From a.janke at gmail.com  Fri Jan  1 09:18:44 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 2 Jan 2010 01:18:44 +1100
Subject: [MINC-users] mincresample - what is the expected behavior
In-Reply-To: <4B3D0CBC.3060503@phenogenomics.ca>
References: <4B3D0CBC.3060503@phenogenomics.ca>
Message-ID: <d747ed51001010618q2280a513reafb7646f76833eb@mail.gmail.com>

Hi Matthijs,

On Fri, Jan 1, 2010 at 07:42, Matthijs van Eede
<matthijs at phenogenomics.ca> wrote:
> I have a question about the expected behavior of mincresample when using
> a transformation file with a combination of rotations and translations.
> The problem is as follows. There is a source file which has its center
> of gravity in -510,0,0 and a target file which has its center of gravity
> in 0,0,0. The source image should be translated to the target image and
> then rotated by -4,1,-13. If I specify two transformation (xfm) files,
> one for the translation and one for the rotation and apply these
> sequentially, the resulting transformation is correct., i.e., it has its
> center of gravity in the origin and rotated around that. However, if I
> create one transformation file which contains both transformations, I
> "loose" my file; its new center of gravity is not in 0,0,0 but in
> 14,118,2 suggesting that the rotation was applied before the
> transformation. Is this the expected behavior for mincresample?


mincresample doesn't know about translations and rotations as these
are just one way of decomposing a affine matrix transformation. Note
that for each affine transformation matrix there are often multiple
ways of decomposing it into rotations and translations. In order to
avoid this problem mincresample treats all such transformations as
affine as defined by a 4x4 matrix (well, really a 3x3 with a column
matrix tacked onto the end for translations and 0,0,0,1 in the last
row but I digress).

You would be better of thinking of this as a problem in setting up
your affine transformation matrices. You would typically define/create
these using param2xfm and it is here that the order of operations is
important.  So first lets define the transformation matrix:

spencer:~$ param2xfm -translation 510 0 0 trans.xfm

spencer:~$ cat trans.xfm
MNI Transform File
%Sat Jan  2 01:14:17 2010>>> param2xfm -translation 510 0 0 trans.xfm
%(Package mni_autoreg 0.99.6, compiled by @murdoch
(x86_64-unknown-linux-gnu) on Thu Oct 22 12:03:54 EST 2009)

Transform_Type = Linear;
Linear_Transform =
 1 0 0 510
 0 1 0 0
 0 0 1 0;

Now our rotations matrix:

spencer:~$ param2xfm -rotations -3 1 -13 rot.xfm

spencer:~$ cat rot.xfm
MNI Transform File
%Sat Jan  2 01:14:35 2010>>> param2xfm -rotations -3 1 -13 rot.xfm
%(Package mni_autoreg 0.99.6, compiled by @murdoch
(x86_64-unknown-linux-gnu) on Thu Oct 22 12:03:54 EST 2009)

Transform_Type = Linear;
Linear_Transform =
 0.974221646785736 0.223752781748772 0.0287548266351223 0
 -0.224916785955429 0.97324013710022 0.0470740348100662 0
 -0.0174524057656527 -0.0523279905319214 0.998477458953857 0;

Now add them together:

spencer:~$ xfmconcat trans.xfm rot.xfm out.xfm

And have a look at the result:

spencer:~$ cat out.xfm
MNI Transform File
%Sat Jan  2 01:14:44 2010>>> xfmconcat trans.xfm rot.xfm out.xfm

Transform_Type = Linear;
Linear_Transform =
 0.974221646785736 0.223752781748772 0.0287548266351223 496.853039860725
 -0.224916785955429 0.97324013710022 0.0470740348100662 -114.707560837269
 -0.0174524057656527 -0.0523279905319214 0.998477458953857 -8.90072694048288;

Note that the 4th column probably isn't what you'd expect.

Hope this helps.


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

From matthijs at phenogenomics.ca  Fri Jan  1 22:55:19 2010
From: matthijs at phenogenomics.ca (Matthijs van Eede)
Date: Fri, 1 Jan 2010 22:55:19 -0500
Subject: [MINC-users] mincresample - what is the expected behavior
Message-ID: <30345739.62511262404519005.JavaMail.root@mail2.phenogenomics.ca>

Hi Andrew,

Thank you very much! I am trying to debug a minctracc error I am getting and got confused when minctracc said the following:

after parameter optimization
-center      -508.71222    0.90644   -5.98667
-translation  508.09448    0.51216   -1.63015
-rotation      -3.84787    1.13791  -13.16369
-scale          1.00000    1.00000    1.00000
-shear          0.00000    0.00000    0.00000

and xfm2param gave me the following on the transformation that was created by minctracc:

-center         0.00000    0.00000    0.00000
-translation  494.63181 -114.92624  -11.68648
-rotation      -3.84787    1.13791  -13.16369
-scale          1.00000    1.00000    1.00000
-shear          0.00000   -0.00000   -0.00000

When I saw that large difference in the translation, I tried to simulate the problem by using param2xfm and specifying the translation and rotation at the same time with the output of minctracc, but given your response I now found that this is indeed not where things go wrong. Things go wrong when I now use this transformation as input for a sequential minctracc call in order to refine the initial registration. That second transformation I get from minctracc is:

-center         0.00000    0.00000    0.00000
-translation  495.03180 -114.52625  -11.28648
-rotation      -2.84787    2.13791  -16.16369
-scale          1.00000    1.00000    1.00000
-shear          0.00000   -0.00000    0.00000

So minctracc seems to have mainly improved on the rotation side with respect to the input transformation, but the translation part looks mostly unchanged. Could it be that now there is a problem in terms of concatenating transforms? I.e., does minctracc concatenate the input transformation with the transformation it finds after the optimization? Because when I use this second transformation on my source image it is lost/gone.

Thanks,
Matthijs

----- Original Message -----
From: Andrew Janke <a.janke at gmail.com>
Sent: Fri, 1/1/2010 9:18am
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] mincresample - what is the expected behavior

Hi Matthijs,

On Fri, Jan 1, 2010 at 07:42, Matthijs van Eede
<matthijs at phenogenomics.ca> wrote:
> I have a question about the expected behavior of mincresample when using
> a transformation file with a combination of rotations and translations.
> The problem is as follows. There is a source file which has its center
> of gravity in -510,0,0 and a target file which has its center of gravity
> in 0,0,0. The source image should be translated to the target image and
> then rotated by -4,1,-13. If I specify two transformation (xfm) files,
> one for the translation and one for the rotation and apply these
> sequentially, the resulting transformation is correct., i.e., it has its
> center of gravity in the origin and rotated around that. However, if I
> create one transformation file which contains both transformations, I
> "loose" my file; its new center of gravity is not in 0,0,0 but in
> 14,118,2 suggesting that the rotation was applied before the
> transformation. Is this the expected behavior for mincresample?


mincresample doesn't know about translations and rotations as these
are just one way of decomposing a affine matrix transformation. Note
that for each affine transformation matrix there are often multiple
ways of decomposing it into rotations and translations. In order to
avoid this problem mincresample treats all such transformations as
affine as defined by a 4x4 matrix (well, really a 3x3 with a column
matrix tacked onto the end for translations and 0,0,0,1 in the last
row but I digress).

You would be better of thinking of this as a problem in setting up
your affine transformation matrices. You would typically define/create
these using param2xfm and it is here that the order of operations is
important.  So first lets define the transformation matrix:

spencer:~$ param2xfm -translation 510 0 0 trans.xfm

spencer:~$ cat trans.xfm
MNI Transform File
%Sat Jan  2 01:14:17 2010>>> param2xfm -translation 510 0 0 trans.xfm
%(Package mni_autoreg 0.99.6, compiled by @murdoch
(x86_64-unknown-linux-gnu) on Thu Oct 22 12:03:54 EST 2009)

Transform_Type = Linear;
Linear_Transform =
 1 0 0 510
 0 1 0 0
 0 0 1 0;

Now our rotations matrix:

spencer:~$ param2xfm -rotations -3 1 -13 rot.xfm

spencer:~$ cat rot.xfm
MNI Transform File
%Sat Jan  2 01:14:35 2010>>> param2xfm -rotations -3 1 -13 rot.xfm
%(Package mni_autoreg 0.99.6, compiled by @murdoch
(x86_64-unknown-linux-gnu) on Thu Oct 22 12:03:54 EST 2009)

Transform_Type = Linear;
Linear_Transform =
 0.974221646785736 0.223752781748772 0.0287548266351223 0
 -0.224916785955429 0.97324013710022 0.0470740348100662 0
 -0.0174524057656527 -0.0523279905319214 0.998477458953857 0;

Now add them together:

spencer:~$ xfmconcat trans.xfm rot.xfm out.xfm

And have a look at the result:

spencer:~$ cat out.xfm
MNI Transform File
%Sat Jan  2 01:14:44 2010>>> xfmconcat trans.xfm rot.xfm out.xfm

Transform_Type = Linear;
Linear_Transform =
 0.974221646785736 0.223752781748772 0.0287548266351223 496.853039860725
 -0.224916785955429 0.97324013710022 0.0470740348100662 -114.707560837269
 -0.0174524057656527 -0.0523279905319214 0.998477458953857 -8.90072694048288;

Note that the 4th column probably isn't what you'd expect.

Hope this helps.


--
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 Jan  2 06:13:56 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 2 Jan 2010 22:13:56 +1100
Subject: [MINC-users] mincresample - what is the expected behavior
In-Reply-To: <30345739.62511262404519005.JavaMail.root@mail2.phenogenomics.ca>
References: <30345739.62511262404519005.JavaMail.root@mail2.phenogenomics.ca>
Message-ID: <d747ed51001020313y54f39deci1652c1aca45ed8b7@mail.gmail.com>

> Thank you very much! I am trying to debug a minctracc error I am getting and got confused when minctracc said the following:
>
> after parameter optimization
> -center ? ? ?-508.71222 ? ?0.90644 ? -5.98667
> -translation ?508.09448 ? ?0.51216 ? -1.63015
> -rotation ? ? ?-3.84787 ? ?1.13791 ?-13.16369
> -scale ? ? ? ? ?1.00000 ? ?1.00000 ? ?1.00000
> -shear ? ? ? ? ?0.00000 ? ?0.00000 ? ?0.00000
>
> and xfm2param gave me the following on the transformation that was created by minctracc:
>
> -center ? ? ? ? 0.00000 ? ?0.00000 ? ?0.00000
> -translation ?494.63181 -114.92624 ?-11.68648
> -rotation ? ? ?-3.84787 ? ?1.13791 ?-13.16369
> -scale ? ? ? ? ?1.00000 ? ?1.00000 ? ?1.00000
> -shear ? ? ? ? ?0.00000 ? -0.00000 ? -0.00000
>
> When I saw that large difference in the translation, I tried to simulate the problem by using param2xfm and specifying the translation and rotation at the same time with the output of minctracc, but given your response I now found that this is indeed not where things go wrong.

Correct, or at least the above output is not incorrect, xfm2param has
to make assumptions when doing an Euler angle decomposition (3
rotations) of an affine transformation matrix.  One of these is that
it will assume the centre of rotation is 0,0,0. You can change this
with the -center argument and this then will give you a differing set
of rotations and transformations. Another assumption is that the
rotation can never be more than 90deg in any direction, this is not
always true in the general case but minctracc will not find a rotation
larger than this due to the "gimball lock" problem. (See:
http://en.wikipedia.org/wiki/Euler_angles).

That said minctracc optimises using an Euler angle representation and then
converts this to an affine matrix at the end in order to save the result.

> Things go wrong when I now use this transformation as input for a sequential minctracc call in order to refine the initial registration. That second transformation I get from minctracc is:
>
> -center ? ? ? ? 0.00000 ? ?0.00000 ? ?0.00000
> -translation ?495.03180 -114.52625 ?-11.28648
> -rotation ? ? ?-2.84787 ? ?2.13791 ?-16.16369
> -scale ? ? ? ? ?1.00000 ? ?1.00000 ? ?1.00000
> -shear ? ? ? ? ?0.00000 ? -0.00000 ? ?0.00000
>
> So minctracc seems to have mainly improved on the rotation side with respect to the input transformation, but the translation part looks mostly unchanged. Could it be that now there is a problem in terms of concatenating transforms?

I would dobt it.

> i.e., does minctracc concatenate the input transformation with the transformation it finds after the optimization?

Yes.

> Because when I use this second transformation on my source image it is lost/gone.

Depends on what you are doing with mincresample. When you resample you
are going to have to ensure that your output sampling will cover the
area where your image has been transformed too (in your case 500mm in
X).   The general formula is like this:

   minctracc source.mnc target.mnc out.xfm

   mincresample -like target.mnc -transformation out.xfm source.mnc out.mnc

Meaning the output sampling is taken from the target file.


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


From parya.momayyezsiahkal at mail.mcgill.ca  Sun Jan  3 00:58:41 2010
From: parya.momayyezsiahkal at mail.mcgill.ca (Parya Momayyezsiahkal)
Date: Sun, 3 Jan 2010 00:58:41 -0500
Subject: [MINC-users] minc 1 installation
Message-ID: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>

Hi all,

I have recently installed Ubuntu 9.10 on my iMac and was trying to install minc1 libraries.
While ./configure runs fine, I'll get the following error meassge when make is run:

libsrc/image_conversion.c: In function 'miicv_create':
libsrc/image_conversion.c:206: error: 'MAX_NC_OPEN' undeclared (first use in this function)
libsrc/image_conversion.c:206: error: (Each undeclared identifier is reported only once
libsrc/image_conversion.c:206: error: for each function it appears in.)

As far as I know, MAX_NC_OPEN has been defined in netcdf.h which is located in the /usr/include/ directory in my case. The netcdf library is also located in /usr/lib which I assume is a standard location on Ubuntu.
I am really confused now and I would appreciate if anyone can help me with this.

Thanks,
Parya

From nikelski at bic.mni.mcgill.ca  Sun Jan  3 15:49:15 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Sun, 3 Jan 2010 12:49:15 -0800
Subject: [MINC-users] minc 1 installation
In-Reply-To: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>
References: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>
Message-ID: <e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com>

Hi Parya,

   Ahhh, so many questions ...

(1) Just curious, why did you install ubuntu on your mac? Why not run
minc natively?
(2) Did you install ubuntu on a VM, or did you really wipe out OS X?
(3) Why not use the pre-built minc packages?
(4) Did you also build hdf5 and netcdf yourself? Did the "make check"
work for both?
(5) Did you use the default configure switches, or did you add any
extra? I use something like ..

# set the new BIC install directory
export BIC_BUILD_PATH=/usr/local/bic/new_build
export BIC_INSTALL_PATH=/usr/local/bic/new_build
#
./configure  \
    --prefix=$BIC_INSTALL_PATH  \
    --with-build-path=$BIC_BUILD_PATH  \
    --enable-shared  \
    --enable-static  \
    --enable-acr-nema

HTH. Happy building.

-Jim


On Sat, Jan 2, 2010 at 9:58 PM, Parya Momayyezsiahkal
<parya.momayyezsiahkal at mail.mcgill.ca> wrote:
> Hi all,
>
> I have recently installed Ubuntu 9.10 on my iMac and was trying to install minc1 libraries.
> While ./configure runs fine, I'll get the following error meassge when make is run:
>
> libsrc/image_conversion.c: In function 'miicv_create':
> libsrc/image_conversion.c:206: error: 'MAX_NC_OPEN' undeclared (first use in this function)
> libsrc/image_conversion.c:206: error: (Each undeclared identifier is reported only once
> libsrc/image_conversion.c:206: error: for each function it appears in.)
>
> As far as I know, MAX_NC_OPEN has been defined in netcdf.h which is located in the /usr/include/ directory in my case. The netcdf library is also located in /usr/lib which I assume is a standard location on Ubuntu.
> I am really confused now and I would appreciate if anyone can help me with this.
>
> Thanks,
> Parya
> _______________________________________________
> 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

From parya.momayyezsiahkal at mail.mcgill.ca  Sun Jan  3 18:19:49 2010
From: parya.momayyezsiahkal at mail.mcgill.ca (Parya Momayyezsiahkal)
Date: Sun, 3 Jan 2010 18:19:49 -0500
Subject: [MINC-users] minc 1 installation
In-Reply-To: <e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com>
References: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>,
	<e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com>
Message-ID: <077D717CC5336C42939EAC0561788F81EF325CE493@EXMBXVS4B.campus.mcgill.ca>

Hi Jim,

Here are the answers to tour questions:

1) I use Ubuntu at work, and I wanted to have the same system at home. And also, I am not that comfortable with Xtool Debugger for C++ code development, and eclipse which is much easier to work with has so many bugs on Mac.
2) I have partitioned the disk space to dual boot Ubuntu and Mac OS x.
3) I want to have minc-1 libraries. For minc2, I have used the pre-built minc package. And also when I try to to install minc package using Synaptic package manager, I 'll get the message saying:
Depends: netcdf which is not installable.
4) No I have not built hdf5 and netcdf myself.
5) I tried the --prefix option, the LDFlags option, LIBS option, but none of them helped.

thanks,
Parya
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of EJ Nikelski [nikelski at bic.mni.mcgill.ca]
Sent: Sunday, January 03, 2010 3:49 PM
To: MINC users mailing list
Subject: Re: [MINC-users] minc 1 installation

Hi Parya,

   Ahhh, so many questions ...

(1) Just curious, why did you install ubuntu on your mac? Why not run
minc natively?
(2) Did you install ubuntu on a VM, or did you really wipe out OS X?
(3) Why not use the pre-built minc packages?
(4) Did you also build hdf5 and netcdf yourself? Did the "make check"
work for both?
(5) Did you use the default configure switches, or did you add any
extra? I use something like ..

# set the new BIC install directory
export BIC_BUILD_PATH=/usr/local/bic/new_build
export BIC_INSTALL_PATH=/usr/local/bic/new_build
#
./configure  \
    --prefix=$BIC_INSTALL_PATH  \
    --with-build-path=$BIC_BUILD_PATH  \
    --enable-shared  \
    --enable-static  \
    --enable-acr-nema

HTH. Happy building.

-Jim


On Sat, Jan 2, 2010 at 9:58 PM, Parya Momayyezsiahkal
<parya.momayyezsiahkal at mail.mcgill.ca> wrote:
> Hi all,
>
> I have recently installed Ubuntu 9.10 on my iMac and was trying to install minc1 libraries.
> While ./configure runs fine, I'll get the following error meassge when make is run:
>
> libsrc/image_conversion.c: In function 'miicv_create':
> libsrc/image_conversion.c:206: error: 'MAX_NC_OPEN' undeclared (first use in this function)
> libsrc/image_conversion.c:206: error: (Each undeclared identifier is reported only once
> libsrc/image_conversion.c:206: error: for each function it appears in.)
>
> As far as I know, MAX_NC_OPEN has been defined in netcdf.h which is located in the /usr/include/ directory in my case. The netcdf library is also located in /usr/lib which I assume is a standard location on Ubuntu.
> I am really confused now and I would appreciate if anyone can help me with this.
>
> Thanks,
> Parya
> _______________________________________________
> 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 a.janke at gmail.com  Sun Jan  3 18:58:42 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 4 Jan 2010 10:58:42 +1100
Subject: [MINC-users] minc 1 installation
In-Reply-To: <077D717CC5336C42939EAC0561788F81EF325CE493@EXMBXVS4B.campus.mcgill.ca>
References: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>
	<e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com> 
	<077D717CC5336C42939EAC0561788F81EF325CE493@EXMBXVS4B.campus.mcgill.ca>
Message-ID: <d747ed51001031558i43494971t6bbbff7843019634@mail.gmail.com>

Hi Parya,

> 1) I use Ubuntu at work, and I wanted to have the same system at home. And also, I am not that comfortable with Xtool Debugger for C++ code development, and eclipse which is much easier to work with has so many bugs on Mac.
> 2) I have partitioned the disk space to dual boot Ubuntu and Mac OS x.
> 3) I want to have minc-1 libraries. For minc2, I have used the pre-built minc package. And also when I try to to install minc package using Synaptic package manager, I 'll get the message saying:
> Depends: netcdf which is not installable.

Which versions of minc are you using?  I just downloaded the last minc
1.x release (1.5.1) and built it successfully on Ubuntu Karmic Koala
(9.10).

harold:minc-1.5.1$ ./mincmath -version
program: 1.5.1
libminc: 1.5.1
netcdf : "3.6.2" of Sep 24 2009 17:09:40 $

The MAX_NC_OPEN problem is a known issue that was fixed a while back.
Also which versions of the minc2 packages are you using and from
where?


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

From sean at rogue-research.com  Tue Jan  5 10:27:46 2010
From: sean at rogue-research.com (Sean McBride)
Date: Tue, 5 Jan 2010 10:27:46 -0500
Subject: [MINC-users] minc 1 installation
In-Reply-To: <d747ed51001031558i43494971t6bbbff7843019634@mail.gmail.com>
References: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>
	<e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com> 
	<077D717CC5336C42939EAC0561788F81EF325CE493@EXMBXVS4B.campus.mcgill.ca>
	<d747ed51001031558i43494971t6bbbff7843019634@mail.gmail.com>
Message-ID: <20100105152746.1354248713@kingu.local>

On 1/4/10 10:58 AM, Andrew Janke said:

>The MAX_NC_OPEN problem is a known issue that was fixed a while back.

IIRC, you fixed this in minc2.  Did you fix it in minc1 also?

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




From parya.momayyezsiahkal at mail.mcgill.ca  Tue Jan  5 12:23:33 2010
From: parya.momayyezsiahkal at mail.mcgill.ca (Parya Momayyezsiahkal)
Date: Tue, 5 Jan 2010 12:23:33 -0500
Subject: [MINC-users] minc 1 installation
In-Reply-To: <20100105152746.1354248713@kingu.local>
References: <077D717CC5336C42939EAC0561788F81EF325CE491@EXMBXVS4B.campus.mcgill.ca>
	<e12172551001031249sbf84843je033500cc30a1c12@mail.gmail.com>
	<077D717CC5336C42939EAC0561788F81EF325CE493@EXMBXVS4B.campus.mcgill.ca>
	<d747ed51001031558i43494971t6bbbff7843019634@mail.gmail.com>,
	<20100105152746.1354248713@kingu.local>
Message-ID: <077D717CC5336C42939EAC0561788F81F207A1E4A1@EXMBXVS4B.campus.mcgill.ca>

I finally managed to install minc1.
Downloaded the .tgz file again, and reran everything. It Worked this time.

Thanks,
Parya
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Sean McBride [sean at rogue-research.com]
Sent: Tuesday, January 05, 2010 10:27 AM
To: MINC users mailing list; Andrew Janke
Subject: Re: [MINC-users] minc 1 installation

On 1/4/10 10:58 AM, Andrew Janke said:

>The MAX_NC_OPEN problem is a known issue that was fixed a while back.

IIRC, you fixed this in minc2.  Did you fix it in minc1 also?

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



_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From mrkind.liu at gmail.com  Thu Jan  7 20:55:31 2010
From: mrkind.liu at gmail.com (Hailing Liu)
Date: Fri, 8 Jan 2010 10:55:31 +0900
Subject: [MINC-users] about Minc installation
Message-ID: <9d8a64141001071755x61167a1fscd95405c131687c2@mail.gmail.com>

Hello, I am a fresher to Minc. I tried to install Minc under Linux Redhat.
I think I have installed netcdf correctly. but when I install Minc, the
system give me some messages like this "checking for library netcdf...
no" ,"configure: error: cannot find required library netcdf".  I have
compiled my .bash_profile by adding following command:
export PATH=$NETCDF/bin:$PATH
export LD_LIBRARY_PATH=/netcdf/lib:$LD_LIBRARY_PATH
So I can't find the problem, can you give me some advice or instruction,
thank you very much.

From se at hst.aau.dk  Fri Jan  8 04:43:06 2010
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Fri, 8 Jan 2010 10:43:06 +0100 (CET)
Subject: [MINC-users] about Minc installation
In-Reply-To: <9d8a64141001071755x61167a1fscd95405c131687c2@mail.gmail.com>
Message-ID: <984353336.658971262943786011.JavaMail.root@zimbra-store01.hst.aau.dk>

Hi Hailing,

Usually libnetcdf.so is installed in /usr/lib not /netcdf/lib
However, the linker should look there by default, so check if you have libnetcdf.so in /usr/lib
Also, how did you install netcdf? What versions of netcdf and minc?

Simon
----- "Hailing Liu" <mrkind.liu at gmail.com> wrote:

> Hello, I am a fresher to Minc. I tried to install Minc under Linux
> Redhat.
> I think I have installed netcdf correctly. but when I install Minc,
> the
> system give me some messages like this "checking for library
> netcdf...
> no" ,"configure: error: cannot find required library netcdf".  I have
> compiled my .bash_profile by adding following command:
> export PATH=$NETCDF/bin:$PATH
> export LD_LIBRARY_PATH=/netcdf/lib:$LD_LIBRARY_PATH
> So I can't find the problem, can you give me some advice or
> instruction,
> thank you very much.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From pbellec at bic.mni.mcgill.ca  Wed Jan 13 23:23:47 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Wed, 13 Jan 2010 23:23:47 -0500
Subject: [MINC-users]  emma
Message-ID: <6fe841c71001132023x7d4d1654q3551e589bf27f6fa@mail.gmail.com>

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