# \#nifti

**URL:** https://discourse.itk.org/tag/nifti/26.md

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

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## [Non axis aligned orientation in real world data?](https://discourse.itk.org/t/non-axis-aligned-orientation-in-real-world-data/6639)

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**Author:** [@Jakub\_Mitura](https://discourse.itk.org/u/Jakub_Mitura)\
**Replies:** 6\
**Last updated:** [May 21, 2024, 7:26pm UTC](https://discourse.itk.org/t/non-axis-aligned-orientation-in-real-world-data/6639 "2024-05-21T19:26:01Z")

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Hello from your experience is it happening that direction cosine matrix is not axis aligned for studies like CT PET MRI . I mean when orientation is not RAS or LPS … can not be summarized in 3 letter code because it is o…

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## [Checking simpleitk.Image Equality](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 5\
**Last updated:** [November 29, 2023, 3:37pm UTC](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323 "2023-11-29T15:37:19Z")

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Hi! I have two methods to the same task. I’d like to check, whether the result of the two methods gives equal outcomes. The files are nifti Images. I can check if their numpy part is the same easily: output1=sitk.Read…

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## [Add empty slice at the end of the CT image](https://discourse.itk.org/t/add-empty-slice-at-the-end-of-the-ct-image/6182)

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**Author:** [@agatadefr](https://discourse.itk.org/u/agatadefr)\
**Replies:** 3\
**Last updated:** [September 7, 2023, 12:30pm UTC](https://discourse.itk.org/t/add-empty-slice-at-the-end-of-the-ct-image/6182 "2023-09-07T12:30:17Z")

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Hello, I have a simple question. i need to resize CT scan saved in nifty file. I need to add one black slice at the end of the 3D image (in Z direction). I would appreciate for any help/suggestion. How can I do that i…

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## [Problem in image and its mask superposition](https://discourse.itk.org/t/problem-in-image-and-its-mask-superposition/5867)

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**Author:** [@Sunita\_Patel](https://discourse.itk.org/u/Sunita_Patel)\
**Replies:** 3\
**Last updated:** [April 14, 2023, 8:52am UTC](https://discourse.itk.org/t/problem-in-image-and-its-mask-superposition/5867 "2023-04-14T08:52:16Z")

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Dear SITK team, We are trying to generate image and its mask from RTStruct file. The dimension of the image is: 256 256 216 The dimension of the mask is: 256 256 216 While visualizing we observed that mask is not sup…

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## [Simple region-growing segmentation of the small intestine is terrible, using many seed points and 3D T2 MRI data](https://discourse.itk.org/t/simple-region-growing-segmentation-of-the-small-intestine-is-terrible-using-many-seed-points-and-3d-t2-mri-data/4942)

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**Author:** [@aliabidi](https://discourse.itk.org/u/aliabidi)\
**Replies:** 8\
**Last updated:** [April 28, 2022, 4:55pm UTC](https://discourse.itk.org/t/simple-region-growing-segmentation-of-the-small-intestine-is-terrible-using-many-seed-points-and-3d-t2-mri-data/4942 "2022-04-28T16:55:15Z")

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I am currently trying to apply region growing to 3D T2 MRI scans which I have been given, to segment the end of the small intenstine (i.e. the terminal ileum). I am using several features from SimpleITK. The problem is, …

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## [nifti to dicom conversion introduces negative intensities](https://discourse.itk.org/t/nifti-to-dicom-conversion-introduces-negative-intensities/4798)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 23\
**Last updated:** [February 20, 2022, 5:06pm UTC](https://discourse.itk.org/t/nifti-to-dicom-conversion-introduces-negative-intensities/4798 "2022-02-20T17:06:56Z")

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Hello everyone! When I try to convert a nifti file to a dicom series with ImageSeriesWriter, I encounter weird behavior when inspecting the results with ITK-SNAP. For a few cases the intensity range shifts from only pos…

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## [How can I generate and save volume rendered images of brain arteries](https://discourse.itk.org/t/how-can-i-generate-and-save-volume-rendered-images-of-brain-arteries/4575)

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**Author:** [@Aleena\_Suhail](https://discourse.itk.org/u/Aleena_Suhail)\
**Replies:** 9\
**Last updated:** [November 16, 2021, 2:04pm UTC](https://discourse.itk.org/t/how-can-i-generate-and-save-volume-rendered-images-of-brain-arteries/4575 "2021-11-16T14:04:18Z")

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how can I generate and save images that are in nii (nifti) format into volume rendered image using simpleITK

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## [Interpolate a given point from nifti DVF image volume](https://discourse.itk.org/t/interpolate-a-given-point-from-nifti-dvf-image-volume/4543)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 7\
**Last updated:** [November 9, 2021, 2:19pm UTC](https://discourse.itk.org/t/interpolate-a-given-point-from-nifti-dvf-image-volume/4543 "2021-11-09T14:19:09Z")

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I have extracted a mesh points from a given nifti image which has a dimension of (203, 127, 161). Additionally, I have a deformation vector field as an another nifti file which is generated using the aforementioned 3D n…

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## [MIP](https://discourse.itk.org/t/mip/4521)

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**Author:** [@Aleena\_Suhail](https://discourse.itk.org/u/Aleena_Suhail)\
**Replies:** 11\
**Last updated:** [October 25, 2021, 9:29pm UTC](https://discourse.itk.org/t/mip/4521 "2021-10-25T21:29:46Z")

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Hi I am trying to generate MIP for 3d brain mra images for aneurysm detection however I am struggling with which libraries to use and how to achieve this with python code

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## [NIfTI-1 or NIfTI-2 Data format](https://discourse.itk.org/t/nifti-1-or-nifti-2-data-format/4330)

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**Author:** [@Iryna\_Galytska](https://discourse.itk.org/u/Iryna_Galytska)\
**Replies:** 4\
**Last updated:** [August 16, 2021, 8:08am UTC](https://discourse.itk.org/t/nifti-1-or-nifti-2-data-format/4330 "2021-08-16T08:08:00Z")

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Could you please advise which data format is used when saving image file e.g. with GetImageFromArray(voxel\_buffer) and ImageFileWriter() NIfTI-1 or NIfTI-2 ? is there posibility to specify explicitly data format (NIfTI-1…

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## [3D niigz Affine Registration](https://discourse.itk.org/t/3d-niigz-affine-registration/4007)

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**Author:** [@qxs](https://discourse.itk.org/u/qxs)\
**Replies:** 3\
**Last updated:** [August 5, 2021, 9:32am UTC](https://discourse.itk.org/t/3d-niigz-affine-registration/4007 "2021-08-05T09:32:33Z")

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Hello All, I have some 3D CT brain images in nii.gz format. I would like to use one image as fixed image and another as moving image. I also have some blood vessels in vtk format in Image Coordinate System and in World…

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## [Nifti: ImageFileReader + ImageFileWriter changes orientation matrix](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064)

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**Author:** [@crossmanith](https://discourse.itk.org/u/crossmanith)\
**Replies:** 3\
**Last updated:** [April 26, 2021, 12:48pm UTC](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064 "2021-04-26T12:48:22Z")

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Hi, I’m reading a Nifti File and writing it back without applying any other filter: using ReaderType = itk::ImageFileReader; ReaderType::Pointer in=ReaderType::New(); in-\>SetFileName( ifname ); in-\>Update(); using …

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## [2D multiplanar (sagittal) from cross sequence](https://discourse.itk.org/t/2d-multiplanar-sagittal-from-cross-sequence/3861)

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**Author:** [@AmericaBG](https://discourse.itk.org/u/AmericaBG)\
**Replies:** 12\
**Last updated:** [February 16, 2021, 3:20pm UTC](https://discourse.itk.org/t/2d-multiplanar-sagittal-from-cross-sequence/3861 "2021-02-16T15:20:33Z")

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Hi! There goes my problem: I want to obtain 2D sagittal slices from a 3D volume composed of cross images. So far so good. My problem arrives when I want to resample/reform this sagittal images with a STIR sequence fro…

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## [Direction/Orientation matrix DICOM vs Nifti](https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289)

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**Author:** [@rcorredorj](https://discourse.itk.org/u/rcorredorj)\
**Replies:** 5\
**Last updated:** [July 16, 2020, 3:41pm UTC](https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289 "2020-07-16T15:41:50Z")

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Hi everyone, I’m having discrepancies between the orientation matrix read from DICOMs or from a Nifti generated from the same DICOM series. I’d like to understand what is going on. I have a DICOM series that I read in …

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## [Using SimpleITK to Convert Dicom to Nifiti With Misleading Series Tags](https://discourse.itk.org/t/using-simpleitk-to-convert-dicom-to-nifiti-with-misleading-series-tags/679)

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**Author:** [@bsmarine](https://discourse.itk.org/u/bsmarine)\
**Replies:** 18\
**Last updated:** [January 17, 2019, 6:57pm UTC](https://discourse.itk.org/t/using-simpleitk-to-convert-dicom-to-nifiti-with-misleading-series-tags/679 "2019-01-17T18:57:10Z")

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Hi All, I’m trying to convert a CT abdomen triple-phase dicom data folder into nifti 3D data by series. The approach I’m using is below and works great, BUT for some of the data the slices are not in the correct order d…

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## [NIFTI Orientation Issues](https://discourse.itk.org/t/nifti-orientation-issues/431)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 13\
**Last updated:** [December 12, 2017, 1:58am UTC](https://discourse.itk.org/t/nifti-orientation-issues/431 "2017-12-12T01:58:58Z")

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Hello, I am having trouble with NIFTI orientations (again). I am using the Bruker reader I contributed to read in a 2dseq file and then save to NIFTI. When I then read that file with FSL or nibabel, the orientation come…