miykael / nipype-beginner-s-guide

Beginner's guide for Nipype

Nipype Beginner's Guide

This homepage provides a beginner's guide for Nipype, a user-friendly software written in Python that provides a uniform interface to existing neuroimaging softwares like SPM, FSL, FreeSurfer, Camino, AFNI, Slicer, etc.

Website

Nipype Beginner's Guide is located here: http://miykael.github.com/nipype-beginner-s-guide/

Nipype website is located here: http://nipy.sourceforge.net/nipype/

Documentation

A PDF-Version of this beginner's guide can be found here: http://github.com/miykael/nipype-beginner-s-guide/blob/master/NipypeBeginnersGuide.pdf?raw=true

Examples

All examples and codes which are used in the guide can be found here: http://github.com/miykael/nipype-beginner-s-guide/blob/master/scripts

Contact

You can contact me on: [email protected]

License

This beginner's guide was mostly written by Michael Notter. But some of its ideas and content is from the original Nipype homepage (http://nipy.sourceforge.net/nipype/) and other various homepages (e.g. http://mindhive.mit.edu/imaging).

Copyright (c) 2009-2014, NIPY Developers
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

    * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.

    * Neither the name of the NIPY Developers nor the names of any
       contributors may be used to endorse or promote products derived
       from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

nipype-beginner-s-guide's Issues

Error: tutorial_1_create_dataset.sh - No such file or directory

Running OS X Version 10.11.4 with BASH version: 3.2.57(1)-release

It seems like the for loop on line 17 has a different behaviour depending on the BASH version you use:

for id in {01..10}

The output I get is:

0
1
2
3
4
5
6
7
8
9
10

There seems to be no padding zeros for the values that are single digit. This results in the script not being able to find any of the subject folders.

Changing line 17 to the following seemed to have fixed the issue for me:

for id in $(seq -w 1 10)

reconall error in script tutorial_2_recon_python.py

Hi,

I am trying to run this script and am getting an error of reconall at line 41 since that is not defined anywhere in the script. Do I need to do something else to make the script work ?

Appreciate the effort put in creating these scripts.

I used node of spm.realign, but it doesn't work. the code is following:

error: dot could not be found on host 1.0.0.127.in-addr.arpa (tutorial_3_first_steps.py)

When I tried to run the script, it gives the error:

IOError: dot could not be found on host 1.0.0.127.in-addr.arpa
Interface CommandLine failed to run.

I have everything configured as stated in the website.