[MINC-users] emma

[Pierre Bellec]

Dear Soren and minc users,

I was going through the minc-users archive and I ran into this post. Sorry
for waiting two months to get back to you ! The reason is that I only just
registered to minc-users (shame on me !).

Anyway, I confirm that the NIAK reader/writer for matlab are simple overlays
on the minc tools (mincheader, raw2minc and minc2raw to be more precise).

I also confirm that the native NetCFD and HDF5 libraries of matlab would
allow to code a stand-alone reader/writer, much faster and elegant than the
NIAK things actually. As an anecdote, "load volume.mnc" will work in octave
with MINC2 ... sweet... . Writing this reader/writer is quite a bit of work
still because NetCDF/HDF5 are much more general formats than MINC, so it is
necessary to write a complete extra layer. I started a couple of times to
work on such a code (it is actually the issue 39 on the NIAK project) and I
did not find any blocker in matlab. Unfortunately, the octave HDF5 libraries
are much less versatile, and I didn't find a way of extracting the header
information. Because compatibility with both Matlab and Octave is a strong
specification of NIAK and that it did not seem possible to achieve that
without using the minc tools, I sticked to the wraper approach.

If you ever go through the trouble of implementing these reader/writter, I
would be very interested to integrate those in NIAK. In any case, f that's
something you are or may be be working on feel free to contact me I have
some notes on a MINC2 reader based on HDF5 libraries that I wrote before I
decided to abandon that project and that you might find useful.

Best regards,

Pierre

>From sorench at gmail.com Sun Nov 1 18:52:18 2009
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 2 Nov 2009 07:52:18 +0800
Subject: [MINC-users] emma
In-Reply-To: <e12172550910291052v7f6d5bf3k6cb5fcc6e01b946a at mail.gmail.com>
References: <d6e2d6550910281956i59057f83hd9c57ce793ca9c8d at mail.gmail.com>
<d747ed50910282003w5e1062eu11c9295da476b3ca at mail.gmail.com>
<e12172550910291052v7f6d5bf3k6cb5fcc6e01b946a at mail.gmail.com>
Message-ID: <d6e2d6550911011552n92216a9r97c6ebc54fc665d3 at mail.gmail.com>

Thanks to you both.
I checked out Niak but and it looks interesting but at the moment I am
looking for something simple to include in Matlab stand-alone apps and
since Niak still needs the minc libraries installed I will probably
end up using the matlab NetCDF interface (I currently only have MINC1
files) as it simplifies portability.
I look forward to trying out mniMincIO when available too.

Thanks for pointers
Soren

On Fri, Oct 30, 2009 at 1:52 AM, EJ Nikelski <nikelski at bic.mni.mcgill.ca>
wrote:
> Hi all,
>
> ? Just a quick FYI related to this post. ?Work on the new mniMincIO
> package (version 1.0) is now pretty much complete, and will be made
> available as soon as I finish the documentation and take it for a test
> drive on a non-trivial internal project. This package uses the Minc2
> API and can replace all EMMA functionality (plus a lot more).
>
> ? ?It's purpose is to provide an easy to use rapid application
> development (RAD) environment, which will make working with Minc
> volumes an attractive alternative to the other volume formats.
> Unlike EMMA, mniMincIO is built as an R package, and as such, RAD
> development can be done using the very powerful (functional) R
> language. ?More info to follow.
>
> Cheers,
>
> -Jim
>
>
>
> On Wed, Oct 28, 2009 at 8:03 PM, Andrew Janke <a.janke at gmail.com>
wrote:
>> Hi Soren,
>>
>> On Thu, Oct 29, 2009 at 13:56, Soren Christensen <sorench at gmail.com>
wrote:
>>> Sorry, wrt. my previous question I realized I was referencing
>>> softlinks that were not redirected on windows and there are no
>>> problems with EMMA
>>
>> Good to hear. I was dreading having to put vista back onto my new
>> (Ubuntu) laptop just to test this...
>>
>>> I noticed Matlab now has both NETCDF and HDF support so I wonder if it
>>> would be an option to replace (since this has been debated) EMMA with
>>> a Matlab based interface that one could speculate would be easier to
>>> maintain over time and OSs.
>>
>> Well There is work on new project called niak now by Pierre Bellec
>>
>> ? http://code.google.com/p/niak/
>>
>> I have now dumped emma in favour of this if only because it supports
>> octave as well.
>> I don't know if it works on XP, Vista or 7 but if you can get EMMA
>> going on windows then odds are you will be able to sort out niak.
>>
>> --
>> Andrew Janke
>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>> Canberra->Australia ? ?+61 (402) 700 883
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> --
> =================================
> Jim Nikelski, Ph.D.
> Postdoctoral Research Fellow
> Bloomfield Centre for Research in Aging
> Lady Davis Institute for Medical Research
> Sir Mortimer B. Davis - Jewish General Hospital
> McGill University
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
-- 

Pierre Bellec
Home page: http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
Address:   McConnel Brain Imaging Center, Webster 2B
          Montreal Neurological Institute
          3801 University Street
          Montreal, Quebec, Canada H3A 2B4
tel:       (001)(514) 398 5220
fax:      (001)(514) 398 8948