From sorench at gmail.com  Mon Nov  1 23:48:15 2010
From: sorench at gmail.com (Soren Christensen)
Date: Tue, 2 Nov 2010 14:48:15 +1100
Subject: [MINC-users] mincresample of negative zsteps
In-Reply-To: <AANLkTikaHNunv=mFofQbrLyNhuZq8ybwwRsaddFH1Oo9@mail.gmail.com>
References: <AANLkTi=DcDCKUaDcgRKB=k0r+y5JXyC3raFCwK++cWN_@mail.gmail.com>
	<AANLkTikaHNunv=mFofQbrLyNhuZq8ybwwRsaddFH1Oo9@mail.gmail.com>
Message-ID: <AANLkTi=4MOX3ZxG9TBmja14XMpv79RKpmMeHNfuUQ+sT@mail.gmail.com>

Hi Andrew,
 Sorry, have been away for a while and just trying to look into this now.

Yes the files have cosines - and as far as I can tell non-suspicious looking
too:
mincheader template.mnc  | grep cos
        zspace:direction_cosines = -0., -0., 1. ;
        yspace:direction_cosines = -0., 1., -0. ;
        xspace:direction_cosines = 1., -0., -0. ;
mincheader to_be_resampled.mnc  | grep cos
        zspace:direction_cosines = -0., -0., 1. ;
        yspace:direction_cosines = -0., 1., -0. ;
        xspace:direction_cosines = 1., -0., -0. ;


I am not sure where the problem arises (is it that zspace is my slowest
varying dim and the -1 you allude to?)

In any case, I can work around it by reshaping to positive zsteps:
mincreshape -dimsize zspace=-1 +zdirection -clobber template.mnc
new_template.mnc

Using new_template.mnc as target solves it. So it seems the problem has to
do with the "likefile" in mincresample having negative zsteps.

Thanks for the suggestions!

Cheers
Soren



On Wed, Oct 20, 2010 at 4:02 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren,
>
> On Sat, Oct 16, 2010 at 13:10, Soren Christensen <sorench at gmail.com>
> wrote:
> >  I have trouble understanding why I get a positive zstep when
> > resampling like a file with a negative zstep:
> >
> > The effect of this seems to be that the resampling is done outside of
> > the volume of to_be_resampled.mnc and I get an empty image as result.
> >
> > Can anyone see what is happening?
>
> As of right now no. My initial guess is you are being bitten by the
> non-image dimension behavior. (search for -1 in man mincreshape) but I
> am not sure if this is the case.
>
> Do the files have direction cosines?
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Nov  2 00:23:06 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 2 Nov 2010 15:23:06 +1100
Subject: [MINC-users] mincresample of negative zsteps
In-Reply-To: <AANLkTi=4MOX3ZxG9TBmja14XMpv79RKpmMeHNfuUQ+sT@mail.gmail.com>
References: <AANLkTi=DcDCKUaDcgRKB=k0r+y5JXyC3raFCwK++cWN_@mail.gmail.com>
	<AANLkTikaHNunv=mFofQbrLyNhuZq8ybwwRsaddFH1Oo9@mail.gmail.com>
	<AANLkTi=4MOX3ZxG9TBmja14XMpv79RKpmMeHNfuUQ+sT@mail.gmail.com>
Message-ID: <AANLkTinA9Enu6wsPivuAHZ5hEO544JzeiVSiZ84c0R1D@mail.gmail.com>

I think so ( in this case). Peter oroginally made a distinction
between the slice and in-plane dimensions for reasons known to him. I
think a lot of the reason was around slice scaling of image ranges.

In any case it can sometimes make for some interesting (and at times)
unexpected results. :(


a

On Tue, Nov 2, 2010 at 14:48, Soren Christensen <sorench at gmail.com> wrote:
> I am not sure where the problem arises (is it that zspace is my slowest
> varying dim and the -1 you allude to?)
>

From sorench at gmail.com  Tue Nov  2 02:21:43 2010
From: sorench at gmail.com (Soren Christensen)
Date: Tue, 2 Nov 2010 17:21:43 +1100
Subject: [MINC-users] mincresample of negative zsteps
In-Reply-To: <AANLkTinA9Enu6wsPivuAHZ5hEO544JzeiVSiZ84c0R1D@mail.gmail.com>
References: <AANLkTi=DcDCKUaDcgRKB=k0r+y5JXyC3raFCwK++cWN_@mail.gmail.com>
	<AANLkTikaHNunv=mFofQbrLyNhuZq8ybwwRsaddFH1Oo9@mail.gmail.com>
	<AANLkTi=4MOX3ZxG9TBmja14XMpv79RKpmMeHNfuUQ+sT@mail.gmail.com>
	<AANLkTinA9Enu6wsPivuAHZ5hEO544JzeiVSiZ84c0R1D@mail.gmail.com>
Message-ID: <AANLkTikCaXQXGuVSqMpGzxoy-gcc5eBJCMBamYoP6U6U@mail.gmail.com>

Thanks Andrew,
 I just bumped into another issue with mincresample this afternoon - this
time with ordinary positive zsteps:

Shouldn't the resampled file below get a zstep of 4?    what could be the
reason it becomes 3.74669 only?

mincinfo roi_no_header.mnc
file: roi_no_header.mnc
image: unsigned byte 0 to 255
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                      9      unknown      unknown
    yspace                    512      unknown      unknown
    xspace                    512      unknown      unknown

mincinfo template.mnc
file: template.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                      9            4     -513.102
    yspace                    512     -0.40625       102.84
    xspace                    512     -0.40625      103.797


mincresample -like template.mnc -nearest roi_no_header.mnc
roi_l_template.mnc

file: roi_l_template.mnc
image: unsigned byte 0 to 255
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                      9      3.74669     -513.102
    yspace                    512     -0.40625       102.84
    xspace                    512     -0.40625      103.797



Cheers
Soren


On Tue, Nov 2, 2010 at 3:23 PM, Andrew Janke <a.janke at gmail.com> wrote:

> I think so ( in this case). Peter oroginally made a distinction
> between the slice and in-plane dimensions for reasons known to him. I
> think a lot of the reason was around slice scaling of image ranges.
>
> In any case it can sometimes make for some interesting (and at times)
> unexpected results. :(
>
>
> a
>
> On Tue, Nov 2, 2010 at 14:48, Soren Christensen <sorench at gmail.com> wrote:
> > I am not sure where the problem arises (is it that zspace is my slowest
> > varying dim and the -1 you allude to?)
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Nov  2 18:06:30 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 3 Nov 2010 09:06:30 +1100
Subject: [MINC-users] mincresample of negative zsteps
In-Reply-To: <AANLkTikCaXQXGuVSqMpGzxoy-gcc5eBJCMBamYoP6U6U@mail.gmail.com>
References: <AANLkTi=DcDCKUaDcgRKB=k0r+y5JXyC3raFCwK++cWN_@mail.gmail.com>
	<AANLkTikaHNunv=mFofQbrLyNhuZq8ybwwRsaddFH1Oo9@mail.gmail.com>
	<AANLkTi=4MOX3ZxG9TBmja14XMpv79RKpmMeHNfuUQ+sT@mail.gmail.com>
	<AANLkTinA9Enu6wsPivuAHZ5hEO544JzeiVSiZ84c0R1D@mail.gmail.com>
	<AANLkTikCaXQXGuVSqMpGzxoy-gcc5eBJCMBamYoP6U6U@mail.gmail.com>
Message-ID: <AANLkTiknhW5OkrkZo81+tUG2pPNztjT_Vt8pNguR92KH@mail.gmail.com>

Hi Soren,

> ?I just bumped into another issue with mincresample this afternoon - this
> time with ordinary positive zsteps:
>
> Shouldn't the resampled file below get a zstep of 4? ? ?what could be the
> reason it becomes 3.74669 only?

>From a quick look I think you are being bitten by the same defalut
behaviour (it's not a bug! it's described to perform this way!) of
mincresample. From a look at what you are doing however I think you
could just use minccopy instead if all you want to do is put the data
from one file into another with some step and starts defined.

Certainly resampling one file (with no sampling defined) like another
(that does have sampling defined) is going to be somewhat undefined in
any case.


a

From a.janke at gmail.com  Tue Nov  2 18:08:28 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 3 Nov 2010 09:08:28 +1100
Subject: [MINC-users] Ubuntu Maverick Packages available.
In-Reply-To: <AANLkTikhNGiTgSFC_kvHh1pydYjgP=QEaKgA7epQnANS@mail.gmail.com>
References: <AANLkTikyD8dPw9nLYXE3a6ONzoWRRs3cX_1OXWi7BKbP@mail.gmail.com>
	<AANLkTikhNGiTgSFC_kvHh1pydYjgP=QEaKgA7epQnANS@mail.gmail.com>
Message-ID: <AANLkTi=fX7L_X7s_P+0QEuNvWqTH9eeRd=WsSboxk_=N@mail.gmail.com>

Hi Mishkin,

> Just upgraded to 10.10 on my 32bit thinkpad, but ran into a problem
> when installing minc. Here are the steps I took and error msgs:
>
> 1. Added this to /etc/apt/sources.list
> deb http://packages.bic.mni.mcgill.ca/ubuntu-maverick ./

Time to get a new thinkpad. :)  I have so far only made the amd64
versions of the pacakges as I currently don't have a 32bit machine
with maverick on it. I guess i am going to have to run up a virtual
machine or someting.

a

From Jared at bic.mni.mcgill.ca  Thu Nov  4 11:54:51 2010
From: Jared at bic.mni.mcgill.ca (Jared Rowley)
Date: Thu, 4 Nov 2010 11:54:51 -0400
Subject: [MINC-users] cropping obj files
Message-ID: <AANLkTimgSHp5VOHw53EYUKHMNJ-G+1PGpPr=JXDsUiT_@mail.gmail.com>

Hi All,

I have an object file (.obj) that is a series of lines.  I want to crop or
mask this file. Display doesn't work to crop lines as far as I know. Does
anyone have a tool that would do this?

Thanks so much,

Jared

-- 
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3

From lconcha at gmail.com  Thu Nov  4 14:26:03 2010
From: lconcha at gmail.com (Luis Concha)
Date: Thu, 4 Nov 2010 12:26:03 -0600
Subject: [MINC-users] cropping obj files
Message-ID: <AANLkTikMd3DKHKC-hh=ZBLcJ3QeOBcqfYyb3iwQAz97k@mail.gmail.com>

I have used paraview to do this before. You must first convert your obj to a
vtk file. I have a matlab function to do this (you must first load the obj
to matlab using SurfStat). I do not know if the mailing list supports
attachments, but here it goes.

Luis





On Thu, Nov 4, 2010 at 10:00 AM, <minc-users-request at bic.mni.mcgill.ca>wrote:

> Send MINC-users mailing list submissions to
>        minc-users at bic.mni.mcgill.ca
>
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> or, via email, send a message with subject or body 'help' to
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> than "Re: Contents of MINC-users digest..."
>
>
> Today's Topics:
>
>   1. cropping obj files (Jared Rowley)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 4 Nov 2010 11:54:51 -0400
> From: Jared Rowley <Jared at bic.mni.mcgill.ca>
> Subject: [MINC-users] cropping obj files
> To: minc-users at bic.mni.mcgill.ca
> Message-ID:
>        <AANLkTimgSHp5VOHw53EYUKHMNJ-G+1PGpPr=JXDsUiT_ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All,
>
> I have an object file (.obj) that is a series of lines.  I want to crop or
> mask this file. Display doesn't work to crop lines as far as I know. Does
> anyone have a tool that would do this?
>
> Thanks so much,
>
> Jared
>
> --
> Jared Rowley
> Translational Neuroimaging Laboratory
> McGill Centre for Studies in Aging
> Douglas Hospital Research Center
> McGill University
> 6825 LaSalle Blvd.
> Montreal, QC Canada
> H4H 1R3
>
>
> ------------------------------
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> End of MINC-users Digest, Vol 64, Issue 3
> *****************************************
>

From bailey at bic.mni.mcgill.ca  Mon Nov 15 17:53:27 2010
From: bailey at bic.mni.mcgill.ca (Lara Bailey)
Date: Mon, 15 Nov 2010 17:53:27 -0500
Subject: [MINC-users] mincmorph -successive usage
Message-ID: <AANLkTim5fR7p88K1h3GrTXByB+e=1K3qjLgUUsV6b8L=@mail.gmail.com>

Hello,
I can't seem to get mincmorph -successive D to work for multiple dilations..
Anyone know how to use it?
Lara

From a.janke at gmail.com  Mon Nov 15 18:02:41 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 16 Nov 2010 09:02:41 +1000
Subject: [MINC-users] mincmorph -successive usage
In-Reply-To: <AANLkTim5fR7p88K1h3GrTXByB+e=1K3qjLgUUsV6b8L=@mail.gmail.com>
References: <AANLkTim5fR7p88K1h3GrTXByB+e=1K3qjLgUUsV6b8L=@mail.gmail.com>
Message-ID: <AANLkTinZY=BLY6rqFXmR6TdajqxjSRt6OqbdeAxr4U3m@mail.gmail.com>

Hi laura.

mincmorph -successive 'DDD' in.mnc out.mnc

Should do 3 successive dilations for you.

If the input is not a binary image you will have to put in a B[x,y]
operation first where x and y are the floor and ceiling you want to
binarise in.

Andrew

On 2010-11-16, Lara Bailey <bailey at bic.mni.mcgill.ca> wrote:
> Hello,
> I can't seem to get mincmorph -successive D to work for multiple dilations..
> Anyone know how to use it?
> Lara
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From pbellec at bic.mni.mcgill.ca  Tue Nov 16 13:42:59 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Tue, 16 Nov 2010 13:42:59 -0500
Subject: [MINC-users] Ubuntu Maverick Packages available.
In-Reply-To: <AANLkTi=fX7L_X7s_P+0QEuNvWqTH9eeRd=WsSboxk_=N@mail.gmail.com>
References: <AANLkTikyD8dPw9nLYXE3a6ONzoWRRs3cX_1OXWi7BKbP@mail.gmail.com>
	<AANLkTikhNGiTgSFC_kvHh1pydYjgP=QEaKgA7epQnANS@mail.gmail.com>
	<AANLkTi=fX7L_X7s_P+0QEuNvWqTH9eeRd=WsSboxk_=N@mail.gmail.com>
Message-ID: <AANLkTim8ZzWtTRA7FKtm+GTLwF2xX+DgZRB_Zn_=rJ8Y@mail.gmail.com>

Hi Andrew,

Thanks so much for releasing the new bundle. But I am with Mishkin on that
one, I tried to install it on an ubuntu virtual machine for MAC and I got
stuck because the machine was configured in 32 bits. The same thing happened
on two laptops with Lucid. If you have a chance, a 32 bit version of the
package would be very much appreciated.

Best regards,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de G?riatrie de Montr?al
D?partement d'informatique et de recherche op?rationnelle
Universit? de Montr?al
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #336730


2010/11/2 Andrew Janke <a.janke at gmail.com>

> Hi Mishkin,
>
> > Just upgraded to 10.10 on my 32bit thinkpad, but ran into a problem
> > when installing minc. Here are the steps I took and error msgs:
> >
> > 1. Added this to /etc/apt/sources.list
> > deb http://packages.bic.mni.mcgill.ca/ubuntu-maverick ./
>
> Time to get a new thinkpad. :)  I have so far only made the amd64
> versions of the pacakges as I currently don't have a 32bit machine
> with maverick on it. I guess i am going to have to run up a virtual
> machine or someting.
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From pbellec at bic.mni.mcgill.ca  Tue Nov 16 14:27:32 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Tue, 16 Nov 2010 14:27:32 -0500
Subject: [MINC-users] Re :  MINC2 on Mac OS 10.5
Message-ID: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>

Dear MINC users,

I have been trying this morning to install the minc tools & associated
software on a MAC OS 10.5 using the package found in :
http://packages.bic.mni.mcgill.ca/osx-10.5/
Minc2 won't install because it cannot find the (shared) HDF5 libraries. It
turns out that every single shared version of these libraries I found (fink
etc) comes in 32 bit, and the MINC packages are 64 bits. I finally pulled
out a 64 bit HDF5 library from Matlab (one dirty hack, just to test) but
then mincinfo complained about szip. Which again I haven't been able to find
in 64 bit shared version. So first question is, how is it possible to
install a version of HDF5 which work with these packages ? I found an old
thread from two years ago describing pretty much all the steps I went
through :
http://www2.bic.mni.mcgill.ca/pipermail/minc-users/2008-July/002127.html
The tar ball of Alex won't work for me because raw2minc (or minc2raw) is
broken, according to the original post of Alex. Beyond that, what is the
rationale for using dynamic libraries in the first place ? Every time I try
to install the minc tools I run into issues with HDF5/NETCDF. This topic
came back many times and I believe that now Andrew has decided to go for
static builds, but I just wanted to mention again that I think it is totally
worth it.

In any case, this version of minc2 is rather old (2.0.15).   It would be
great to have the 2.1 release. In my new institution, there are a lot of MAC
and I am eager to share tools, but so far I got stuck at the installation
phase. Please let me know if that is something that can be expected to come
out in the near future. Otherwise, Mathieu Desrosiers at CRIUGM offered to
create a static build of the minc bundle that we will then share as a tar
ball.

Thanks a lot in advance for your help,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de G?riatrie de Montr?al
D?partement d'informatique et de recherche op?rationnelle
Universit? de Montr?al
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #336730

From burt.crepeault at crulrg.ulaval.ca  Tue Nov 16 15:32:12 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Tue, 16 Nov 2010 15:32:12 -0500
Subject: [MINC-users] Re : MINC2 on Mac OS 10.5
In-Reply-To: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
References: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
Message-ID: <AANLkTimHTP0PDBV=AYQWX6jdvVQ-Ca7sE2xOAXYkW5wx@mail.gmail.com>

Pierre,

I was having the same problem about a year ago (someone really should pull
that old OS X page from the site) and my only solution was to compile the
whole thing myself, including libraries. That was not a task I really wanted
to get into but it turned out not so bad. Anyway, I now have 2.0.18,
unfortunately in 32 bits, and some knowledge on how to do it yourself if
you're interested.

Burt.


-------------
Burt Cr?peault
Centre de recherche de l'universit? Laval - Robert-Giffard
2601 de la Canardi?re, suite F-4400
Qu?bec QC G1J 2G3
418-663-5741, ext 6844


On Tue, Nov 16, 2010 at 14:27, Pierre Bellec <pbellec at bic.mni.mcgill.ca>wrote:

> Dear MINC users,
>
> I have been trying this morning to install the minc tools & associated
> software on a MAC OS 10.5 using the package found in :
> http://packages.bic.mni.mcgill.ca/osx-10.5/
> Minc2 won't install because it cannot find the (shared) HDF5 libraries. It
> turns out that every single shared version of these libraries I found (fink
> etc) comes in 32 bit, and the MINC packages are 64 bits. I finally pulled
> out a 64 bit HDF5 library from Matlab (one dirty hack, just to test) but
> then mincinfo complained about szip. Which again I haven't been able to
> find
> in 64 bit shared version. So first question is, how is it possible to
> install a version of HDF5 which work with these packages ? I found an old
> thread from two years ago describing pretty much all the steps I went
> through :
> http://www2.bic.mni.mcgill.ca/pipermail/minc-users/2008-July/002127.html
> The tar ball of Alex won't work for me because raw2minc (or minc2raw) is
> broken, according to the original post of Alex. Beyond that, what is the
> rationale for using dynamic libraries in the first place ? Every time I try
> to install the minc tools I run into issues with HDF5/NETCDF. This topic
> came back many times and I believe that now Andrew has decided to go for
> static builds, but I just wanted to mention again that I think it is
> totally
> worth it.
>
> In any case, this version of minc2 is rather old (2.0.15).   It would be
> great to have the 2.1 release. In my new institution, there are a lot of
> MAC
> and I am eager to share tools, but so far I got stuck at the installation
> phase. Please let me know if that is something that can be expected to come
> out in the near future. Otherwise, Mathieu Desrosiers at CRIUGM offered to
> create a static build of the minc bundle that we will then share as a tar
> ball.
>
> Thanks a lot in advance for your help,
>
> Pierre Bellec, PhD
> Chercheur adjoint
> Centre de recherche de l'institut de G?riatrie de Montr?al
> D?partement d'informatique et de recherche op?rationnelle
> Universit? de Montr?al
> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
> (001)(514) 340 3540 #336730
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From claude at bic.mni.mcgill.ca  Tue Nov 16 15:34:55 2010
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 16 Nov 2010 15:34:55 -0500
Subject: [MINC-users] Re :  MINC2 on Mac OS 10.5
In-Reply-To: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
Message-ID: <201011162034.oAGKYtfa015066@cassio.bic.mni.mcgill.ca>

Pierre,

Back in May 2010, I compiled some basic minc tools on Darwin 10.6 on
Samir's computer. Read carefully: it's 10.6, not 10.5. If you want to
try:

http://www.bic.mni.mcgill.ca/users/claude/darwin-10.6.tar.gz

It comes with a newer version than minc-2.0.15. It's mostly a static
build, likely 64 bits. It's not the full stuff, but it's a good start.

Claude

> Dear MINC users,
>
> I have been trying this morning to install the minc tools & associated
> software on a MAC OS 10.5 using the package found in :
> http://packages.bic.mni.mcgill.ca/osx-10.5/
> Minc2 won't install because it cannot find the (shared) HDF5 libraries. It
> turns out that every single shared version of these libraries I found (fink
> etc) comes in 32 bit, and the MINC packages are 64 bits. I finally pulled
> out a 64 bit HDF5 library from Matlab (one dirty hack, just to test) but
> then mincinfo complained about szip. Which again I haven't been able to find
> in 64 bit shared version. So first question is, how is it possible to
> install a version of HDF5 which work with these packages ? I found an old
> thread from two years ago describing pretty much all the steps I went
> through :
> http://www2.bic.mni.mcgill.ca/pipermail/minc-users/2008-July/002127.html
> The tar ball of Alex won't work for me because raw2minc (or minc2raw) is
> broken, according to the original post of Alex. Beyond that, what is the
> rationale for using dynamic libraries in the first place ? Every time I try
> to install the minc tools I run into issues with HDF5/NETCDF. This topic
> came back many times and I believe that now Andrew has decided to go for
> static builds, but I just wanted to mention again that I think it is totally
> worth it.
>
> In any case, this version of minc2 is rather old (2.0.15).   It would be
> great to have the 2.1 release. In my new institution, there are a lot of MAC
> and I am eager to share tools, but so far I got stuck at the installation
> phase. Please let me know if that is something that can be expected to come
> out in the near future. Otherwise, Mathieu Desrosiers at CRIUGM offered to
> create a static build of the minc bundle that we will then share as a tar
> ball.
>
> Thanks a lot in advance for your help,
>
> Pierre Bellec, PhD
> Chercheur adjoint
> Centre de recherche de l'institut de G=E9riatrie de Montr=E9al
> D=E9partement d'informatique et de recherche op=E9rationnelle
> Universit=E9 de Montr=E9al
> http://simexp-lab.org/brainwiki/doku.php?id=3Dpierrebellec
> (001)(514) 340 3540 #336730
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sean at rogue-research.com  Tue Nov 16 15:42:29 2010
From: sean at rogue-research.com (Sean McBride)
Date: Tue, 16 Nov 2010 15:42:29 -0500
Subject: [MINC-users] Re :  MINC2 on Mac OS 10.5
In-Reply-To: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
References: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
Message-ID: <20101116204229.1741485038@mail.rogue-research.com>

On Tue, 16 Nov 2010 14:27:32 -0500, Pierre Bellec said:

>In any case, this version of minc2 is rather old (2.0.15).   It would be
>great to have the 2.1 release.

I seem to remember 2.1 was released!  But the web pages are woefully out
of date...

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



From pbellec at bic.mni.mcgill.ca  Tue Nov 16 15:58:01 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Tue, 16 Nov 2010 15:58:01 -0500
Subject: [MINC-users] Re : MINC2 on Mac OS 10.5
In-Reply-To: <20101116204229.1741485038@mail.rogue-research.com>
References: <AANLkTi=Bf_JrtYKC7J17LLcAvodJ1iAsYWg3hDhJA=dU@mail.gmail.com>
	<20101116204229.1741485038@mail.rogue-research.com>
Message-ID: <AANLkTi=rVwkdOpDSaos=5FqeFfjANKWoHhgegx6iqq_A@mail.gmail.com>

Thanks everyone for the feedback.

@Burt
This is precisely what I would like to avoid. But if I really need to, I'll
try with the help of Mathieu and I will get back to you if we run into
problems. I am waiting on Andrew though, because if he decides to release
new packages (or a bundle !!) that would be the best solution (much cleaner
& easier installation, no work on my end :) ).

@Claude
I will try your tar ball, but I am kind of pessimistic as I do need quite a
bit of different packages.

@Sean
It has been released in the general sense, but not for the Mac plateform as
far as I know. At least, it is absent of the MNI repository :
http://packages.bic.mni.mcgill.ca/osx-10.5/

Regards,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de G?riatrie de Montr?al
D?partement d'informatique et de recherche op?rationnelle
Universit? de Montr?al
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #336730


2010/11/16 Sean McBride <sean at rogue-research.com>

> On Tue, 16 Nov 2010 14:27:32 -0500, Pierre Bellec said:
>
> >In any case, this version of minc2 is rather old (2.0.15).   It would be
> >great to have the 2.1 release.
>
> I seem to remember 2.1 was released!  But the web pages are woefully out
> of date...
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng                 sean at rogue-research.com
> Rogue Research                        www.rogue-research.com
> Mac Software Developer              Montr?al, Qu?bec, Canada
>
>
>

From vladimir.fonov at gmail.com  Tue Nov 16 16:03:01 2010
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Tue, 16 Nov 2010 16:03:01 -0500
Subject: [MINC-users] Re :  MINC2 on Mac OS 10.5
In-Reply-To: <201011162034.oAGKYtfa015066@cassio.bic.mni.mcgill.ca>
References: <201011162034.oAGKYtfa015066@cassio.bic.mni.mcgill.ca>
Message-ID: <4CE2F185.6020203@gmail.com>

Hello,

On 10-11-16 03:34 PM, Claude LEPAGE wrote:
> Back in May 2010, I compiled some basic minc tools on Darwin 10.6 on
> Samir's computer. Read carefully: it's 10.6, not 10.5. If you want to
> try:
>
> http://www.bic.mni.mcgill.ca/users/claude/darwin-10.6.tar.gz
>
> It comes with a newer version than minc-2.0.15. It's mostly a static
> build, likely 64 bits. It's not the full stuff, but it's a good start.

I've been recently building mincified ITKsnap for MAC OS X and learned 
that it's relatively easy to compile MINC2 2.0.18 in 32 bits for 10.5 
and 64bit for 10.6, reverse seem to be extremely difficult.

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

From assemlal at bic.mni.mcgill.ca  Tue Nov 16 16:49:43 2010
From: assemlal at bic.mni.mcgill.ca (Haz-Edine Assemlal - L. Collins Lab)
Date: Tue, 16 Nov 2010 16:49:43 -0500 (EST)
Subject: [MINC-users] Re :  MINC2 on Mac OS 10.5
In-Reply-To: <Pine.LNX.4.64.1010211055310.27601@cassio.bic.mni.mcgill.ca>
References: <Pine.LNX.4.64.1010211055310.27601@cassio.bic.mni.mcgill.ca>
Message-ID: <Pine.LNX.4.64.1011161642470.25043@cassio.bic.mni.mcgill.ca>

Pierre,

You might be interested in the following updated MacPorts files for 
MINC2.1. It compiles and runs fine on MacOsX 10.6, you may want to give 
it a try on MacOsX 10.5.

Best,
Haz-Edine


On Thu, 21 Oct 2010, Haz-Edine Assemlal - L. Collins Lab wrote:

> Hi everyone,
>
> I have updated the MacPort of MINC 2.1 so it compiles fine on Snow Leopard. 
> The corresponding Portfile is attached in this email.
>
> Best,
> Haz-Edine

From v.popescu at vumc.nl  Fri Nov 19 05:02:07 2010
From: v.popescu at vumc.nl (Popescu, V. )
Date: Fri, 19 Nov 2010 11:02:07 +0100
Subject: [MINC-users] changing orietation at conversion nifti-minc
In-Reply-To: <mailman.3.1290013202.29046.minc-users@bic.mni.mcgill.ca>
Message-ID: <6D6611E81E29754A80F752BFCDB5303502D731EE@vumc-mb02.vumc.nl>

Dear all,
I am trying to run N3 on a nifti image (compressed).  
It works fine on one machine with N3 version 1.7.2.2 (2009/05/04) and it
changes the orientation of the image at the first step (the conversion
to .mnc) on the other machine with N3 version 1.12 (2009/12/16). 
Does anybody know a way out of this?
Thanks in advance!
Veronica

From michel.audette at kitware.com  Tue Nov 23 13:36:03 2010
From: michel.audette at kitware.com (Michel Audette)
Date: Tue, 23 Nov 2010 10:36:03 -0800
Subject: [MINC-users] methods for registering brainmap.org activation data
	to subject data
Message-ID: <AANLkTin0Cf9DZbzx1LCDDYcDupEb9jVzG0syqNXKGa2t@mail.gmail.com>

Dear Minc fellow users,

I am interested in using existing fMRI-based activation maps, such as are
apparently available at brainmap.org (e.g.: Sleuth, GingerALE), and warping
these maps to subject data. What MINC-based registration procedure will
achieve this? Is there anyone at MNI who is using these maps in the manner
that I am considering?

Best wishes,

Michel

-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From pbellec at bic.mni.mcgill.ca  Tue Nov 23 13:52:07 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Tue, 23 Nov 2010 13:52:07 -0500
Subject: [MINC-users] methods for registering brainmap.org activation
 data to subject data
In-Reply-To: <AANLkTin0Cf9DZbzx1LCDDYcDupEb9jVzG0syqNXKGa2t@mail.gmail.com>
References: <AANLkTin0Cf9DZbzx1LCDDYcDupEb9jVzG0syqNXKGa2t@mail.gmail.com>
Message-ID: <AANLkTikJZ4rwGN6We5dMYD=Dz9ZGG5J4=mp6wn0=hC1s@mail.gmail.com>

Dear Michel,

I am not sure to understand what you are trying to do. If I am correct,
Sleuth just produces coordinates. ALE will give you maps, in stereotaxic
space. Do you want to bring those maps in the space of individual subjects
?? You will then need to estimate a transformation from the individual space
to stereotaxic space (the most common tool to do that is MRI2TAL I believe,
even though there are other scripts around, please ask if you need more
details). You will then need to use MINCRESAMPLE with the inverse transform
to resample your ALE map in the individual subject space.

I hope this helps,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de G?riatrie de Montr?al
D?partement d'informatique et de recherche op?rationnelle
Universit? de Montr?al
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #336730


2010/11/23 Michel Audette <michel.audette at kitware.com>

> Dear Minc fellow users,
>
> I am interested in using existing fMRI-based activation maps, such as are
> apparently available at brainmap.org (e.g.: Sleuth, GingerALE), and
> warping
> these maps to subject data. What MINC-based registration procedure will
> achieve this? Is there anyone at MNI who is using these maps in the manner
> that I am considering?
>
> Best wishes,
>
> Michel
>
> --
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From michel.audette at kitware.com  Tue Nov 23 14:02:13 2010
From: michel.audette at kitware.com (Michel Audette)
Date: Tue, 23 Nov 2010 11:02:13 -0800
Subject: [MINC-users] methods for registering brainmap.org activation
 data to subject data
In-Reply-To: <AANLkTikJZ4rwGN6We5dMYD=Dz9ZGG5J4=mp6wn0=hC1s@mail.gmail.com>
References: <AANLkTin0Cf9DZbzx1LCDDYcDupEb9jVzG0syqNXKGa2t@mail.gmail.com>
	<AANLkTikJZ4rwGN6We5dMYD=Dz9ZGG5J4=mp6wn0=hC1s@mail.gmail.com>
Message-ID: <AANLkTinxa+kbyyf_fz4gN0GBAVJNahbDgvVC3CTWg8cr@mail.gmail.com>

Hi Pierre,

thanks for your kind reply. The bolded part is exactly what I have in mind.
MRI2TAL sounds  like a good fit then.

Moreover, brainmap.org seems to discriminate between Talairach coordinates
and MNI coordinates. I was under the impression up to now that the two were
the same thing (I did not use this research in my PhD thesis while at MNI
:-D ). Can you explain the difference?

(If I understand correctly, the brainmap.org data is referred to the Average
Brain. Which coordinate system is attached to this image?)

Best wishes,

Michel

On Tue, Nov 23, 2010 at 10:52 AM, Pierre Bellec
<pbellec at bic.mni.mcgill.ca>wrote:

> Dear Michel,
>
> I am not sure to understand what you are trying to do. If I am correct,
> Sleuth just produces coordinates. *ALE will give you maps, in stereotaxic
> space. Do you want to bring those maps in the space of individual subjects
> ?? *You will then need to estimate a transformation from the individual
> space
> to stereotaxic space (the most common tool to do that is MRI2TAL I believe,
> even though there are other scripts around, please ask if you need more
> details). You will then need to use MINCRESAMPLE with the inverse transform
> to resample your ALE map in the individual subject space.
>
> I hope this helps,
>
> Pierre Bellec, PhD
> Chercheur adjoint
> Centre de recherche de l'institut de G?riatrie de Montr?al
> D?partement d'informatique et de recherche op?rationnelle
> Universit? de Montr?al
> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
> (001)(514) 340 3540 #336730
>
>
> 2010/11/23 Michel Audette <michel.audette at kitware.com>
>
> > Dear Minc fellow users,
> >
> > I am interested in using existing fMRI-based activation maps, such as are
> > apparently available at brainmap.org (e.g.: Sleuth, GingerALE), and
> > warping
> > these maps to subject data. What MINC-based registration procedure will
> > achieve this? Is there anyone at MNI who is using these maps in the
> manner
> > that I am considering?
> >
> > Best wishes,
> >
> > Michel
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.