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Questions tagged [nipype]

Nipype: Neuroimaging in Python Pipelines and Interfaces It enables the use different imaging processing tools like fsl, spm, afni, freesurfer and others more.

Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, Camino, MRtrix, AFNI, Slicer), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Nipype allows you to:

  • easily interact with tools from different software packages
  • combine processing steps from different software packages
  • develop new workflows faster by reusing common steps from old ones
  • process data faster by running it in parallel on many cores/machines
  • make your research easily reproducible
  • share your processing workflows with the community
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Down-sample mri T1 image in python with Nipy

I have a T1 image (NIFTI), already aligned, with dimension 121 x 145 x 121. The image is loaded by nibabel. The voxel size is 1.5 x 1.5 x 1.5 mm. I want to down-sample it to an image with 2.0 x 2.0 x 2.0 mm resolution and keep the images aligned. I…
RemiDav
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Building Singularity recipe from Nipype docker image CommandNotFound

I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment …
user9761559
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Error in Nibabel when running Nipype tutorial

Having problem with slicing niimg from nibabel.get_data(). When this function of Nipype tutorial was used, def plot_slice(fname, z_idx=5): # Load the image and collect the data # and orientation information img = nib.load(fname) …
Nufa
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How to connect two simple functions using NiPype?

I am trying to replace our internal pipeline infrastructure with NiPype. As a test, I want to connect to simple functions where the first gets an input and after some calculation returns an output which gets used for the second function as an…
haehn
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Nipype SPM12 / Matlab Compiler Runtime interface functions

I'm trying to run SPM functions via Nipype but i get the same error when calling different SPM functions. I can successfully connect to the Matlab compiler runtime and execute commands via nipype like so: import nipype.interfaces.matlab as…
Elias Rau
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Taking two outputs from two different nodes and feeding them as a list to another node as one single input

it's Pablo! I'm trying to make a script for DTI. I already have it with functions and nipype but now I'm trying with nodes yet there is one node which needs a list of two inputs -Merge()- to merge both images. However, it only accepts one input and…
Paul
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python problem from nipype.interfaces.ants import N4BiasFieldCorrection

OSError: No command "N4BiasFieldCorrection" found on host pc. Please check that the corresponding package is installed. i have problem using nipype.can you plese help? from nipype.interfaces.ants import N4BiasFieldCorrection n4 =…
Abhayadev
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TypeError: environment can only contain strings

I'm using nipype for an image processing project. My python version is 3.6, and I got this error File "D:\softwares\Annoconda3\lib\site- packages\nipype\interfaces\base\core.py", line 750, in run_command close_fds=False, File…
percy
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SPM Dicom Convert in python (Ipython/ Nipype)

I am new to python or more specifically ipython. I have been running through the steps to run what should be a very simple Dicom Conversion in a statistical package called SPM for an MRI image file as described by NiPype. I can't get it to run and…
brainimaging_new_to_unix
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subprocess get stucks at poller.poll()

I'm trying to run a simple matlab interface on Nipype as below, but somehow it gets stuck in run() code. My command line does not proceed anymore . But it works perfectly if I copy mlab.cmdline (matlab -nodesktop -nosplash -singleCompThread -r…
yasin.yazici
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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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OSError: This docstring was not generated by Nipype

Hey i am runing the following piece of code: import nipype.interfaces.spm as spm realign = spm.Realign() And getting the following error: raise IOError("This docstring was not generated by Nipype!\n") from e OSError: This docstring was not…
greenity
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Access Values of an interface in python

I read in a fMRI image where I want to calculate a certain measurement. initial_data =…
Dr. S
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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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Nipype Custom Interface not showing output

I am trying to build a custom interface that will dynamically generate the outputspec attribute based on the dictionary input. However, the output is not showing up when I do .help() Here is what I have previously and if I run help() it will show…
amyleeslie
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