Documentation refers to missing data repository?

[justbennet]

Summary

Missing example data for FSL interface

Actual behavior

Data is missing

Expected behavior

Data is present

How to replicate the behavior

I am trying to work through the script in the Nipype examples, fsl_fmri.py, from here

http://nipype.readthedocs.io/en/latest/users/examples/fmri_fsl.html

and I think also from /usr/share/doc/python-nipype-doc/examples/fmri_fsl.py.

That says it will work on the 'Nipype tutorial data set', but I think the Nipype tutorial has disappeared, and it's maybe been replaced by the link to Michael Notter's Nipype Tutorial, which uses Openfmri dataset ds000114.

Instead, I think the data for the example on the filesystem is at

https://figshare.com/articles/nipype_tutorial_data/3395806

which, when the Download button gets pressed, goes to

https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5305348/nipypetutorial.tar

I found a reference to that at

http://nipype.readthedocs.io/en/0.12.0/users/pipeline_tutorial.html

which has a warning at the top that this is not the most up-to-date version.

You are not using the most up to date version of the library. 0.13.1 is the newest version.

I found the 'correct' example data in the README at

https://github.com/nipy/nipype/tree/master/examples

where it is referenced specifically by version number as

http://nipype.readthedocs.io/en/0.12.0/users/pipeline_tutorial.html

The README that is included with Neurodebian is probably still an old one, as it uses just

http://nipy.org/nipype/users/pipeline_tutorial.html

which now leads to a 404 File not found page.

Sorry for the messy details, but I think maybe I've caught things in transition. It seems like some of this needs to be dealt with at Nipype, some maybe at NeuroDebian, though if the change is made upstream, it will propagate. I would like to submit a PR somewhere to someone to make it easier to locate the right sample data to use with the example scripts, but I am not sure what to submit and where.

Platform details:

This is more about the web site and documentation. Fixes will float downstream to NeuroDebian.

Execution environment

NA, I think

[mgxd]

Ah yes, there have been some changes to our documentation / tutorials throughout the years and this has fallen through the cracks.

If you would like to help maintain the documentation, adding the download link for the old nipype tutorial data set to the headers in the relevant examples would be super helpful.

[justbennet]

Is it OK to add a bit of extra verbiage for the beginners? Something like:

A workflow that uses fsl to perform a first level analysis on the nipype
tutorial data set, which can be downloaded from

    https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/5305348/nipypetutorial.tar

That will expand into a folder `nipype-tutorial`, and this example assumes that you are
in that folder.

    python fmri_fsl.py

I am using the URL above instead of the reference to FigShare because the download speed is better than twice as fast, and it is usable by a wider variety of GUI and command line download tools.