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Questions tagged [nifti]

A data format used in biomedical imaging, proposed by the Neuroimaging Informatics Technology Initiative.

It can be used to represent the 2 current formats, NIfTI-1 or NIfTI-2, as well as the organization behind it, the Neuroimaging Informatics Technology Initiative.

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Medical Imaging Data - how to convert .raw/mhd to Nifti/nii

Is there a way in Python or any other language to convert .raw/mhd image data to Nifti/nii? I can load the .raw/mhd file in python via SimpleITK as in this post: Reading *.mhd/*.raw format in python import skimage.io as io img =…
user844597
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How to read Nifti(.nii) files stored in HDFS with pyspark?

I'm trying to make a model to train with images of nii format.I could read files from local filesystem with nibabel library But I dont find any proper library to read nii files from hdfs using pyspark. I also tried to read using spark binary. None…
Jayakrishnan U
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How to open a binary file in my case .nii file using node.js

I want to open a binary file, or at least when I try to open this with the vscode editor, is say that, can't be opened, because is a binary file. Can someone explain to me what I can do in order to open this type of files and read the content? About…
George C.
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How can I Loop Through 3D NIFTI Image in Python

For a project I am doing, I want to write a script that can calculate the total brain volume of an MRI image in the nifti format (.nii extension). What I don't know how to do is loop through all the individual voxels and extract the integer data…
arnavlohe15
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How to convert nii slices to a squence？

I have a file in format of nii.gz with 20 slices. But there are some problem that I just need the top 13 slices. So I use the load_nii or simpleITK to get the array of the 20 silces. What I want to do is just use the top 13 slices(now is array) to…
Salmon
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convert list of img/hdr file to nifti1image in python

I have list of img/hdr file. Suppose that length of list is 50 and size of img is 60*60*60. I would like to convert it to Nifti1image whose size is (60*60*60*50). import nibabel import nipy img_list=[] for file in os.listdir(path): if…
kyabaria
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How to do affine transformation for nifti image?

When i use niftiinfo for extracting the information of nifti image I got the following error.Is it possible to do affine transformation so that niftiinfo works properly info = niftiinfo('Subject01.nii'); Error using affine3d/set.T (line 340) …
user3217708
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What is the format of the values in the img matrix given by load_untouch_nii in MATLAB?

I am working with MRI scans in NIFTI (.nii) format using MATLAB. My code is the following: pha_nii=load_untouch_nii(filename_unzip_pha); Where filename_unzip_pha is the name of a raw phase MRI scan in .nii format. According to documentation,…
C.P.
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Nrrd to Nifti file conversion

I am looking to convert ~1000 .nrrd files into Nifit (.nii.gz) format. I've been using 3DSlicer's ResampleScalarVectorDWIVolume command-line module to accomplish this task. But this process is really slow. It takes ~4 minutes to convert each file on…
avi.ks
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how to save images in png using MITK

Hi i am uisng MITK Workbench 2016.11.0. I want to save image in PNG or JPEG or TIFF using MITK. But there are only 5 options available: NRRD, NIFTI, VTK, VTK LEGACY IMAGE.
Hitesh
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Copy one Nifti header to another

I have a 'prob_map' variable in matlab ( a probability map) which I want to save it in '.nii' format. I did it by 2 lines code: nii = make_nii(prob_map); save_nii(nii,'prob.nii'); This is done successfully however the header info is not…
patric
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Is it possible to apply an arbitrary transformation matrix to an image in SPM?

I have a somewhat specific task I'd like to do in SPM. Basically, I have some input NII file scan.nii and I would like to apply an arbitrary affine transformation to it, defined by x y z p r yw. x,y,z,p,r,yw represent the translations and rotations…
Karl
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Calculate peak height of histogram in R

I'm trying to extract some metrics from an histogram in R. For that I have an image in nifti and I plot the correspondent histogram. After that I want to extract mean, median, peak height, peak value and peak width. For that I have the following…
anaF
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ITK-SNAP segmentation displays same intensity value even after registration

I'm using ITK-SNAP to compare the intensities of several Regions of Interest between several conditions. For some subjects, I need to realign one image to another by using the Registration tool. However, I noticed that the intensity values of a…
Pollux
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Python: Using NiBabel to write .hdr/.img nifti files

Attempting to go from dicom to nifti using nibabel. looking for the way to save the header and image seperately, ive done the rest. nibabel.Nifti1Header has a write_to function but only takes a fileobj. how do i pass the Nifti1Header instance with a…
PatfordS
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