[Neuroimaging] Neuroimaging Digest, Vol 13, Issue 5

[Samuel St-Jean]

A quick beginner guide to python would probably help you 
https://www.python.org/about/gettingstarted/

As a quick tip, most stuff can be easily installed with pip like this

pip install dipy nibabel numpy scipy pywavelets

or any other library available from pypi. For other software, most of 
them are also easily installable through a setup.py file, but I strongly 
suggest to read a bit about python and how it works first.

As for denoising, well, there is nlmeans in dipy (good for structural 
imaging for example), some other algorithms are probably available in 
pytohn if you look around and apparently a pr for wavelet mixing 
denoising is in the works, but it has not been reviewed so far, and you 
would need to checkout and use the guy branch to try it out.

Try to get the examples/some test code running, importing modules and 
such on your own and we can see afterward how it goes.


Le 2016-06-05 à 18:19, Vivek Joshi a écrit :
> Hello
> Can you tell me the steps to install dipy from a release.
> Steps to install modules like pywavelets nibabel and modules for 
> adaptive denoising.
> Thank you
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> Subject: Neuroimaging Digest, Vol 13, Issue 5
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> Today's Topics:
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>    1. errors installing other modules in dipy (Vivek Joshi)
>    2. Re: errors installing other modules in dipy (Ariel Rokem)
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> Message: 1
> Date: Sun, 5 Jun 2016 16:00:07 +0530
> From: Vivek Joshi <vivekjoshi1894 at gmail.com>
> To: neuroimaging at python.org
> Subject: [Neuroimaging] errors installing other modules in dipy
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>
> hello
> I ve installed dipy using the instructions given in the dipy website. But
> when trying to install other modules my setup.py got overwritten. Now i m
> getting errors trying to fetch sherbrooke_3shell dataset.
> Also i want to denoise the dataset using wavelet denoising. For that i 
> need
> to install other modules. How to do that?
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> Message: 2
> Date: Sun, 5 Jun 2016 08:51:50 -0700
> From: Ariel Rokem <arokem at gmail.com>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] errors installing other modules in dipy
> Message-ID:
> <CA+X4w0yQh7aVkXUV3BurMk-zM9cqk1JR78_GRh=eubC0RD6SHg at mail.gmail.com>
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>
> Hi Vivek,
>
> On Sun, Jun 5, 2016 at 3:30 AM, Vivek Joshi <vivekjoshi1894 at gmail.com>
> wrote:
>
> > hello
> > I ve installed dipy using the instructions given in the dipy 
> website. But
> > when trying to install other modules my setup.py got overwritten. 
> Now i m
> > getting errors trying to fetch sherbrooke_3shell dataset.
> >
>
> I am not exactly sure what you mean. Could you tell me exactly what 
> you did
> (step by step)? Which instructions did you follow? The ones to install 
> from
> the source code (
> http://nipy.org/dipy/installation.html#installing-from-source)? Or for
> installing a released version (I think that would be better in this case:
> http://nipy.org/dipy/installation.html#installing-a-release)?
>
>
> > Also i want to denoise the dataset using wavelet denoising. For that i
> > need to install other modules. How to do that?
> >
>
> Again - I am not exactly sure what you mean. Do you mean that you want to
> install other libraries (e.g., pywavelets
> <http://www.pybytes.com/pywavelets/>)? You should be able to do that in
> parallel to your Dipy installation.
>
> Cheers,
>
> Ariel
>
>
>
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