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@mail.gmail.com>
References: <d6e2d6550910281956i59057f83hd9c57ce793ca9c8d@mail.gmail.com> 
	<d747ed50910282003w5e1062eu11c9295da476b3ca@mail.gmail.com> 
	<e12172550910291052v7f6d5bf3k6cb5fcc6e01b946a@mail.gmail.com>
Message-ID: <d6e2d6550911011552n92216a9r97c6ebc54fc665d3@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
>


From jween at klaru-baycrest.on.ca  Tue Nov  3 14:06:16 2009
From: jween at klaru-baycrest.on.ca (Jon Erik Ween)
Date: Tue, 3 Nov 2009 14:06:16 -0500
Subject: [MINC-users] How to extract volumes from 4D sets
Message-ID: <8CCB114E-2E5B-46A7-AD8D-BD88F5564BD6@klaru-baycrest.on.ca>

Hello all

Is mincextract the proper way to get a volume out of a 4D set? I have  
dti images but need to extract the b0 from the rest (the b0 is always  
first). Can't quite figure out what parameters to use for mincextract.

Thanks

Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


Confidential: This communication and any attachment(s) may contain  
confidential or privileged information and is intended solely for the  
address(es) or the entity representing the recipient(s). If you have  
received this information in error, you are hereby advised to destroy  
the document and any attachment(s), make no copies of same and inform  
the sender immediately of the error. Any unauthorized use or  
disclosure of this information is strictly prohibited.




From vladimir.fonov at gmail.com  Tue Nov  3 14:27:00 2009
From: vladimir.fonov at gmail.com (Vladimir Fonov)
Date: Tue, 3 Nov 2009 14:27:00 -0500
Subject: [MINC-users] How to extract volumes from 4D sets
In-Reply-To: <8CCB114E-2E5B-46A7-AD8D-BD88F5564BD6@klaru-baycrest.on.ca>
References: <8CCB114E-2E5B-46A7-AD8D-BD88F5564BD6@klaru-baycrest.on.ca>
Message-ID: <fb3c4430911031127n5b831e4bkc433acbd4b0e5634@mail.gmail.com>

Hello,

On Tue, Nov 3, 2009 at 2:06 PM, Jon Erik Ween
<jween at klaru-baycrest.on.ca> wrote:
> Hello all
>
> Is mincextract the proper way to get a volume out of a 4D set? I have
> dti images but need to extract the b0 from the rest (the b0 is always
> first). Can't quite figure out what parameters to use for mincextract.

Maybe it is easier to do mincreshape -dimrange time=0 to the temporary
file, and then use mincextract ?


-- 
Best regards,
 Vladimir S. Fonov ~ v.s.fonov <@> ilmarin.info

From a.janke at gmail.com  Wed Nov  4 04:40:41 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 4 Nov 2009 20:40:41 +1100
Subject: [MINC-users] Karmic (Koala) Ubuntu packages
Message-ID: <d747ed50911040140o348479fub1183edb53305624@mail.gmail.com>

Hi all,

I am currently uploading packages (both amd64 and i386) for Ubuntu
Karmic Koala here:

? http://packages.bic.mni.mcgill.ca/ubuntu-karmic/

Let me know if you have any problems with them, they should be all
uploaded in the next hour of so.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


From vladimir.fonov at gmail.com  Wed Nov  4 09:33:53 2009
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Wed, 04 Nov 2009 09:33:53 -0500
Subject: [MINC-users] Karmic (Koala) Ubuntu packages
In-Reply-To: <d747ed50911040140o348479fub1183edb53305624@mail.gmail.com>
References: <d747ed50911040140o348479fub1183edb53305624@mail.gmail.com>
Message-ID: <4AF190D1.9070400@gmail.com>

Hello,

Andrew Janke wrote:
> I am currently uploading packages (both amd64 and i386) for Ubuntu
> Karmic Koala here:
> 
>   http://packages.bic.mni.mcgill.ca/ubuntu-karmic/
> 
> Let me know if you have any problems with them, they should be all
> uploaded in the next hour of so.

By the way, is there any chance that 
http://packages.bic.mni.mcgill.ca/deb/ gets updated with latest version 
of the tools?

-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From a.janke at gmail.com  Thu Nov  5 07:57:57 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 5 Nov 2009 23:57:57 +1100
Subject: [MINC-users] Karmic (Koala) Ubuntu packages
In-Reply-To: <4AF190D1.9070400@gmail.com>
References: <d747ed50911040140o348479fub1183edb53305624@mail.gmail.com> 
	<4AF190D1.9070400@gmail.com>
Message-ID: <d747ed50911050457l2c02c163o237b99517b6f59a2@mail.gmail.com>

> By the way, is there any chance that
> http://packages.bic.mni.mcgill.ca/deb/ gets updated with latest version
> of the tools?

For the Debian lenny users I just built these:

   http://packages.bic.mni.mcgill.ca/debian-lenny/

Let me know if they work for you, if they do I think I will delete the
old deb directory.

Note that the models packages are missing for now as I will run out of
quota (700MB of them) if I upload them from home tonight.  I'll upload
them in the morning when my ADSL account is in offpeak!


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From a.janke at gmail.com  Thu Nov  5 20:52:48 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 6 Nov 2009 12:52:48 +1100
Subject: [MINC-users] debian lenny packages now available
Message-ID: <d747ed50911051752k5e0eb9fct620fcde72a6be75a@mail.gmail.com>

Hi all,

I have had a few requests for these so here you are:

   http://packages.bic.mni.mcgill.ca/debian-lenny/

I am looking into making some Fedora 11/12 packages too so stay tuned.
(or email me if you want these to kick me along the process).


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From mishkind at gmail.com  Sat Nov  7 01:03:39 2009
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Sat, 7 Nov 2009 01:03:39 -0500
Subject: [MINC-users] debian lenny packages now available
In-Reply-To: <d747ed50911051752k5e0eb9fct620fcde72a6be75a@mail.gmail.com>
References: <d747ed50911051752k5e0eb9fct620fcde72a6be75a@mail.gmail.com>
Message-ID: <9c5abb60911062203x5f42e09dw121afcb516dfbbb6@mail.gmail.com>

Hi,

Running ubuntu 9.10 (karmic koala, i386) at home, and am pleased to
say that so far all the minc tools work fine.
I did notice however that brain-view was missing from the
/ubuntu-karmic/ directory, I tried installing via the .deb package.

But got the following:

thinkpad[~/pial]$ brain-view
brain-view: error while loading shared libraries: libCoin.so.40:
cannot open shared object file: No such file or directory

thinkpad[~/pial]$ sudo apt-get install libcoin40c2
thinkpad[~/pial]$ brain-view
Segmentation fault

thinkpad[~/pial]$ sudo apt-get install libcoin40-dev
The following packages will be REMOVED:
  libcoin60-dev libsoqt3-dev mincbundle
The following NEW packages will be installed:
  libcoin40-dev
0 upgraded, 1 newly installed, 3 to remove and 0 not upgraded.
Need to get 3,418kB of archives.
After this operation, 6,361kB disk space will be freed.
Do you want to continue [Y/n]? n

Looks like some sort of libCoin dependency problem. Any help on
getting brain-view to work without having to un-install mincbundle?

thanks,
mishkin




On Thu, Nov 5, 2009 at 8:52 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi all,
>
> I have had a few requests for these so here you are:
>
> ? http://packages.bic.mni.mcgill.ca/debian-lenny/
>
> I am looking into making some Fedora 11/12 packages too so stay tuned.
> (or email me if you want these to kick me along the process).
>
>
> --
> 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
>


From a.janke at gmail.com  Sat Nov  7 04:56:39 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 7 Nov 2009 20:56:39 +1100
Subject: [MINC-users] debian lenny packages now available
In-Reply-To: <9c5abb60911062203x5f42e09dw121afcb516dfbbb6@mail.gmail.com>
References: <d747ed50911051752k5e0eb9fct620fcde72a6be75a@mail.gmail.com> 
	<9c5abb60911062203x5f42e09dw121afcb516dfbbb6@mail.gmail.com>
Message-ID: <d747ed50911070156h57e69afdk545d3f7367c38527@mail.gmail.com>

> Running ubuntu 9.10 (karmic koala, i386) at home, and am pleased to
> say that so far all the minc tools work fine.
> I did notice however that brain-view was missing from the
> /ubuntu-karmic/ directory, I tried installing via the .deb package.

Meaning the debian lenny variant?

> Looks like some sort of libCoin dependency problem.

Unfortunately from my digging into this the problem is a bit more
insidious and from what I can tell a problem with a QT3->QT4 upgrade
in the various distros. I am hoping that Jason can shed some light on
this as brain-view is his baby.

> Any help on
> getting brain-view to work without having to un-install mincbundle?

Well uninstalling mincbundle should not be a problem in itself, it is
just a meta-package akin so ubuntu-desktop that I use to track
dependencies.


a

From sean at rogue-research.com  Fri Nov 13 17:41:18 2009
From: sean at rogue-research.com (Sean McBride)
Date: Fri, 13 Nov 2009 17:41:18 -0500
Subject: [MINC-users] MINC and supporting HDF5 1.8.x
Message-ID: <20091113224118.163982854@kingu.local>

Hi all,

There have been many posts on this list about the fact that MINC
requires HDF5 1.6.x not 1.8.x.  Is this still so?  If so, will it be
rectified?

Just today, 1.8.4 and 1.6.10 were released:
http://www.hdfgroup.org/newsletters/newsletter109.html

Notice that it says:
"HDF5 1.6.10 is the LAST RELEASE of HDF5 1.6"

The HDF folks say "1.8 libraries should work seamlessly with the
applications written for 1.6 and earlier. Please see "API Compatibility
Macros in HDF5" document for more information
http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html 
Please let us know about any problems you encounter when using 1.6
application with 1.8 (and later)."

So what's the status of MINC and HDF5 1.8?

Thanks,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada




From a.janke at gmail.com  Wed Nov 18 07:27:53 2009
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 18 Nov 2009 23:27:53 +1100
Subject: [MINC-users] MINC and supporting HDF5 1.8.x
In-Reply-To: <20091113224118.163982854@kingu.local>
References: <20091113224118.163982854@kingu.local>
Message-ID: <d747ed50911180427q6c59e02aj10632a69d9b2fe09@mail.gmail.com>

Hi Sean,

Sorry for the delay with this reply but you set me to porting MINC to
HDF 1.8.x ..

> There have been many posts on this list about the fact that MINC
> requires HDF5 1.6.x not 1.8.x. ?Is this still so? ?If so, will it be
> rectified?

Yes it is still the case. I don't know what you mean by rectified, the
1.6.x release will still be good for some time yet. But yes in time
we/I will port MINC to 1.8.x (like right now! :)

> So what's the status of MINC and HDF5 1.8?

Well after a few hours (mainly reading the spec to see what changed) I
have a working version of MINC:

spencer:minc$ mincmath -version
program: 2.0.19
libminc: 2.0.19
netcdf : "3.6.2" of Sep 24 2009 17:09:40 $
HDF5   : 1.8.4

I need to do more testing but so far all the unit tests I have are
flawless. If you are interested I could send you a unified diff to the
current CVS HEAD of MINC of my changes but I won't be committing them
to CVS anytime soon because I haven't had enough time to test it
properly yet.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883