nifti

Change entire images slices of NIFTI in Python 3.7

由 喜夏-厌秋 提交于 2021-02-07 23:01:51
问题 I'm actually work on MRI images using Python. The image format is the NIFTI format I get how to visualise slices on x, y or z axe, but now, I want tu use Sobel filtering on each of them and create a new NIFTI image with those slices. For that: I load the main .nii.gz image (img = nib.load(im_path)) I load again the main .nii.gz image with a new name "img_sobel" (img_sobel = nib.load(im_path)) Create a loop for each slice Sobel filtering the slice Replace this slice on the corresponding slice

Accessing files inside a .zip archive without extracting them

由 有些话、适合烂在心里 提交于 2019-12-23 02:43:10
问题 I am attempting to read a NIFTI file inside a .zip without having to extract the directory to the root directory. More specifically, I am working with the ADNI database and the files are stored by subjectID in individual .zip files. Inside the .zip file there is all the data pertaining to that subject, I would like to extract the NIFTI file (.nii.gz) from within the .zip without extracting the files. Currently I have the following code snippet def openNIFTI(filename): return nib.load(filename

VTK - How to read Tensors/Matrix per cell from a NIFTI Image?

由 ﹥＞﹥吖頭↗ 提交于 2019-12-12 03:46:47
问题 I'm trying to implement a MRT-DTI real-time fibertracking visualization tool based on VTK . Therefore we need to read the DTI tensors /matrices per cell stored in a NIFTI Image (.nii) and I really can't figure out how to do this. It's not a problem to retrieve a single scalar value from the NIFTI file, but I don't know how to get the tensor (3x3/4x4 matrix). We would really appreciate any help ! Since the NIFTIImageReader is supposed to read a tensor NIFTI image as a multi-component vtkImage

How to convert Nifti file to Numpy array?

由 邮差的信 提交于 2019-12-06 02:38:21
问题 I have 3D array in Nifti file (.ii.gz) and I want to save it as a 3D numpy array. I used Nibabel to convert Numpy to Nifti1. Can I do the opposite? 回答1: From nipy import numpy as np import nibabel as nib img = nib.load(example_filename) a = np.array(img.dataobj) 来源： https://stackoverflow.com/questions/44422248/how-to-convert-nifti-file-to-numpy-array

How to convert Nifti file to Numpy array?

由 无人久伴 提交于 2019-12-04 08:21:30
I have 3D array in Nifti file (.ii.gz) and I want to save it as a 3D numpy array. I used Nibabel to convert Numpy to Nifti1. Can I do the opposite? From nipy import numpy as np import nibabel as nib img = nib.load(example_filename) a = np.array(img.dataobj) 来源： https://stackoverflow.com/questions/44422248/how-to-convert-nifti-file-to-numpy-array

How to transfer Nifti file into .mat Matlab file?

由 时光毁灭记忆、已成空白 提交于 2019-12-02 20:10:20
问题 I have a Nifti file, the size of which is 62*62*38. How can I transfer the Nifti file to .mat Matlab file? 回答1: This can read NIFTI as well as many other medical image file types into MATLAB arrays, which you can then save as .mat files. 回答2: Most medical imaging data can be manipulated effectively using some kind of toolbox, such as SPM. However, if you need to gain access to the raw matrix I've always used NIfTI tools from the Mathworks file exchange site (here). There are two functions

How to transfer Nifti file into .mat Matlab file?

由 牧云@^-^@ 提交于 2019-12-02 10:11:36
I have a Nifti file, the size of which is 62*62*38. How can I transfer the Nifti file to .mat Matlab file? This can read NIFTI as well as many other medical image file types into MATLAB arrays, which you can then save as .mat files. Most medical imaging data can be manipulated effectively using some kind of toolbox, such as SPM. However, if you need to gain access to the raw matrix I've always used NIfTI tools from the Mathworks file exchange site ( here ). There are two functions that are relevant here: load_nii and load_untouched_nii . The first function load_nii takes care of situations
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