nipype | Workflows and interfaces for neuroimaging packages

by nipy Python Version: 1.8.6 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

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

Support

Quality

Security

License

Reuse

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

Quality

nipype has no bugs reported.

Security

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

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.

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

Trending Discussions on nipype

How to search the output of a script and save a subsection to a file?

Building Singularity recipe from Nipype docker image CommandNotFound

Using networkX to output a tree structure

Can Crontab be used to manage packages if it requires input only some of the time

"command 'bet' could not be found on host" error while using BET in FSL on Windows 10 via Python 3.5

QUESTION

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:

...

ANSWER

Answered 2019-Sep-20 at 19:49

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

Source https://stackoverflow.com/questions/58033909

QUESTION

Building Singularity recipe from Nipype docker image CommandNotFound

Asked 2018-May-09 at 17:52

I have the following Singularity container recipe:

...

ANSWER

Answered 2018-May-09 at 17:52

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

Source https://stackoverflow.com/questions/50259231

QUESTION

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).

...

ANSWER

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.

Source https://stackoverflow.com/questions/48380550

QUESTION

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.

...

ANSWER

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 auto_package_updater.sh 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:

Source https://stackoverflow.com/questions/48002613

QUESTION

"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:

...

ANSWER

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.

Source https://stackoverflow.com/questions/47444272

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

Vulnerabilities

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.

Support

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 .

Find more information at: