slices turn into png forma…

---

## [Export segmentation with multiple labels as nifti doesn't work](https://discourse.slicer.org/t/export-segmentation-with-multiple-labels-as-nifti-doesnt-work/32677)

<div class="topic-metadata">

**Author:** [@lvdw](https://discourse.slicer.org/u/lvdw)\
**Replies:** 3\
**Last updated:** [November 8, 2023, 5:08pm UTC](https://discourse.slicer.org/t/export-segmentation-with-multiple-labels-as-nifti-doesnt-work/32677 "2023-11-08T17:08:02Z")

</div>

Hi, System: Linux Ubuntu Slicer: 5.2.2 Input: nifti (both source volume and segmentation map) So I have some sort of lesion map (nifti) I want to edit. This lesion map consists of non-overlapping segmentations rangin…

---

## [Loosing 4th dimension after segmentation ](https://discourse.slicer.org/t/loosing-4th-dimension-after-segmentation/29881)

<div class="topic-metadata">

**Author:** [@chopraamhk](https://discourse.slicer.org/u/chopraamhk)\
**Replies:** 4\
**Last updated:** [June 12, 2023, 2:13pm UTC](https://discourse.slicer.org/t/loosing-4th-dimension-after-segmentation/29881 "2023-06-12T14:13:58Z")

</div>

Hi, My original nifti file is having 4dimensions , i.e., ( 196, 240, 100, 1). I have done segmentation in 3d slicer using 2 labels, and after saving the segmented file, it is giving me output as 3d. My new dimensions ar…

---

## [Shifted ROIs (exported from LifeX)](https://discourse.slicer.org/t/shifted-rois-exported-from-lifex/29333)

<div class="topic-metadata">

**Author:** [@leoraffy](https://discourse.slicer.org/u/leoraffy)\
**Replies:** 2\
**Last updated:** [May 10, 2023, 4:12pm UTC](https://discourse.slicer.org/t/shifted-rois-exported-from-lifex/29333 "2023-05-10T16:12:31Z")

</div>

Hi, I am working on a project which requires me to perform radiomics analysis on 3DSlicer on ROIs exported from LifeX. Every ROI exported from LifeX is shifted compared to the PET series when I open it on 3D Slicer, eve…

---

## [Are G and Y channels infered?](https://discourse.slicer.org/t/are-g-and-y-channels-infered/29027)

<div class="topic-metadata">

**Author:** [@Ilias\_P](https://discourse.slicer.org/u/Ilias_P)\
**Replies:** 1\
**Last updated:** [April 20, 2023, 11:50am UTC](https://discourse.slicer.org/t/are-g-and-y-channels-infered/29027 "2023-04-20T11:50:58Z")

</div>

I have some nii.gz files which, when I open using imajeJ , or any python library such as SimpleITK or Monai I get a stack of MRI images, as if taken from top to bottom. That being said, when I open the same file with sli…

---

## [Change data type for nifti export of SEG](https://discourse.slicer.org/t/change-data-type-for-nifti-export-of-seg/27549)

<div class="topic-metadata">

**Author:** [@alireza](https://discourse.slicer.org/u/alireza)\
**Replies:** 1\
**Last updated:** [January 31, 2023, 11:05am UTC](https://discourse.slicer.org/t/change-data-type-for-nifti-export-of-seg/27549 "2023-01-31T11:05:50Z")

</div>

Hi, thanks in advance Is nifti export of Segmentations in 3D Slicer, Nifti2? or Nifti1? Seems like 3D Slicer uses signed short (16 bit) for data type of the exported nifti. Is it possible to force it to use unsigned ch…

---

## [Add a user warning prompt when NIfTI imported as a segment is not a binary mask](https://discourse.slicer.org/t/add-a-user-warning-prompt-when-nifti-imported-as-a-segment-is-not-a-binary-mask/27298)

<div class="topic-metadata">

**Author:** [@mikbuch](https://discourse.slicer.org/u/mikbuch)\
**Replies:** 0\
**Last updated:** [January 17, 2023, 1:34pm UTC](https://discourse.slicer.org/t/add-a-user-warning-prompt-when-nifti-imported-as-a-segment-is-not-a-binary-mask/27298 "2023-01-17T13:34:38Z")

</div>

Hi, I struggled a bit with importing NIfTI images as a segment (“Segmentation”) to the Slicer. It took ma a while to realize that the image I was trying to import was not a binary mask (0s and 1s), but a probability map…

---

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

<div class="topic-metadata">

**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")

</div>

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…

---

## [2D nifti sagittal slice won't open in 3DSlicer](https://discourse.slicer.org/t/2d-nifti-sagittal-slice-wont-open-in-3dslicer/24407)

<div class="topic-metadata">

**Author:** [@BayesMonk](https://discourse.slicer.org/u/BayesMonk)\
**Replies:** 8\
**Last updated:** [July 21, 2022, 8:16am UTC](https://discourse.slicer.org/t/2d-nifti-sagittal-slice-wont-open-in-3dslicer/24407 "2022-07-21T08:16:37Z")

</div>

Hi, I have a 2D sagittal slice stored in Nifti. It won’t open in slicer and I get the following error: Exception thrown in event: D:\\D\\S\\Slicer-1-build\\ITK\\Modules\\Core\\Common\\include\\itkImageBase.hxx:184: itk::ERROR…

---

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

<div class="topic-metadata">

**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")

</div>

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…

---

## [Create DICOM series using python](https://discourse.slicer.org/t/create-dicom-series-using-python/22871)

<div class="topic-metadata">

**Author:** [@Shambhavi\_Malik](https://discourse.slicer.org/u/Shambhavi_Malik)\
**Replies:** 3\
**Last updated:** [April 9, 2022, 12:22pm UTC](https://discourse.slicer.org/t/create-dicom-series-using-python/22871 "2022-04-09T12:22:38Z")

</div>

I have nifti (.nii.gz) scalar volumes and I wanted to convert them into DICOM format and extract information from the metadata (IOP and IPP). I had done this manually using the 3D Slicer GUI. As there are multiple nifti …

---

## [Dose Volume Histogram Plotting issue](https://discourse.slicer.org/t/dose-volume-histogram-plotting-issue/22781)

<div class="topic-metadata">

**Author:** [@Js165](https://discourse.slicer.org/u/Js165)\
**Replies:** 10\
**Last updated:** [March 31, 2022, 11:07pm UTC](https://discourse.slicer.org/t/dose-volume-histogram-plotting-issue/22781 "2022-03-31T23:07:35Z")

</div>

Hi, I am trying to plot a dose-volume histogram (DVH) graph using SlicerRT. I have a segmentation file in NIFTI format and a dose file in DICOM format. I am uploading the segmentation file as “segmentation” and the dose…

---

## [How to segment one/more organs using 3DSlicer and add to the existing segmentation file?](https://discourse.slicer.org/t/how-to-segment-one-more-organs-using-3dslicer-and-add-to-the-existing-segmentation-file/22444)

<div class="topic-metadata">

**Author:** [@Js165](https://discourse.slicer.org/u/Js165)\
**Replies:** 2\
**Last updated:** [March 11, 2022, 6:47pm UTC](https://discourse.slicer.org/t/how-to-segment-one-more-organs-using-3dslicer-and-add-to-the-existing-segmentation-file/22444 "2022-03-11T18:47:43Z")

</div>

I have original CT scans (.nii format) and a corresponding segmentation file (.nii format). Now I want to manually segment one/more organs using 3DSlicer and add to the existing segmentation file (.nii format). I am not …

---

## [Problem about pixel value shift and orientation and origin between nifti and converted dicom series](https://discourse.slicer.org/t/problem-about-pixel-value-shift-and-orientation-and-origin-between-nifti-and-converted-dicom-series/22103)

<div class="topic-metadata">

**Author:** [@Liu\_Lance](https://discourse.slicer.org/u/Liu_Lance)\
**Replies:** 4\
**Last updated:** [February 24, 2022, 3:47pm UTC](https://discourse.slicer.org/t/problem-about-pixel-value-shift-and-orientation-and-origin-between-nifti-and-converted-dicom-series/22103 "2022-02-24T15:47:38Z")

</div>

Hello, I was trying to convert the nifti data to the dicom series. I figure out myself how to use the GUI of 3d slicer to export the loaded volume to dicom series. However, there are some problems in the output. 1. the…

---

## [How to save brain structural edited masks (segment edited) in nifti for freesurfer use?](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429)

<div class="topic-metadata">

**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:04am UTC](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429 "2021-07-02T04:04:46Z")

</div>

Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some editing, and I used Slicer Segment Editor for it (opened mask as label \> imported labelmap as segmentation \> …

---

## [Nifti to DICOM-RT structure conversion](https://discourse.slicer.org/t/nifti-to-dicom-rt-structure-conversion/17919)

<div class="topic-metadata">

**Author:** [@laura.gelcano](https://discourse.slicer.org/u/laura.gelcano)\
**Replies:** 3\
**Last updated:** [June 4, 2021, 4:02pm UTC](https://discourse.slicer.org/t/nifti-to-dicom-rt-structure-conversion/17919 "2021-06-04T16:02:42Z")

</div>

Operating system: Windows 10 Slicer version: Slicer 4.11.20200930 Hi all, I have a binary mask in a Nifti file and I want to convert it into a DicomRT structure. I have tried 3D Slicer to perform this conversion using…

---

## [Converting Segmentation to Volume automatically w/ Python or Matlab](https://discourse.slicer.org/t/converting-segmentation-to-volume-automatically-w-python-or-matlab/16829)

<div class="topic-metadata">

**Author:** [@Hball99](https://discourse.slicer.org/u/Hball99)\
**Replies:** 1\
**Last updated:** [April 3, 2021, 2:50am UTC](https://discourse.slicer.org/t/converting-segmentation-to-volume-automatically-w-python-or-matlab/16829 "2021-04-03T02:50:04Z")

</div>

Hello there! I have 200+ CT-Volumes with matching segmentations. The Volumes are in .nrrd format and the segmentations are in seg.nrrd format. I need both of those as .nii.gz format and I want to script the conversion fr…

[Next page](https://discourse.slicer.org/tag/nifti/36.md?match_all_tags=true&page=1&tags%5B%5D=nifti)