nipype | Workflows and interfaces for neuroimaging packages

 by   nipy Python Version: 1.8.6 License: Non-SPDX

kandi X-RAY | nipype Summary

kandi X-RAY | nipype Summary

nipype is a Python library typically used in Data Science applications. nipype has no bugs, it has no vulnerabilities, it has build file available and it has high support. However nipype has a Non-SPDX License. You can install using 'pip install nipype' or download it from GitHub, PyPI.

Workflows and interfaces for neuroimaging packages

            kandi-support Support

              nipype has a highly active ecosystem.
              It has 686 star(s) with 519 fork(s). There are 50 watchers for this library.
              It had no major release in the last 12 months.
              There are 383 open issues and 939 have been closed. On average issues are closed in 142 days. There are 31 open pull requests and 0 closed requests.
              It has a negative sentiment in the developer community.
              The latest version of nipype is 1.8.6

            kandi-Quality Quality

              nipype has no bugs reported.

            kandi-Security Security

              nipype has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              nipype has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              nipype releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.

            Top functions reviewed by kandi - BETA

            kandi has reviewed nipype and discovered the below as its top functions. This is intended to give you an instant insight into nipype implemented functionality, and help decide if they suit your requirements.
            • Generates a GantT TantT plot
            • Create event dictionary
            • Calculate the time series for a given resource
            • Generates HTML lines for a time series
            • Build rst file
            • Connect the workflow to the workflow
            • Return the relative path from start to start
            • Print crash files matching regex
            • Return True if text contains doctest
            • Run the interface
            • Connect to the workflow
            • Run nifti1
            • Run the optimizer
            • Send all pending jobs to all workers
            • Send all the pending jobs to the workers
            • List the output files
            • List outputs
            • Run the simulation
            • Run the CFFlib
            • List all outputs in s3 bucket
            • Make the command line for matlab
            • Run the network interface
            • Submit the graph
            • Submit a graph to SGE
            • Generate matlab script
            • Lists the outputs
            • Parse inputs
            Get all kandi verified functions for this library.

            nipype Key Features

            No Key Features are available at this moment for nipype.

            nipype Examples and Code Snippets

            No Code Snippets are available at this moment for nipype.

            Community Discussions


            How to search the output of a script and save a subsection to a file?
            Asked 2019-Sep-20 at 19:49

            I have a command nipype.interface.afni.Warp which gives me the following python terminal output:



            Answered 2019-Sep-20 at 19:49

            I think your command-line arguments to python3 are incorrect in Python's Popen call. With



            Building Singularity recipe from Nipype docker image CommandNotFound
            Asked 2018-May-09 at 17:52

            I have the following Singularity container recipe:



            Answered 2018-May-09 at 17:52

            The issue comes down to the way you are activating the environment. Normally, you would do:



            Using networkX to output a tree structure
            Asked 2018-Jan-22 at 18:46

            I am using networkX to generate a tree structure as follows (I am following the answer of this question).



            Answered 2018-Jan-22 at 17:08

            I think this issue was solved on networkx 2.x, but before that you should be explicit import of the function like this.



            Can Crontab be used to manage packages if it requires input only some of the time
            Asked 2017-Dec-28 at 06:57

            I essentially have a suite of python packages, binaries, and other programs requiring constant updates and I wanted to see if I could create a crontab entry that would run a BASH script that basically just runs these updates monthly. I have successfully created a crontab entry that calls a shorter test script I wrote for this purpose. The script is not the issue but it is as follows if it helps answer the question, which I doubt.



            Answered 2017-Dec-28 at 06:57

            crontab(5) entries describe commands to be run periodically (or, with @reboot at boot time). These commands are interpreted by /bin/sh (the POSIX shell, see sh(1p)...) with a prior substitution of the % character.

            Notice that these commands are running in a different environment (see environ(7)...) than your interactive shell has. Hence, you may need to set your PATH variable (and perhaps other environment variables, such as LD_LIBRARY_PATH if you need it) explicitly in your shell script (instead of source /Users/mycomputer/.bash_profile which smells really bad ...) .

            is that cron will crash if it gets to a point where it needs input,

            No, cron(8) is a daemon -started by init or systemd at boot time- and does not crash (unless you got hit by a bug in cron itself, which is very unlikely). It always runs (and if you crash it -which is highly unlikely, you cannot run any crontab job afterwards). What could happen is that your particular cron job is blocked ...

            Is there a way I can automate the process of inputting 'y'?

            You could consider using yes(1) (which emits a potentially infinite stream of y lines) and pipe its output (see pipe(7)). For example, if pip install --upgrade nibabel nipype could want many y you might put in your shell script:



            "command 'bet' could not be found on host" error while using BET in FSL on Windows 10 via Python 3.5
            Asked 2017-Nov-23 at 01:31

            I need to perform brain extraction on .nii images. I am using Anaconda on Windows 10 and have an environment based on Python 3.5.4. On Nipype I found the BET from FSL and I followed the code:



            Answered 2017-Nov-23 at 01:31

            You can only use FSL on Windows via Docker, Virtual Machine, or Windows Subsystem for Linux. Running it naively is not possible.


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install nipype

            You can install using 'pip install nipype' or download it from GitHub, PyPI.
            You can use nipype like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.


            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            pip install nipype

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            gh repo clone nipy/nipype

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