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Questions tagged [nibabel]

Nibabel is an open source python package for processing neuroimaging files. It supports processing of ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT file formats.

Nibabel is an open source python package for processing neuroimaging files. It supports processing of ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT file formats.

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Nibabel

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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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get the zdata with event from a orthoviewer of medical image

I want get the zdata, from navigation toolbar, when I load a .nii file. I want do that with the event def _onclick(event): import matplotlib matplotlib.use('TkAgg') from tkinter import filedialog from tkinter import * from…
user9535201
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Pass an argument in class to ApplicationWindow()

how I can pass as argument the variable fig in class Orthocanvas to aw = ApplicationWindow? global fig class OrthoCanvas(FigureCanvas): def __init__(self, parent=None, width=5, height=4, dpi=100): fig = Figure(figsize=(width, height),…
user9535201
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Center cropping of 3D images for MRI images

I have a list of 3D MRI images, and I would like to crop these images to the center so that I leave only the ROI, any suggestions on how to do that? I tried the following code, but it returned the original size at the end... Any idea how to crop all…
Mrmr
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How can I find groups in an array?

I have a binary 3d array that has small groups of 1 and large groups of 1. I want to search the array and when a 1 is found I want to search the surrounding values in the x,y,z directions and count how many 1 are connected. If there are less than x…
rzaratx
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