[Neuroimaging] Site Contributions

Tue Oct 27 16:20:42 EDT 2015

Hey Julien,

On Tue, Oct 27, 2015 at 12:04 PM, Julien Cohen-Adad <jcohen at polymtl.ca>
wrote:

> Hi everyone,
>
> would it be possible to add our neuroimaging project to the nipy website?
> https://github.com/neuropoly/spinalcordtoolbox
>
>
I am +1 for adding the toolbox to the project directory.

How about putting in a PR on the website Github repo for this?

http://nipy.org/contribute.html#add-a-package

> it is 100% python and notably uses nibabel and dipy.
>
> cheers
> julien
>
>
> --
> Julien Cohen-Adad, PhD
> Assistant Professor, Polytechnique Montreal
> Associate Director, Functional Neuroimaging Unit, University of Montreal
> Phone: 514 340 5121 (office: 2264);  Skype: jcohenadad
> Web: www.neuro.polymtl.ca
>
> On Tue, Oct 27, 2015 at 2:44 PM, Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>
>> Epic awesomeness! Thank you Vanessa!
>>
>> On Tue, Oct 27, 2015 at 2:40 PM, Ariel Rokem <arokem at gmail.com> wrote:
>>
>>> Great work! Will resubmit my blog-post PR through the new mechanism.
>>>
>>> On Tue, Oct 27, 2015 at 11:38 AM, vanessa sochat <vsochat at stanford.edu>
>>> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> I just added the missing CNAME file, apologies for the oversight, I did
>>>> not know it was there :) It looks like nipy.org is working as well now
>>>> too - please let me know if you see any issues.
>>>>
>>>> Circle is expected to have some changes in the next week, so I am going
>>>> to wait for the weekend to debug the building of artifacts. Will let you
>>>> know when I fix that up!
>>>>
>>>> Best,
>>>>
>>>> Vanessa
>>>>
>>>> On Tue, Oct 27, 2015 at 11:30 AM, vanessa sochat <vsochat at stanford.edu>
>>>> wrote:
>>>>
>>>>> Hi Everyone,
>>>>>
>>>>> Site is live!
>>>>>
>>>>> https://nipy.github.io/
>>>>>
>>>>> Ariel - I'm not sure how to set up the nipy.org. Would you mind
>>>>> taking a look and fixing that up?
>>>>>
>>>>> Circle is having some bugs with the artifact generation, I think I can
>>>>> probably fix it, but not during the work week. Ben - I added your
>>>>> contribution to the README but didn't get the other comment in time. The
>>>>> good news is now anyone and everyone can submit changes as PR. I encourage
>>>>> everyone to familiarize yourself with tumblr, and start contributing
>>>>> content, PRs to tweak it.
>>>>>
>>>>> Best,
>>>>>
>>>>> Vanessa
>>>>>
>>>>> On Tue, Oct 27, 2015 at 11:10 AM, vanessa sochat <vsochat at stanford.edu
>>>>> > wrote:
>>>>>
>>>>>> Got it! Thanks! :)
>>>>>>
>>>>>> On Tue, Oct 27, 2015 at 11:07 AM, Ariel Rokem <arokem at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> On Tue, Oct 27, 2015 at 10:56 AM, vanessa sochat <
>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>
>>>>>>>> Hi Ariel,
>>>>>>>>
>>>>>>>> Please add me as an admin to nipy.github.io, so I can set up
>>>>>>>> circle for CI. Thanks!
>>>>>>>>
>>>>>>>>
>>>>>>> I believe I just did that. Let me know how you get on.
>>>>>>>
>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> Vanessa
>>>>>>>>
>>>>>>>> On Tue, Oct 27, 2015 at 10:42 AM, vanessa sochat <
>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>
>>>>>>>>> Just as a proof of concept for adding a project - I just added a
>>>>>>>>> new entry to the data file (copy pasting basically), copied one file, and
>>>>>>>>> the entire process took me like, 48 seconds :)
>>>>>>>>>
>>>>>>>>> On Tue, Oct 27, 2015 at 10:36 AM, Ben Cipollini <bcipolli at ucsd.edu
>>>>>>>>> > wrote:
>>>>>>>>>
>>>>>>>>>> Thanks Vanessa!
>>>>>>>>>>
>>>>>>>>>> On Tue, Oct 27, 2015 at 10:35 AM, vanessa sochat <
>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> I will do some tweaks and get the site working. There will be a
>>>>>>>>>>> change for the URL so there might be some bugs with my initial release, but
>>>>>>>>>>> I'll get it fixed asap. Will send an update later.
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Oct 27, 2015 at 6:48 AM, Ariel Rokem <arokem at gmail.com>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Oh, one more:
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Oct 27, 2015 at 6:40 AM, Ariel Rokem <arokem at gmail.com>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Vanessa,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have a few comments/suggestions:
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1. I would rather not have the front page be the project
>>>>>>>>>>>>> directory. In my opinion, the front page should instead explain briefly
>>>>>>>>>>>>> what this is, and lead visitors to the various other parts of the website.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2. There are a few issues with formatting in the Code of
>>>>>>>>>>>>> Conduct page (bullet points appear as continued lines)
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 3. Please include mindboggle in the project directory (it's
>>>>>>>>>>>> been recently added!).
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Other than these two, I think this is ready to be introduced
>>>>>>>>>>>>> as a PR against the nipy/nipy.github.com repository (you
>>>>>>>>>>>>> don't need any admin rights to do that, but I also just added you to "team
>>>>>>>>>>>>> blog" on the github nipy org, so you can even do the merge yourself, if you
>>>>>>>>>>>>> want).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Ariel
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Oct 26, 2015 at 12:56 PM, vanessa sochat <
>>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Eleftherios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> It definitely would be possible! I'm not any sort of admin in
>>>>>>>>>>>>>> the nipy space, so the farthest I could take it is having the repo for
>>>>>>>>>>>>>> someone to deploy on nipy.github.io. The code is here:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> https://github.com/vsoch/nipy-jekyll
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> and deployment on my github pages:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> http://vsoch.github.io/nipy-jekyll/
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I mostly stopped working on it because I accomplished all the
>>>>>>>>>>>>>> things that I set out to do (jekyll site, preview on continuous integration
>>>>>>>>>>>>>> with circle, standard ways to add new content, and an easy way to multiple
>>>>>>>>>>>>>> ways to add content a la github
>>>>>>>>>>>>>> <http://vsoch.github.io/nipy-jekyll/contribute.html>, or for
>>>>>>>>>>>>>> those who aren't comfortable with pushing and pulling, la
>>>>>>>>>>>>>> social media <http://neuroimaging.tumblr.com>). I think I
>>>>>>>>>>>>>> had suggested moving forward for people to try out tumblr (and start
>>>>>>>>>>>>>> contributing content!), and if people were happy, to move it over to the
>>>>>>>>>>>>>> nipy repo. If the outcome of the work was not a desired solution, I was
>>>>>>>>>>>>>> content to just let it be. However if there is interest, that is definitely
>>>>>>>>>>>>>> still a possibility.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Vanessa
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Mon, Oct 26, 2015 at 12:34 PM, Eleftherios Garyfallidis <
>>>>>>>>>>>>>> garyfallidis at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Vanessa and all,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Would it be possible to switch to your much nicer new
>>>>>>>>>>>>>>> website? I still see the older version being up.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Do you have a plan for this? Or you waiting for some
>>>>>>>>>>>>>>> feedback on our side?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>>>> Eleftherios
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 12:57 PM, Ben Cipollini <
>>>>>>>>>>>>>>> bcipolli at ucsd.edu> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I think they're good for mobile sites. I think they're
>>>>>>>>>>>>>>>> generally expanded by default on full screens, and compacted on mobile. So
>>>>>>>>>>>>>>>> I suggest to keep it, but have a regular menu that's showing on full
>>>>>>>>>>>>>>>> screens and hidden on mobile.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 9:51 AM, vanessa sochat <
>>>>>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> That's a good suggestion, and I'll add as an issue so I
>>>>>>>>>>>>>>>>> can find it easily when the next round of changes comes around. Generally,
>>>>>>>>>>>>>>>>> these "hamburger" menu things are useless functionality wise, and only
>>>>>>>>>>>>>>>>> serve to aesthetically "get rid of the navigation" to have a clean looking
>>>>>>>>>>>>>>>>> site. In our case, it is probably just annoying to have the extra clicks.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Wed, Sep 2, 2015 at 8:50 AM, Ben Cipollini <
>>>>>>>>>>>>>>>>> bcipolli at ucsd.edu> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> This looks great. It's also cool to see "ask a question"
>>>>>>>>>>>>>>>>>> integrated into the website, though we'll still have to hash things out for
>>>>>>>>>>>>>>>>>> that.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Rather than open a github issue (which few may see), I'll
>>>>>>>>>>>>>>>>>> make a suggestion here: can we have the menu expanded by default when
>>>>>>>>>>>>>>>>>> accessing via a full-size screen?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> It feels odd to me to have to expand the menu in order to
>>>>>>>>>>>>>>>>>> navigate anywhere, by default. To me, navigation options should be obvious,
>>>>>>>>>>>>>>>>>> unless pressed for space.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Sun, Aug 30, 2015 at 1:14 PM, vanessa sochat <
>>>>>>>>>>>>>>>>>> vsochat at stanford.edu> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Everyone,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I've finished work on the "contribute" page with my
>>>>>>>>>>>>>>>>>>> thinking for how to contribute various content:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> http://vsoch.github.io/nipy-jekyll/contribute.html
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> and as an example, put up a quick blog post:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> http://neuroimaging.tumblr.com/
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The old "example" blog posts are hidden (private) and
>>>>>>>>>>>>>>>>>>> can be viewed if you are a contributor. I'd like to add anyone and everyone
>>>>>>>>>>>>>>>>>>> interested to contribute as "official" contributors via tumblr - if you are
>>>>>>>>>>>>>>>>>>> interested please send me your email address. I've already invited some of
>>>>>>>>>>>>>>>>>>> you for which I know the email.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Vanessa
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>>>>> Stanford University
>>>>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>>>> Stanford University
>>>>>>>>>>> (603) 321-0676
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Neuroimaging mailing list
>>>>>>>>>> Neuroimaging at python.org
>>>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Vanessa Villamia Sochat
>>>>>>>>> Stanford University
>>>>>>>>> (603) 321-0676
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Vanessa Villamia Sochat
>>>>>>>> Stanford University
>>>>>>>> (603) 321-0676
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Neuroimaging mailing list
>>>>>>>> Neuroimaging at python.org
>>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Neuroimaging mailing list
>>>>>>> Neuroimaging at python.org
>>>>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Vanessa Villamia Sochat
>>>>>> Stanford University
>>>>>> (603) 321-0676
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Vanessa Villamia Sochat
>>>>> Stanford University
>>>>> (603) 321-0676
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Vanessa Villamia Sochat
>>>> Stanford University
>>>> (603) 321-0676
>>>>
>>>> _______________________________________________
>>>> Neuroimaging mailing list
>>>> Neuroimaging at python.org
>>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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