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Questions tagged [nipy]

The project "Neuroimaging in Python" which develops tools for neuroimage processing, f.e. the well known cross-software pipeline "Nipype" interface for fsl, spm and others more.

The project "Neuroimaging in Python" which develops tools for neuroimage processing, f.e. the well known cross-software pipeline "Nipype" interface for fsl, spm and freesurfer.

Project website: http://nipy.sourceforge.net/software/projects/

Because the difference between Nipy and Nipype need a closer look, this tag will probably often be used when using Nipype would be enough. Use this tag when you want to reference to the other sub projects listes on the project website:

  • nipy
  • nitime
  • nibabel
  • dipy
  • pbrain
7 questions
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Resizing a 3D image (and resampling)

I have 3D image of a brain (let's call it flash) and it's currently 263 x 256 x 185. I want to resize it to be the size of another image(call it whole_brain_bravo); 256 x 256 x 176, and (hopefully) use a lanczos interpolation to resample…
faskiat
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Windows PermissionError & tempfile module

We use tempfile module to generate temporary files & dirs during our tests. We recently started testing on Windows as well and ran into a bunch of Windows PermissionErrors. I initially thought this may be because Windows, unlike Unix does not allow…
kchawla-pi
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Plotting multiple matplotlib axes class object

My problem is the following: I'm trying to plot in a readable way 6 different design matrix. The function creating the display for this design matrix is part of the nipy module and is describe as this: class…
Mathieu
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Is there any nipype interface for avscale (FSL script)?

I am trying to use nipype to analyze transformation matrixes that were created by FSL. FSL has a script called "avscale" that analyzes those transformation matrixes (*.mat files). I was wondering whether nipype has any interface that wrap that…
duchin
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Using nipype to apply a FLIRT registration to an additional image error

I am trying to do some registration in python using the nipype package. It worked for basic registration: from nipype.interfaces import fsl from nipype.testing import example_data flt = fsl.FLIRT(bins=640, cost_func='mutualinfo') flt.inputs.in_file…
tylerthemiler
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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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ImportError when importing Python module written in C in cloned Git repo

I've just cloned the NiPy repository, but when I try to import nipy.algorithms.registration, I get the following error: In [1]: import…
abcd
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