[DOC] fmriprep-docker documentation #1515

franklin-feingold · 2019-02-22T22:04:09Z

Changes proposed in this pull request

This PR will address #1488 and #1129. This PR provides additional documentation to fmriprep-docker

Documentation that should be reviewed

Provided documentation to fmriprep-docker

2/22 update

Added documentation to fmriprep-docker call

local version of this file deleted spaces at the end of certain sentences, added them back in

welcome · 2019-02-22T22:04:12Z

Thanks for opening this pull request! We have detected this is the first time for you to contribute to fMRIPrep. Please check out our contributing guidelines.
We invite you to list yourself as a fMRIPrep contributor, so if your name is not already mentioned, please modify the .zenodo.json file with your data right above Russ' entry. Example:

{
   "name": "Contributor, New FMRIPrep",
   "affiliation": "Department of fMRI prep'ing, Open Science Made-Up University",
   "orcid": "<your id>"
},
{
   "name": "Poldrack, Russell A.",
   "affiliation": "Department of Psychology, Stanford University",
   "orcid": "0000-0001-6755-0259"
},

Of course, if you want to opt-out this time there is no problem at all with adding your name later. You will be always welcome to add it in the future whenever you feel it should be listed.

franklin-feingold · 2019-02-23T01:08:21Z

I'm not sure why the ds tests failed, I am only changing the documentation

oesteban

left some suggestions and comments 👍 . Thanks a lot for this!

oesteban · 2019-02-23T02:02:11Z

docs/installation.rst

@@ -26,20 +26,33 @@ In order to run fmriprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
 Once Docker is installed, the recommended way to run fmriprep is to use the
 fmriprep-docker_ wrapper, which requires Python and an Internet connection.
+``fmriprep-docker`` is a streamlined command to run fmriprep without having to
+properly mount directories (``fmriprep-docker`` does this for you)


Suggested change

properly mount directories (``fmriprep-docker`` does this for you)

properly mount directories (``fmriprep-docker`` does this for you).

Just to rewrite the whole sentence:

``fmriprep-docker`` is a command that allows you to write your command line as if you were running ``fmriprep`` directly, and converts it into a ``docker`` command.

oesteban · 2019-02-23T02:02:54Z

docs/installation.rst


 To install::

    $ pip install --user --upgrade fmriprep-docker

-When run, ``fmriprep-docker`` will generate a Docker command line for you,
-print it out for reporting purposes, and then run the command, e.g.::
+When you run, ``fmriprep-docker`` it will generate a Docker command line for you,


Suggested change

When you run, ``fmriprep-docker`` it will generate a Docker command line for you,

When you run ``fmriprep-docker``, it will generate a Docker command line for you,

oesteban · 2019-02-23T02:04:38Z

docs/installation.rst

-When run, ``fmriprep-docker`` will generate a Docker command line for you,
-print it out for reporting purposes, and then run the command, e.g.::
+When you run, ``fmriprep-docker`` it will generate a Docker command line for you,
+print it out for reporting purposes, and then run the command without further action


Suggested change

print it out for reporting purposes, and then run the command without further action

print it out for reporting purposes, and then execute it without further action

oesteban · 2019-02-23T02:14:21Z

docs/installation.rst


    $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
        -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
        /data /out participant
    ...

+For ``fmriprep-docker`` all the options you would typically pass to fmriprep,


I'm confused by this paragraph. I think it should differentiate between docker arguments that you can pass in (e.g. environment variables and mounting dirs) and the arguments to fmriprep.

@oesteban Not sure exactly what you're suggesting here. As in we should add a section for additional fmriprep-docker-specific options? For that I would direct readers to The Docker Wrapper CLI, to avoid cluttering the basic "How to run fMRIPrep" page with those details.

oesteban · 2019-02-23T02:14:58Z

docs/installation.rst

+
+We have published a `step-by-step tutorial
+<http://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/>`_
+illustrating how to run ``fmriprep-docker``. This tutorial also provides valuable


Start sentence in a new line, down the line that is easier to maintain.

effigies · 2019-02-23T02:39:31Z

docs/installation.rst

@@ -26,20 +26,33 @@ In order to run fmriprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
 Once Docker is installed, the recommended way to run fmriprep is to use the
 fmriprep-docker_ wrapper, which requires Python and an Internet connection.
+``fmriprep-docker`` is a streamlined command to run fmriprep without having to
+properly mount directories (``fmriprep-docker`` does this for you)


Just to rewrite the whole sentence:

``fmriprep-docker`` is a command that allows you to write your command line as if you were running ``fmriprep`` directly, and converts it into a ``docker`` command.

effigies · 2019-02-23T02:41:52Z

docs/installation.rst


    $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
        -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
        /data /out participant
    ...

+For ``fmriprep-docker`` all the options you would typically pass to fmriprep,
+you can use for ``fmriprep-docker``. ``fmriprep-docker`` is mostly mounting
+the paths and environmental variables.


An alternative paragraph:

``fmriprep-docker`` accepts all of the typical options for ``fmriprep``, automatically translating directories into Docker mount points.

effigies · 2019-02-23T02:44:32Z

docs/installation.rst


    $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
        -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
        /data /out participant
    ...

+For ``fmriprep-docker`` all the options you would typically pass to fmriprep,


@oesteban Not sure exactly what you're suggesting here. As in we should add a section for additional fmriprep-docker-specific options? For that I would direct readers to The Docker Wrapper CLI, to avoid cluttering the basic "How to run fMRIPrep" page with those details.

effigies · 2019-02-23T02:45:25Z

Oh, looks like I reviewed at exactly the wrong moment... Let me know if you want me to go through again.

franklin-feingold · 2019-02-23T02:46:19Z

It was at the same time! I'll apply your edits right now and then ping you for your review

applying suggestions and recommendations from Chris M

franklin-feingold · 2019-02-23T02:51:04Z

@effigies - recent commit should have applied both Oscar's and your's comments and suggestions

effigies

A couple minor adjustments.

effigies · 2019-02-23T02:52:15Z

docs/installation.rst

@@ -26,20 +26,34 @@ In order to run fmriprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
 Once Docker is installed, the recommended way to run fmriprep is to use the
 fmriprep-docker_ wrapper, which requires Python and an Internet connection.
+``fmriprep-docker`` is a command that allows you to write your command line 
+as if you were running ``fmriprep`` directly, converts it into a ``docker`` 


"and converts" or "converting"

effigies · 2019-02-23T02:52:59Z

docs/installation.rst

+This tutorial also provides valuable troubleshooting insights and advice on 
+what to do after fmriprep has run.
+
+


Suggested change

franklin-feingold · 2019-02-23T02:59:37Z

adjustments applied - thank you for reviewing!

franklin-feingold added 3 commits February 22, 2019 11:24

Merge pull request #1 from poldracklab/master

8653558

2/22 update

Installation edits

42830d0

Added documentation to fmriprep-docker call

add deleted spaces

3b46aae

local version of this file deleted spaces at the end of certain sentences, added them back in

franklin-feingold requested review from effigies and oesteban February 23, 2019 01:07

oesteban reviewed Feb 23, 2019

View reviewed changes

edits to fmriprep-docker

f08fde1

effigies reviewed Feb 23, 2019

View reviewed changes

edits to fmri-docker (2)

54914f2

applying suggestions and recommendations from Chris M

effigies reviewed Feb 23, 2019

View reviewed changes

minor fmriprep-docker edits

2afad64

effigies merged commit b32bd9e into nipreps:master Feb 25, 2019

This was referenced Feb 25, 2019

fmriprep-docker does not list all args in docs #1129

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Explain fmriprep-docker wrapper more thoroughly in docs #1488

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[DOC] fmriprep-docker documentation #1515

[DOC] fmriprep-docker documentation #1515

franklin-feingold commented Feb 22, 2019

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franklin-feingold commented Feb 23, 2019

	properly mount directories (``fmriprep-docker`` does this for you)
	properly mount directories (``fmriprep-docker`` does this for you).

	When you run, ``fmriprep-docker`` it will generate a Docker command line for you,
	When you run ``fmriprep-docker``, it will generate a Docker command line for you,

	print it out for reporting purposes, and then run the command without further action
	print it out for reporting purposes, and then execute it without further action

		This tutorial also provides valuable troubleshooting insights and advice on
		what to do after fmriprep has run.

[DOC] fmriprep-docker documentation #1515

[DOC] fmriprep-docker documentation #1515

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franklin-feingold commented Feb 22, 2019

Changes proposed in this pull request

Documentation that should be reviewed

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effigies commented Feb 23, 2019

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franklin-feingold commented Feb 23, 2019