From francois.hebert007 at gmail.com  Thu Mar  4 12:58:41 2010
From: francois.hebert007 at gmail.com (francois hebert)
Date: Thu, 4 Mar 2010 12:58:41 -0500
Subject: [MINC-users] surface simplification
Message-ID: <450376071003040958n2ab66e8fx744bd67a297cb1e5@mail.gmail.com>

Hi everyone,

I would like to simplify (reduce the number of vertex) by means of an edge
collapsing algorithm.
My surface is a minc obj file so I would like to know if there is a minc
program that can perform it?


Francois Hebert
Research Assistant
Small Animal Imaging Laboratory
Montreal Neurological Institute
McGill University
Genome building
Rm 3200
ph: 514-398-5849

From laurence at bic.mni.mcgill.ca  Thu Mar  4 13:07:04 2010
From: laurence at bic.mni.mcgill.ca (Laurence Mercier)
Date: Thu, 04 Mar 2010 13:07:04 -0500
Subject: [MINC-users] surface simplification
In-Reply-To: <450376071003040958n2ab66e8fx744bd67a297cb1e5@mail.gmail.com>
References: <450376071003040958n2ab66e8fx744bd67a297cb1e5@mail.gmail.com>
Message-ID: <4B8FF6C8.4080106@bic.mni.mcgill.ca>

Hello Fran?ois,

I while back I used a script from Claude Lepage that did exactly that: 
it reduced the number of triangles from an obj file... I guess he could 
tell you more about it.

Laurence


francois hebert wrote:
> Hi everyone,
> 
> I would like to simplify (reduce the number of vertex) by means of an edge
> collapsing algorithm.
> My surface is a minc obj file so I would like to know if there is a minc
> program that can perform it?
> 
> 
> Francois Hebert
> Research Assistant
> Small Animal Imaging Laboratory
> Montreal Neurological Institute
> McGill University
> Genome building
> Rm 3200
> ph: 514-398-5849
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



From se at hst.aau.dk  Thu Mar  4 15:13:14 2010
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Thu, 4 Mar 2010 21:13:14 +0100 (CET)
Subject: [MINC-users] surface simplification
In-Reply-To: <1797418033.367650.1267733422210.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <1421998174.367654.1267733594222.JavaMail.root@zimbra-store01.hst.aau.dk>

Hi Francois,

Do you need an algorithm to simply remove short edges? Or is it rather a decimation approach, where the geometrical features are preserved, you are after?
I can probably help you with the former, but not the latter.

Simon
----- "francois hebert" <francois.hebert007 at gmail.com> wrote:

> Hi everyone,
> 
> I would like to simplify (reduce the number of vertex) by means of an
> edge
> collapsing algorithm.
> My surface is a minc obj file so I would like to know if there is a
> minc
> program that can perform it?
> 
> 
> Francois Hebert
> Research Assistant
> Small Animal Imaging Laboratory
> Montreal Neurological Institute
> McGill University
> Genome building
> Rm 3200
> ph: 514-398-5849
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From francois.hebert007 at gmail.com  Thu Mar  4 17:05:20 2010
From: francois.hebert007 at gmail.com (francois hebert)
Date: Thu, 4 Mar 2010 17:05:20 -0500
Subject: [MINC-users] surface simplification
In-Reply-To: <1421998174.367654.1267733594222.JavaMail.root@zimbra-store01.hst.aau.dk>
References: <1797418033.367650.1267733422210.JavaMail.root@zimbra-store01.hst.aau.dk>
	<1421998174.367654.1267733594222.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <450376071003041405q3dd7b514l978e33b72a971734@mail.gmail.com>

Hi Simon,

I must say I do not know too much about mesh. From my point of view is more
a decimation approach.
It still can be interesting to try an algorithm that remove short edges.

Francois


2010/3/4 Simon Fristed Eskildsen <se at hst.aau.dk>

> Hi Francois,
>
> Do you need an algorithm to simply remove short edges? Or is it rather a
> decimation approach, where the geometrical features are preserved, you are
> after?
> I can probably help you with the former, but not the latter.
>
> Simon
> ----- "francois hebert" <francois.hebert007 at gmail.com> wrote:
>
> > Hi everyone,
> >
> > I would like to simplify (reduce the number of vertex) by means of an
> > edge
> > collapsing algorithm.
> > My surface is a minc obj file so I would like to know if there is a
> > minc
> > program that can perform it?
> >
> >
> > Francois Hebert
> > Research Assistant
> > Small Animal Imaging Laboratory
> > Montreal Neurological Institute
> > McGill University
> > Genome building
> > Rm 3200
> > ph: 514-398-5849
> > _______________________________________________
> > 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
>

From mona.maneshi at mail.mcgill.ca  Tue Mar  9 14:57:00 2010
From: mona.maneshi at mail.mcgill.ca (Mona Maneshi)
Date: Tue, 9 Mar 2010 14:57:00 -0500
Subject: [MINC-users] Anybody having experience with FSL?
Message-ID: <594FC9D44D69BC4399FB41900A54F84DD406D9AE94@EXMBXVS4A.campus.mcgill.ca>

Hi BIC users,

I just started using FSL to do ICA analysis. I wanted to know if there is anybody around using FSL. I have got some problems in orientation/convention of my data and need to get some help for that.

Thanks in advance,

Mona

From mishkind at gmail.com  Tue Mar  9 15:27:11 2010
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Tue, 9 Mar 2010 15:27:11 -0500
Subject: [MINC-users] Anybody having experience with FSL?
In-Reply-To: <594FC9D44D69BC4399FB41900A54F84DD406D9AE94@EXMBXVS4A.campus.mcgill.ca>
References: <594FC9D44D69BC4399FB41900A54F84DD406D9AE94@EXMBXVS4A.campus.mcgill.ca>
Message-ID: <9c5abb61003091227u7069fb11j94b1ea526e603322@mail.gmail.com>

Hi Mona,
I've never done ICA in FSL, but I've used many of the other tools and
have converted to/from minc.
What exactly do you need help with?
mishkin
514-398-5065
wb-319





On Tue, Mar 9, 2010 at 2:57 PM, Mona Maneshi
<mona.maneshi at mail.mcgill.ca> wrote:
> Hi BIC users,
>
> I just started using FSL to do ICA analysis. I wanted to know if there is anybody around using FSL. I have got some problems in orientation/convention of my data and need to get some help for that.
>
> Thanks in advance,
>
> Mona
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sorench at gmail.com  Wed Mar 10 01:11:45 2010
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 10 Mar 2010 17:11:45 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
Message-ID: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com>

Hi,
 I have trouble with Display and register on Fedora 12.
I compiled minc2 + register and Display presumably without incident, but
when runing Display and register I get the follwoing in the terminal:

Could not get requested colour_map_mode(0), got(1,256)
and
G_draw_pixels(): cannot draw rgb pixels in colour map mode.
G_draw_pixels(): cannot draw rgb pixels in colour map mode.

As a particularly bad omen this error seems to have no direct hits in google
:(
Both programs UI appear to be black/white only.

My guess is this is a GL issue of some sort has anybody seen it before and
know how to fix it?

I may get a GeForce card in stead of the Quadro FX as I also had problems
with Blender freezing, but glxinfo tells me direct rendering is on. I am
using the rpmfusion nvidia drivers.

Cheers
Soren

From a.janke at gmail.com  Wed Mar 10 01:15:36 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 10 Mar 2010 17:15:36 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com>
References: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com>
Message-ID: <d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com>

Hi Soren,

On Wed, Mar 10, 2010 at 17:11, Soren Christensen <sorench at gmail.com> wrote:
> Hi,
> ?I have trouble with Display and register on Fedora 12.
> I compiled minc2 + register and Display presumably without incident, but
> when runing Display and register I get the follwoing in the terminal:
>
> Could not get requested colour_map_mode(0), got(1,256)
> and
> G_draw_pixels(): cannot draw rgb pixels in colour map mode.
> G_draw_pixels(): cannot draw rgb pixels in colour map mode.

Have you tried:

   $ register -rgb ....

?

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

From mishkind at gmail.com  Wed Mar 10 01:27:50 2010
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Wed, 10 Mar 2010 01:27:50 -0500
Subject: [MINC-users] Anybody having experience with FSL?
In-Reply-To: <9c5abb61003091227u7069fb11j94b1ea526e603322@mail.gmail.com>
References: <594FC9D44D69BC4399FB41900A54F84DD406D9AE94@EXMBXVS4A.campus.mcgill.ca>
	<9c5abb61003091227u7069fb11j94b1ea526e603322@mail.gmail.com>
Message-ID: <9c5abb61003092227p55c06616i1b44df07f04ea702@mail.gmail.com>

Hello list,
Perhaps someone with specific knowledge of MELODIC in FSL would be able to
help Mona a bit better.
She seems to have an orientation (or else really bad registration) problem
with her functional data, and the usual mincreshape tricks that I use for
structural datasets don't seem to be working.
good luck Mona,
mishkin


On Tue, Mar 9, 2010 at 3:27 PM, Mishkin Derakhshan <mishkind at gmail.com>wrote:

> Hi Mona,
> I've never done ICA in FSL, but I've used many of the other tools and
> have converted to/from minc.
> What exactly do you need help with?
> mishkin
> 514-398-5065
> wb-319
>
>
>
>
>
> On Tue, Mar 9, 2010 at 2:57 PM, Mona Maneshi
> <mona.maneshi at mail.mcgill.ca> wrote:
> > Hi BIC users,
> >
> > I just started using FSL to do ICA analysis. I wanted to know if there is
> anybody around using FSL. I have got some problems in orientation/convention
> of my data and need to get some help for that.
> >
> > Thanks in advance,
> >
> > Mona
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>

From sorench at gmail.com  Wed Mar 10 01:29:15 2010
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 10 Mar 2010 17:29:15 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com>
References: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com> 
	<d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com>
Message-ID: <d6e2d6551003092229l75e13a89kad20f18a4c28bd02@mail.gmail.com>

Hi Andrew,
 No I did not know about that one - no difference though:

register -rgb idwi.mnc idwi_mir.mnc
Could not get requested colour_map_mode(0), got(1,256)



On Wed, Mar 10, 2010 at 5:15 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren,
>
> On Wed, Mar 10, 2010 at 17:11, Soren Christensen <sorench at gmail.com>
> wrote:
> > Hi,
> >  I have trouble with Display and register on Fedora 12.
> > I compiled minc2 + register and Display presumably without incident, but
> > when runing Display and register I get the follwoing in the terminal:
> >
> > Could not get requested colour_map_mode(0), got(1,256)
> > and
> > G_draw_pixels(): cannot draw rgb pixels in colour map mode.
> > G_draw_pixels(): cannot draw rgb pixels in colour map mode.
>
> Have you tried:
>
>   $ register -rgb ....
>
> ?
>
> --
> 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://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Wed Mar 10 01:41:49 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 10 Mar 2010 17:41:49 +1100
Subject: [MINC-users] Anybody having experience with FSL?
In-Reply-To: <9c5abb61003092227p55c06616i1b44df07f04ea702@mail.gmail.com>
References: <594FC9D44D69BC4399FB41900A54F84DD406D9AE94@EXMBXVS4A.campus.mcgill.ca>
	<9c5abb61003091227u7069fb11j94b1ea526e603322@mail.gmail.com> 
	<9c5abb61003092227p55c06616i1b44df07f04ea702@mail.gmail.com>
Message-ID: <d747ed51003092241t6feef1c0v9b9ccf113e203e0e@mail.gmail.com>

> Perhaps someone with specific knowledge of MELODIC in FSL would be able to
> help Mona a bit better.

Well I don't use MELODIC, but am certain we can help. Mona, can you
post a few more details of your problems?  I am guessing you are using
nii2mnc to convert your images?

perhaps post a few screenshots of the problem?


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

From a.janke at gmail.com  Wed Mar 10 01:43:32 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 10 Mar 2010 17:43:32 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <d6e2d6551003092229l75e13a89kad20f18a4c28bd02@mail.gmail.com>
References: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com> 
	<d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com> 
	<d6e2d6551003092229l75e13a89kad20f18a4c28bd02@mail.gmail.com>
Message-ID: <d747ed51003092243q1574fb5clc2cd6c120b9ce21b@mail.gmail.com>

On Wed, Mar 10, 2010 at 17:29, Soren Christensen <sorench at gmail.com> wrote:
> ?No I did not know about that one - no difference though:
>
> register -rgb idwi.mnc idwi_mir.mnc
> Could not get requested colour_map_mode(0), got(1,256)

Well that's no fun.  Which version of the nvidia drivers and GLUT are
you using and do things like glxgears work?


a

From sorench at gmail.com  Thu Mar 11 02:07:34 2010
From: sorench at gmail.com (Soren Christensen)
Date: Thu, 11 Mar 2010 18:07:34 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <d6e2d6551003102305g5f0953dfr1035fcf5637253e7@mail.gmail.com>
References: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com> 
	<d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com> 
	<d6e2d6551003092229l75e13a89kad20f18a4c28bd02@mail.gmail.com> 
	<d747ed51003092243q1574fb5clc2cd6c120b9ce21b@mail.gmail.com> 
	<d6e2d6551003102305g5f0953dfr1035fcf5637253e7@mail.gmail.com>
Message-ID: <d6e2d6551003102307p79747313m4288101b2871790d@mail.gmail.com>

sorry forgot the GLUT version:
localhost ~# ls -al /usr/lib64/libGLU.so.1
lrwxrwxrwx. 1 root root 20 2010-03-10 09:44 /usr/lib64/libGLU.so.1 ->
libGLU.so.1.3.070701
localhost ~# ls -al /usr/lib64/libGL.so.1
lrwxrwxrwx 1 root root 15 2010-03-11 17:46 /usr/lib64/libGL.so.1 ->
libGL.so.190.53



On Thu, Mar 11, 2010 at 6:05 PM, Soren Christensen <sorench at gmail.com>wrote:

> Sorry for the delay and thanks for the help - was trying to add remove
> drivers did not resolve it. At one stage I had the drivers removed and x
> started without 3D acceleration and Display and register came up normal.
> I have now reinstalled the nvidia driver from the nvidia web site
> (NVIDIA-Linux-x86_64-190.53-pkg2.run) and everything seems to run well (even
> blender) but still the color issue with Display and register.
> Can it be something to do with freeglut?
>
> Here's some diagnostics:
>
> glxgears work fine, 5000 frames/sec as a was getting on F10 where I had no
> problems.
> Here's glxinfo output
> name of display: :0.0
> display: :0  screen: 0
> direct rendering: Yes
> server glx vendor string: NVIDIA Corporation
> server glx version string: 1.4
> server glx extensions:
>
> From Xorg.conf  (I assume this is wher ethe Nvidia installer put the kernel
> module)
> Section "Files"
>     ModulePath      "/usr/lib64/xorg/modules"
> EndSection
>
> Display library dependiencies:
>
> ldd /usr/local/mni2/bin/Display
>     linux-vdso.so.1 =>  (0x00007fff13bff000)
>     libglut.so.3 => /usr/lib64/libglut.so.3 (0x00007f9c4d22e000)
>     libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003d0d000000)
>     libGL.so.1 => /usr/lib64/libGL.so.1 (0x00007f9c4d035000)
>     libhdf5.so.0 => /usr/local/hdf5-1.6.7/lib/libhdf5.so.0
> (0x00007f9c4cd11000)
>     libz.so.1 => /lib64/libz.so.1 (0x00000032c7e00000)
>     libm.so.6 => /lib64/libm.so.6 (0x00000032c6e00000)
>     libc.so.6 => /lib64/libc.so.6 (0x00000032c6a00000)
>     libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000032cc200000)
>     libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000032cae00000)
>     libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x00000032d2600000)
>     libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000032cca00000)
>     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000032d3600000)
>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000032d2200000)
>     libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x00007f9c4b82a000)
>     libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
> (0x00007f9c4b728000)
>     libdl.so.2 => /lib64/libdl.so.2 (0x00000032c7200000)
>     /lib64/ld-linux-x86-64.so.2 (0x00000032c6400000)
>     libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000032ca200000)
>     libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000032caa00000)
>
>
>
>
>
> On Wed, Mar 10, 2010 at 5:43 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> On Wed, Mar 10, 2010 at 17:29, Soren Christensen <sorench at gmail.com>
>> wrote:
>> >  No I did not know about that one - no difference though:
>> >
>> > register -rgb idwi.mnc idwi_mir.mnc
>> > Could not get requested colour_map_mode(0), got(1,256)
>>
>> Well that's no fun.  Which version of the nvidia drivers and GLUT are
>> you using and do things like glxgears work?
>>
>>
>> a
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From sorench at gmail.com  Thu Mar 11 02:05:37 2010
From: sorench at gmail.com (Soren Christensen)
Date: Thu, 11 Mar 2010 18:05:37 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <d747ed51003092243q1574fb5clc2cd6c120b9ce21b@mail.gmail.com>
References: <d6e2d6551003092211k32ce8797xd5ac6b0f40ff76c3@mail.gmail.com> 
	<d747ed51003092215p1466a24dlb3a3889e2993a8dc@mail.gmail.com> 
	<d6e2d6551003092229l75e13a89kad20f18a4c28bd02@mail.gmail.com> 
	<d747ed51003092243q1574fb5clc2cd6c120b9ce21b@mail.gmail.com>
Message-ID: <d6e2d6551003102305g5f0953dfr1035fcf5637253e7@mail.gmail.com>

Sorry for the delay and thanks for the help - was trying to add remove
drivers did not resolve it. At one stage I had the drivers removed and x
started without 3D acceleration and Display and register came up normal.
I have now reinstalled the nvidia driver from the nvidia web site
(NVIDIA-Linux-x86_64-190.53-pkg2.run) and everything seems to run well (even
blender) but still the color issue with Display and register.
Can it be something to do with freeglut?

Here's some diagnostics:

glxgears work fine, 5000 frames/sec as a was getting on F10 where I had no
problems.
Here's glxinfo output
name of display: :0.0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:

>From Xorg.conf  (I assume this is wher ethe Nvidia installer put the kernel
module)
Section "Files"
    ModulePath      "/usr/lib64/xorg/modules"
EndSection

Display library dependiencies:

ldd /usr/local/mni2/bin/Display
    linux-vdso.so.1 =>  (0x00007fff13bff000)
    libglut.so.3 => /usr/lib64/libglut.so.3 (0x00007f9c4d22e000)
    libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003d0d000000)
    libGL.so.1 => /usr/lib64/libGL.so.1 (0x00007f9c4d035000)
    libhdf5.so.0 => /usr/local/hdf5-1.6.7/lib/libhdf5.so.0
(0x00007f9c4cd11000)
    libz.so.1 => /lib64/libz.so.1 (0x00000032c7e00000)
    libm.so.6 => /lib64/libm.so.6 (0x00000032c6e00000)
    libc.so.6 => /lib64/libc.so.6 (0x00000032c6a00000)
    libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000032cc200000)
    libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000032cae00000)
    libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x00000032d2600000)
    libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000032cca00000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000032d3600000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000032d2200000)
    libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x00007f9c4b82a000)
    libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
(0x00007f9c4b728000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00000032c7200000)
    /lib64/ld-linux-x86-64.so.2 (0x00000032c6400000)
    libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000032ca200000)
    libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000032caa00000)




On Wed, Mar 10, 2010 at 5:43 PM, Andrew Janke <a.janke at gmail.com> wrote:

> On Wed, Mar 10, 2010 at 17:29, Soren Christensen <sorench at gmail.com>
> wrote:
> >  No I did not know about that one - no difference though:
> >
> > register -rgb idwi.mnc idwi_mir.mnc
> > Could not get requested colour_map_mode(0), got(1,256)
>
> Well that's no fun.  Which version of the nvidia drivers and GLUT are
> you using and do things like glxgears work?
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From se at hst.aau.dk  Thu Mar 11 04:28:58 2010
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Thu, 11 Mar 2010 10:28:58 +0100 (CET)
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <749350308.415262.1268299644405.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <454381946.415278.1268299738163.JavaMail.root@zimbra-store01.hst.aau.dk>

Soren,

FWIW, if I enable visual effects in ubuntu the UIs of Display and register are messed up. Maybe something similar is happening in fedora? I haven't tracked down the bug.

Simon
----- "Soren Christensen" <sorench at gmail.com> wrote:

> Sorry for the delay and thanks for the help - was trying to add
> remove
> drivers did not resolve it. At one stage I had the drivers removed and
> x
> started without 3D acceleration and Display and register came up
> normal.
> I have now reinstalled the nvidia driver from the nvidia web site
> (NVIDIA-Linux-x86_64-190.53-pkg2.run) and everything seems to run well
> (even
> blender) but still the color issue with Display and register.
> Can it be something to do with freeglut?
> 
> Here's some diagnostics:
> 
> glxgears work fine, 5000 frames/sec as a was getting on F10 where I
> had no
> problems.
> Here's glxinfo output
> name of display: :0.0
> display: :0  screen: 0
> direct rendering: Yes
> server glx vendor string: NVIDIA Corporation
> server glx version string: 1.4
> server glx extensions:
> 
> >From Xorg.conf  (I assume this is wher ethe Nvidia installer put the
> kernel
> module)
> Section "Files"
>     ModulePath      "/usr/lib64/xorg/modules"
> EndSection
> 
> Display library dependiencies:
> 
> ldd /usr/local/mni2/bin/Display
>     linux-vdso.so.1 =>  (0x00007fff13bff000)
>     libglut.so.3 => /usr/lib64/libglut.so.3 (0x00007f9c4d22e000)
>     libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003d0d000000)
>     libGL.so.1 => /usr/lib64/libGL.so.1 (0x00007f9c4d035000)
>     libhdf5.so.0 => /usr/local/hdf5-1.6.7/lib/libhdf5.so.0
> (0x00007f9c4cd11000)
>     libz.so.1 => /lib64/libz.so.1 (0x00000032c7e00000)
>     libm.so.6 => /lib64/libm.so.6 (0x00000032c6e00000)
>     libc.so.6 => /lib64/libc.so.6 (0x00000032c6a00000)
>     libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000032cc200000)
>     libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000032cae00000)
>     libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1
> (0x00000032d2600000)
>     libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000032cca00000)
>     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000032d3600000)
>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000032d2200000)
>     libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x00007f9c4b82a000)
>     libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
> (0x00007f9c4b728000)
>     libdl.so.2 => /lib64/libdl.so.2 (0x00000032c7200000)
>     /lib64/ld-linux-x86-64.so.2 (0x00000032c6400000)
>     libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000032ca200000)
>     libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000032caa00000)
> 
> 
> 
> 
> On Wed, Mar 10, 2010 at 5:43 PM, Andrew Janke <a.janke at gmail.com>
> wrote:
> 
> > On Wed, Mar 10, 2010 at 17:29, Soren Christensen
> <sorench at gmail.com>
> > wrote:
> > >  No I did not know about that one - no difference though:
> > >
> > > register -rgb idwi.mnc idwi_mir.mnc
> > > Could not get requested colour_map_mode(0), got(1,256)
> >
> > Well that's no fun.  Which version of the nvidia drivers and GLUT
> are
> > you using and do things like glxgears work?
> >
> >
> > a
> > _______________________________________________
> > 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

From sorench at gmail.com  Thu Mar 11 17:57:40 2010
From: sorench at gmail.com (Soren Christensen)
Date: Fri, 12 Mar 2010 09:57:40 +1100
Subject: [MINC-users] register and Display issues on Fedora 12
In-Reply-To: <454381946.415278.1268299738163.JavaMail.root@zimbra-store01.hst.aau.dk>
References: <749350308.415262.1268299644405.JavaMail.root@zimbra-store01.hst.aau.dk>
	<454381946.415278.1268299738163.JavaMail.root@zimbra-store01.hst.aau.dk>
Message-ID: <d6e2d6551003111457s609a110etd126f097c4373010@mail.gmail.com>

Thanks for the suggestion Simon but effects are turned off.

However, I managed to get it to work just now and can finally see colour
again..
I removed the freeglut library, installed the previous version, patched it
for gcc4.2 ( http://bugs.gentoo.org/131856) and compiled against that in
stead. That solved it.
It turns out that FreeGlut was updated on November 2009 (4 years after last
update). I appears that somehow this update may cause problems with Display
and register under certain circumstances.

Cheers
Soren



On Thu, Mar 11, 2010 at 8:28 PM, Simon Fristed Eskildsen <se at hst.aau.dk>wrote:

> Soren,
>
> FWIW, if I enable visual effects in ubuntu the UIs of Display and register
> are messed up. Maybe something similar is happening in fedora? I haven't
> tracked down the bug.
>
> Simon
> ----- "Soren Christensen" <sorench at gmail.com> wrote:
>
> > Sorry for the delay and thanks for the help - was trying to add
> > remove
> > drivers did not resolve it. At one stage I had the drivers removed and
> > x
> > started without 3D acceleration and Display and register came up
> > normal.
> > I have now reinstalled the nvidia driver from the nvidia web site
> > (NVIDIA-Linux-x86_64-190.53-pkg2.run) and everything seems to run well
> > (even
> > blender) but still the color issue with Display and register.
> > Can it be something to do with freeglut?
> >
> > Here's some diagnostics:
> >
> > glxgears work fine, 5000 frames/sec as a was getting on F10 where I
> > had no
> > problems.
> > Here's glxinfo output
> > name of display: :0.0
> > display: :0  screen: 0
> > direct rendering: Yes
> > server glx vendor string: NVIDIA Corporation
> > server glx version string: 1.4
> > server glx extensions:
> >
> > >From Xorg.conf  (I assume this is wher ethe Nvidia installer put the
> > kernel
> > module)
> > Section "Files"
> >     ModulePath      "/usr/lib64/xorg/modules"
> > EndSection
> >
> > Display library dependiencies:
> >
> > ldd /usr/local/mni2/bin/Display
> >     linux-vdso.so.1 =>  (0x00007fff13bff000)
> >     libglut.so.3 => /usr/lib64/libglut.so.3 (0x00007f9c4d22e000)
> >     libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003d0d000000)
> >     libGL.so.1 => /usr/lib64/libGL.so.1 (0x00007f9c4d035000)
> >     libhdf5.so.0 => /usr/local/hdf5-1.6.7/lib/libhdf5.so.0
> > (0x00007f9c4cd11000)
> >     libz.so.1 => /lib64/libz.so.1 (0x00000032c7e00000)
> >     libm.so.6 => /lib64/libm.so.6 (0x00000032c6e00000)
> >     libc.so.6 => /lib64/libc.so.6 (0x00000032c6a00000)
> >     libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000032cc200000)
> >     libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000032cae00000)
> >     libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1
> > (0x00000032d2600000)
> >     libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000032cca00000)
> >     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000032d3600000)
> >     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000032d2200000)
> >     libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x00007f9c4b82a000)
> >     libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
> > (0x00007f9c4b728000)
> >     libdl.so.2 => /lib64/libdl.so.2 (0x00000032c7200000)
> >     /lib64/ld-linux-x86-64.so.2 (0x00000032c6400000)
> >     libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000032ca200000)
> >     libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000032caa00000)
> >
> >
> >
> >
> > On Wed, Mar 10, 2010 at 5:43 PM, Andrew Janke <a.janke at gmail.com>
> > wrote:
> >
> > > On Wed, Mar 10, 2010 at 17:29, Soren Christensen
> > <sorench at gmail.com>
> > > wrote:
> > > >  No I did not know about that one - no difference though:
> > > >
> > > > register -rgb idwi.mnc idwi_mir.mnc
> > > > Could not get requested colour_map_mode(0), got(1,256)
> > >
> > > Well that's no fun.  Which version of the nvidia drivers and GLUT
> > are
> > > you using and do things like glxgears work?
> > >
> > >
> > > a
> > > _______________________________________________
> > > 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From davids at bic.mni.mcgill.ca  Fri Mar 12 11:56:59 2010
From: davids at bic.mni.mcgill.ca (David Seminowicz)
Date: Fri, 12 Mar 2010 11:56:59 -0500
Subject: [MINC-users] temporal filtering
Message-ID: <003701cac205$1df9b6d0$59ed2470$@mni.mcgill.ca>

Does anyone have a (Matlab) script or know of good software for applying a
temporal filter (e.g. bandpass) to timecourse datasets?  Thanks, Dave

 

______________________
David A. Seminowicz, Ph.D.
Postdoctoral Fellow
Alan Edwards Centre for Research on Pain
McGill University
Rm M/19 Strathcona Anatomy & Dentistry
3640 University St.
Montreal, Quebec H3A 2B2

 

Ph: 514.398.1271
Fax: 514.398.7464

 


From mferre at bic.mni.mcgill.ca  Mon Mar 15 16:30:04 2010
From: mferre at bic.mni.mcgill.ca (Michael Ferreira)
Date: Mon, 15 Mar 2010 16:30:04 -0400
Subject: [MINC-users] temporal filtering
In-Reply-To: <003701cac205$1df9b6d0$59ed2470$@mni.mcgill.ca>
References: <003701cac205$1df9b6d0$59ed2470$@mni.mcgill.ca>
Message-ID: <4B9E98CC.2070309@bic.mni.mcgill.ca>

Hi Dave,

Have you tried NIAK?  It has high-pass and low-pass filtering options.
You can find more information on it here:
http://wiki.bic.mni.mcgill.ca/index.php/NiakFmriPreprocessing
under the section: "Correction of slow time drifts".

Regards,

mike


David Seminowicz wrote:
> Does anyone have a (Matlab) script or know of good software for applying a
> temporal filter (e.g. bandpass) to timecourse datasets?  Thanks, Dave
> 
>  
> 
> ______________________
> David A. Seminowicz, Ph.D.
> Postdoctoral Fellow
> Alan Edwards Centre for Research on Pain
> McGill University
> Rm M/19 Strathcona Anatomy & Dentistry
> 3640 University St.
> Montreal, Quebec H3A 2B2
> 
>  
> 
> Ph: 514.398.1271
> Fax: 514.398.7464

From pgravel at bic.mni.mcgill.ca  Tue Mar 23 16:26:41 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 23 Mar 2010 16:26:41 -0400 (EDT)
Subject: [MINC-users] Where is mritopet?
In-Reply-To: <4B9E98CC.2070309@bic.mni.mcgill.ca>
References: <003701cac205$1df9b6d0$59ed2470$@mni.mcgill.ca>
	<4B9E98CC.2070309@bic.mni.mcgill.ca>
Message-ID: <Pine.LNX.4.64.1003231622460.14618@grumio.bic.mni.mcgill.ca>

Dear all,

Would anyone know where I could find a copy of the script mritopet? It 
seems to have been "deactivated" from the server...

Best,

Paul



From kevin.casey at mail.mcgill.ca  Wed Mar 24 12:07:54 2010
From: kevin.casey at mail.mcgill.ca (Kevin Casey)
Date: Wed, 24 Mar 2010 12:07:54 -0400
Subject: [MINC-users] Where is mritopet?
In-Reply-To: <mailman.3.1269446402.11708.minc-users@bic.mni.mcgill.ca>
References: <mailman.3.1269446402.11708.minc-users@bic.mni.mcgill.ca>
Message-ID: <201003241207.54813.kevin.casey@mail.mcgill.ca>

mritopet is still available on yorick, but nowhere else as far as I know

yorick:kevin% which mritopet
/usr/local/mni/bin/mritopet

KC


On Wednesday 24 March 2010 12:00:02 pm minc-users-request at bic.mni.mcgill.ca 
wrote:
> Send MINC-users mailing list submissions to
> 	minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> 	minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> 	minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
>
> Today's Topics:
>
>    1. Where is mritopet? (Paul GRAVEL)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Mar 2010 16:26:41 -0400 (EDT)
> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> Subject: [MINC-users] Where is mritopet?
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Cc: Paul Gravel - McGill Account <paul.gravel2 at mail.mcgill.ca>
> Message-ID:
> 	<Pine.LNX.4.64.1003231622460.14618 at grumio.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Dear all,
>
> Would anyone know where I could find a copy of the script mritopet? It
> seems to have been "deactivated" from the server...
>
> Best,
>
> Paul
>
>
>
>
> ------------------------------
>
> _______________________________________________
> 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 56, Issue 6
> *****************************************



From pgravel at bic.mni.mcgill.ca  Wed Mar 24 15:20:39 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 24 Mar 2010 15:20:39 -0400 (EDT)
Subject: [MINC-users] Where is mritopet?
In-Reply-To: <201003241207.54813.kevin.casey@mail.mcgill.ca>
References: <mailman.3.1269446402.11708.minc-users@bic.mni.mcgill.ca>
	<201003241207.54813.kevin.casey@mail.mcgill.ca>
Message-ID: <Pine.LNX.4.64.1003241519440.29308@grumio.bic.mni.mcgill.ca>

Meny thanks to All who responded!  I now have a couple of 
versions!

Best,

Paul

From nikelski at bic.mni.mcgill.ca  Thu Mar 25 17:41:34 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Thu, 25 Mar 2010 14:41:34 -0700
Subject: [MINC-users] ray_trace colour maps and rendering labels
Message-ID: <e12172551003251441w79a5556er34059bce9941082d@mail.gmail.com>

Hi all,

   Two brief brief questions.  I have a volume of labeled structures
(AAL labels) that I want to render onto a cortical surface. Now,
ray_trace does the job, but the default continuous color maps don't do
a very good job of delineating adjacent structures. For example, as
the label numbers for the superior temp gyrus and MTG are quite close,
both get rendered in a subtly different shade of yellow (using the
spectral color map).   Questions:

(1) does anyone have a ray_trace formatted colormap, suitable for
rendering labels, that I can plug into the ray_trace "-usercc"
argument?

(2) does anyone know the required file format needed to use the
ray_trace "-usercc" argument, so that I can cobble my own together?

Thanks,

-Jim


-- 
=================================
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 claude at bic.mni.mcgill.ca  Thu Mar 25 18:13:38 2010
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Thu, 25 Mar 2010 18:13:38 -0400
Subject: [MINC-users] ray_trace colour maps and rendering labels
In-Reply-To: <e12172551003251441w79a5556er34059bce9941082d@mail.gmail.com>
Message-ID: <201003252213.o2PMDcUw006393@grumio.bic.mni.mcgill.ca>

Hi Jim,

I have played with those colours in the past. I forget the details, 
but here are some clues:

bicpl/Volumes/colour_coding.c, function recreate_piecewise_function()

You may be able to create labels from this:

    static  colour_point  spectral_points[] =
                    { { 0.00, 0.0000,0.0000,0.0000, 1.0, RGB_SPACE},
                      { 0.05, 0.4667,0.0000,0.5333, 1.0, RGB_SPACE},
                      { 0.10, 0.5333,0.0000,0.6000, 1.0, RGB_SPACE},
                      { 0.15, 0.0000,0.0000,0.6667, 1.0, RGB_SPACE},
                      { 0.20, 0.0000,0.0000,0.8667, 1.0, RGB_SPACE},
                      { 0.25, 0.0000,0.4667,0.8667, 1.0, RGB_SPACE},
                       ...
                      { 0.85, 1.0000,0.0000,0.0000, 1.0, RGB_SPACE},
                      { 0.90, 0.8667,0.0000,0.0000, 1.0, RGB_SPACE},
                      { 0.95, 0.8000,0.0000,0.0000, 1.0, RGB_SPACE},
                      { 1.00, 0.8000,0.8000,0.8000, 1.0, RGB_SPACE}
                    };

First column runs from 0 to 1 and maps to (MIN,MAX) in your intensity
range. Suppose you want 10 labels being 1,2,3,4,5,6,7,8,9,10.
    { { 0.00,     0.0000,0.0000,0.0000, 1.0, RGB_SPACE},  // label 1 centered at 0.05
      { 0.099999, 0.0000,0.0000,0.0000, 1.0, RGB_SPACE},
      { 0.100001, 0.4667,0.0000,0.5333, 1.0, RGB_SPACE},  // label 2 centered at 0.15
      { 0.199999, 0.4667,0.0000,0.5333, 1.0, RGB_SPACE},
      { 0.200001, 0.5333,0.0000,0.6000, 1.0, RGB_SPACE},  // label 3 centered at 0.25
      { 0.299999, 0.5333,0.0000,0.6000, 1.0, RGB_SPACE},

Also have a look at brain-view-0.7.0/src/brainApp.cc for a list of labels
for painting:

#define NUM_PAINTING_LABELS 32
static unsigned char rgbt[] = { 255, 255, 255,   // white
                                255,   0,   0,   // red
                                  0, 255,   0,   // green
                                  0,   0, 255,   // blue
                                // from http://cloford.com/resources/colours/500col.htm
                                255, 181, 197,   // pink 1
                                205, 105, 201,   // orchid 3
                                132, 112, 255,   // lightslateblue
                                 78, 238, 148,   // seagreen 2
                                255, 255,   0,   // yellow 1
                                255, 185,  15,   // darkgoldenrod 1
                                255, 231, 186,   // wheat 1
                                 56, 142, 142,   // sgi teal
                                197, 193, 170,   // sgi brightgray
                                139,  26,  26,   // firebrick 4
                                139, 137, 137,   // snow 4
                                244, 164,  96,   // sandybrown
                                255, 215,   0,   // gold 1
                                205, 205,   0,   // yellow 3
                                118, 238,   0,   // chartreuse 2
                                189, 252, 201,   // mint
                                 72, 209, 204,   // mediumturquoise
                                255,   0, 255,   // magenta
                                205, 181, 205,   // thistle 1
                                145,  44, 238,   // purple 2
                                 72, 118, 255,   // royalblue 1
                                  0, 255, 127,   // springgreen
                                107, 142,  35,   // olivedrab
                                237, 145,  33,   // carrot
                                158, 158, 158,   // gray 62
                                 26,  26,  26,   // gray 10
                                238,  59,  59,   // brown 2
                                124, 205, 124    // palegreen 3
                              };

Have fun. If you get something nice in bicpl, feed it back my way so that
I can include in the next version.

Claude

From a.janke at gmail.com  Thu Mar 25 19:28:50 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 26 Mar 2010 10:28:50 +1100
Subject: [MINC-users] ray_trace colour maps and rendering labels
In-Reply-To: <e12172551003251441w79a5556er34059bce9941082d@mail.gmail.com>
References: <e12172551003251441w79a5556er34059bce9941082d@mail.gmail.com>
Message-ID: <d747ed51003251628n103736f2y107d29c08fe05830@mail.gmail.com>

Hi Jim

On Fri, Mar 26, 2010 at 08:41, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> (2) does anyone know the required file format needed to use the
> ray_trace "-usercc" argument, so that I can cobble my own together?

I can't help on the first bit but I would guess that they would follow
the same format as minclookup (man minclookup for more). As an example
here is the spectral colourmap that can be passed to minclookup


harold:Downloads$ cat ~rotor/lib/luts/spectral
0.00 0.0000 0.0000 0.0000
0.05 0.4667 0.0000 0.5333
0.10 0.5333 0.0000 0.6000
0.15 0.0000 0.0000 0.6667
0.20 0.0000 0.0000 0.8667
0.25 0.0000 0.4667 0.8667
0.30 0.0000 0.6000 0.8667
0.35 0.0000 0.6667 0.6667
0.40 0.0000 0.6667 0.5333
0.45 0.0000 0.6000 0.0000
0.50 0.0000 0.7333 0.0000
0.55 0.0000 0.8667 0.0000
0.60 0.0000 1.0000 0.0000
0.65 0.7333 1.0000 0.0000
0.70 0.9333 0.9333 0.0000
0.75 1.0000 0.8000 0.0000
0.80 1.0000 0.6000 0.0000
0.85 1.0000 0.0000 0.0000
0.90 0.8667 0.0000 0.0000
0.95 0.8000 0.0000 0.0000
1.00 0.8000 0.8000 0.8000

For a discrete colourmap the first column would be an integer set from 0-255

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

From nikelski at bic.mni.mcgill.ca  Thu Mar 25 22:02:11 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Thu, 25 Mar 2010 19:02:11 -0700
Subject: [MINC-users] ray_trace colour maps and rendering labels
In-Reply-To: <d747ed51003251628n103736f2y107d29c08fe05830@mail.gmail.com>
References: <e12172551003251441w79a5556er34059bce9941082d@mail.gmail.com>
	<d747ed51003251628n103736f2y107d29c08fe05830@mail.gmail.com>
Message-ID: <e12172551003251902k520d70c3le3c3324261496e6d@mail.gmail.com>

Hi,

  Andrew and Claude -- thanks for the help. Between both suggestions,
I should be able to get the job done.

  Can I add one additional follow-up?  First, for context, I've fit
the AAL labels (manual labeling of the colin-27 brain) to the Civet
model (fit to a 4-mm grid), and am now applying my subject's inverted
non-linear transform to the AAL volume in order to fit the labels onto
my subject's linear fit T1 (out of Civet). The results look good, but
... the "real" values in my label volume appear to be stored as floats
-- or so says register, Display and postf.  How do I convert my label
volume into simply having "real" values = voxel values = label values
= integers?

-Jim



On Thu, Mar 25, 2010 at 4:28 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Jim
>
> On Fri, Mar 26, 2010 at 08:41, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
>> (2) does anyone know the required file format needed to use the
>> ray_trace "-usercc" argument, so that I can cobble my own together?
>
> I can't help on the first bit but I would guess that they would follow
> the same format as minclookup (man minclookup for more). As an example
> here is the spectral colourmap that can be passed to minclookup
>
>
> harold:Downloads$ cat ~rotor/lib/luts/spectral
> 0.00 0.0000 0.0000 0.0000
> 0.05 0.4667 0.0000 0.5333
> 0.10 0.5333 0.0000 0.6000
> 0.15 0.0000 0.0000 0.6667
> 0.20 0.0000 0.0000 0.8667
> 0.25 0.0000 0.4667 0.8667
> 0.30 0.0000 0.6000 0.8667
> 0.35 0.0000 0.6667 0.6667
> 0.40 0.0000 0.6667 0.5333
> 0.45 0.0000 0.6000 0.0000
> 0.50 0.0000 0.7333 0.0000
> 0.55 0.0000 0.8667 0.0000
> 0.60 0.0000 1.0000 0.0000
> 0.65 0.7333 1.0000 0.0000
> 0.70 0.9333 0.9333 0.0000
> 0.75 1.0000 0.8000 0.0000
> 0.80 1.0000 0.6000 0.0000
> 0.85 1.0000 0.0000 0.0000
> 0.90 0.8667 0.0000 0.0000
> 0.95 0.8000 0.0000 0.0000
> 1.00 0.8000 0.8000 0.8000
>
> For a discrete colourmap the first column would be an integer set from 0-255
>
> --
> 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://www.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 claude at bic.mni.mcgill.ca  Thu Mar 25 22:47:54 2010
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Thu, 25 Mar 2010 22:47:54 -0400
Subject: [MINC-users] ray_trace colour maps and rendering labels
In-Reply-To: <e12172551003251902k520d70c3le3c3324261496e6d@mail.gmail.com>
Message-ID: <201003260247.o2Q2lsea015699@grumio.bic.mni.mcgill.ca>

Jim,

>   Can I add one additional follow-up?  First, for context, I've fit
> the AAL labels (manual labeling of the colin-27 brain) to the Civet
> model (fit to a 4-mm grid), and am now applying my subject's inverted
> non-linear transform to the AAL volume in order to fit the labels onto
> my subject's linear fit T1 (out of Civet). The results look good, but
> ... the "real" values in my label volume appear to be stored as floats
> -- or so says register, Display and postf.  How do I convert my label
> volume into simply having "real" values =3D voxel values =3D label values
> =3D integers?

Try something like:
  mincreshape -byte -image_range 0 255 -valid_range 0 255 ...

Claude

From nikelski at bic.mni.mcgill.ca  Fri Mar 26 15:47:57 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 26 Mar 2010 12:47:57 -0700
Subject: [MINC-users] ray_trace colour maps and rendering labels
In-Reply-To: <201003260247.o2Q2lsea015699@grumio.bic.mni.mcgill.ca>
References: <e12172551003251902k520d70c3le3c3324261496e6d@mail.gmail.com>
	<201003260247.o2Q2lsea015699@grumio.bic.mni.mcgill.ca>
Message-ID: <e12172551003261247n1266ab59y2d751e4295ac0159@mail.gmail.com>

Hello minc-users,

   Ok, for posterity and for all future Googlers who find their way to
this post, here is what I've figured out about how to create one's own
*discrete* ray_trace-friendly color map -- useful for rendering
labels.  Pretty simple, when you know how ;)

(1) file type is ".ccd", so use this as an extension

(2) the first column must contain the label number, which *must* be
monotonic. That is, keep your labels in ascending order.

(3) subsequent columns are used to define the corresponding color.
This can be done in the usual way: e.g., [ r g b ], [ r g b a ], or [
blue ].  All fields are space-delimited.

(4) each label in the volume being rendered *should* have a
corresponding line in the .ccd file, else ray_trace might make
something up.

(5) unused label values do *not* need a line defined in the .ccd file.
So, if you have a .ccd range of 128, but only need 10 label values,
you need only define the 10 labels that you need.

(6) the ray_trace <min> and <max> values specified on the "-usercc"
argument, *must* have corresponding labels in the .ccd file, else
labels get unexpectedly assigned. So, if in ray_trace you say ...
>>-usercc    user_map.ccd  0 127  volume.mnc  -1 1.0

   ... then your .ccd file better have label entries for "0" and "127".

   That's all that I can think of for now.  If anyone has any other
suggestions, pls feel free to contribute.  Now get out there and spend
your weekend creating label-friendly color maps ... I will <sigh>.

Cheers,

-Jim



On Thu, Mar 25, 2010 at 7:47 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
> Jim,
>
>> ? Can I add one additional follow-up? ?First, for context, I've fit
>> the AAL labels (manual labeling of the colin-27 brain) to the Civet
>> model (fit to a 4-mm grid), and am now applying my subject's inverted
>> non-linear transform to the AAL volume in order to fit the labels onto
>> my subject's linear fit T1 (out of Civet). The results look good, but
>> ... the "real" values in my label volume appear to be stored as floats
>> -- or so says register, Display and postf. ?How do I convert my label
>> volume into simply having "real" values =3D voxel values =3D label values
>> =3D integers?
>
> Try something like:
> ?mincreshape -byte -image_range 0 255 -valid_range 0 255 ...
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.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 pbellec at bic.mni.mcgill.ca  Fri Mar 26 16:06:07 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Fri, 26 Mar 2010 16:06:07 -0400
Subject: [MINC-users] from surface to adjacency
Message-ID: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>

Dear minc users,

I am currently trying to adapt a region-growing procedure for surface data.
The procedure is using a representation of the adjacency matrix between
vertices, i.e. a matrix (vertices times vertices) with 1s for pairs of
vertices that are spatial neighbours on the surface, and 0 otherwise. I sort
of understood that the order of the vertices in the obj file is very
specific and follows an iterative refinement of the surface grid. Can anyone
suggest an approach to generate the adjacency matrix based on the .obj data
?

Thank you in advance,

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

From nikelski at bic.mni.mcgill.ca  Sat Mar 27 02:37:47 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 26 Mar 2010 23:37:47 -0700
Subject: [MINC-users] from surface to adjacency
In-Reply-To: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>
Message-ID: <e12172551003262337n352f7571xc22ce66e2451069f@mail.gmail.com>

Hi Pierre,

   I'm no expert on the structure of .obj files, but I believe that
one of the structures within the file is used to record the
correspondence between vertices and polygons.  Given that our our
cortical surfaces are constructed of triangles, this table has
number_of_polygons rows and 3 columns.  All 3 vertices for any
triangle would be adjacent, and the corresponding matrix rows-columns
could be set to 1.  Just loop over all triangles in the table, and you
should have the matrix that you're looking for.

HTH,

-Jim



On Fri, Mar 26, 2010 at 1:06 PM, Pierre Bellec
<pbellec at bic.mni.mcgill.ca> wrote:
> Dear minc users,
>
> I am currently trying to adapt a region-growing procedure for surface data.
> The procedure is using a representation of the adjacency matrix between
> vertices, i.e. a matrix (vertices times vertices) with 1s for pairs of
> vertices that are spatial neighbours on the surface, and 0 otherwise. I sort
> of understood that the order of the vertices in the obj file is very
> specific and follows an iterative refinement of the surface grid. Can anyone
> suggest an approach to generate the adjacency matrix based on the .obj data
> ?
>
> Thank you in advance,
>
> Pierre Bellec
> Post-doctoral fellow
> McConnel Brain Imaging Center, Webster 2B
> Montreal Neurological Institute
> 3801 University Street
> Montreal, Quebec, Canada H3A 2B4
> http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
> tel: ? ? ? (001)(514) 398 5220
> fax: ? ? ?(001)(514) 398 8948
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.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 vikingy at gmail.com  Sat Mar 27 15:21:42 2010
From: vikingy at gmail.com (vikingy)
Date: Sat, 27 Mar 2010 12:21:42 -0700
Subject: [MINC-users] from surface to adjacency
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>
Message-ID: <201003271221408432484@gmail.com>

Hi Pierre,

I guess the 'mni_getmesh.m' writted by Moo K. Chung is used to do what you want. Here is the link:
http://www.stat.wisc.edu/~mchung/softwares/mesh/mesh.html

Hope it can help you.

Bin Lv 


2010-03-27 



vikingy 



???? Pierre Bellec 
????? 2010-03-26  13:07:31 
???? MINC users mailing list 
??? 
??? [MINC-users] from surface to adjacency 
 
Dear minc users,
I am currently trying to adapt a region-growing procedure for surface data.
The procedure is using a representation of the adjacency matrix between
vertices, i.e. a matrix (vertices times vertices) with 1s for pairs of
vertices that are spatial neighbours on the surface, and 0 otherwise. I sort
of understood that the order of the vertices in the obj file is very
specific and follows an iterative refinement of the surface grid. Can anyone
suggest an approach to generate the adjacency matrix based on the .obj data
?
Thank you in advance,
Pierre Bellec
Post-doctoral fellow
McConnel Brain Imaging Center, Webster 2B
Montreal Neurological Institute
3801 University Street
Montreal, Quebec, Canada H3A 2B4
http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
tel:       (001)(514) 398 5220
fax:      (001)(514) 398 8948
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From pbellec at bic.mni.mcgill.ca  Sat Mar 27 15:29:22 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Sat, 27 Mar 2010 15:29:22 -0400
Subject: [MINC-users] from surface to adjacency
In-Reply-To: <201003271221408432484@gmail.com>
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>
	<201003271221408432484@gmail.com>
Message-ID: <6fe841c71003271229x75a2622ana0b70024c4d66860@mail.gmail.com>

Thanks so much, Bin, this is exactly what I was looking for (the NBR output
is what I use rather than an actual adjacency matrix representation).

Best regards,

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


2010/3/27 vikingy <vikingy at gmail.com>

>  Hi Pierre,
>
> I guess the 'mni_getmesh.m' writted by Moo K. Chung is used to do what you
> want. Here is the link:
> http://www.stat.wisc.edu/~mchung/softwares/mesh/mesh.html<http://www.stat.wisc.edu/%7Emchung/softwares/mesh/mesh.html>
>
> Hope it can help you.
>
> Bin Lv
>
>
> 2010-03-27
> ------------------------------
>  vikingy
> ------------------------------
> *????* Pierre Bellec
> *?????* 2010-03-26  13:07:31
> *????* MINC users mailing list
> *???*
> *???* [MINC-users] from surface to adjacency
>   Dear minc users,
>
> I am currently trying to adapt a region-growing procedure for surface data.
> The procedure is using a representation of the adjacency matrix between
> vertices, i.e. a matrix (vertices times vertices) with 1s for pairs of
>
> vertices that are spatial neighbours on the surface, and 0 otherwise. I sort
> of understood that the order of the vertices in the obj file is very
>
> specific and follows an iterative refinement of the surface grid. Can anyone
> suggest an approach to generate the adjacency matrix based on the .obj data
> ?
>  Thank you in advance,
>  Pierre Bellec
> Post-doctoral fellow
> McConnel Brain Imaging Center, Webster 2B
> Montreal Neurological Institute
> 3801 University Street
> Montreal, Quebec, Canada H3A 2B4
> http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
> tel:       (001)(514) 398 5220
> fax:      (001)(514) 398 8948
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From pgravel at bic.mni.mcgill.ca  Tue Mar 30 12:48:41 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 30 Mar 2010 12:48:41 -0400 (EDT)
Subject: [MINC-users] mincheader for minc2
In-Reply-To: <201003271221408432484@gmail.com>
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com>
	<201003271221408432484@gmail.com>
Message-ID: <Pine.LNX.4.64.1003301246150.22026@grumio.bic.mni.mcgill.ca>

Dear All,

Would anyone know where I could find mincheader for minc2 files?

I have tried /usr/local/bic/bin/mincheader infile.mnc but I get the 
following error message:
ncopen: filename "infile.mnc": NetCDF: Unknown file format
miopen: MINC package entry point

However: /usr/local/bic/bin/mincinfo infile.mnc does work.

Thanks in advance!

Paul



From a.janke at gmail.com  Tue Mar 30 20:27:02 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 31 Mar 2010 11:27:02 +1100
Subject: [MINC-users] mincheader for minc2
In-Reply-To: <Pine.LNX.4.64.1003301246150.22026@grumio.bic.mni.mcgill.ca>
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com> 
	<201003271221408432484@gmail.com>
	<Pine.LNX.4.64.1003301246150.22026@grumio.bic.mni.mcgill.ca>
Message-ID: <d747ed51003301727hf015f91j1ff7475007c78a8f@mail.gmail.com>

On Wed, Mar 31, 2010 at 03:48, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> Would anyone know where I could find mincheader for minc2 files?
>
> I have tried /usr/local/bic/bin/mincheader infile.mnc but I get the
> following error message:
> ncopen: filename "infile.mnc": NetCDF: Unknown file format
> miopen: MINC package entry point
>
> However: /usr/local/bic/bin/mincinfo infile.mnc does work.

Well this is all very strange.  What does mincdump -h return?

You seem to somehow have a few versions of MINC installs mixed up.  Is
this your own machine or one at the BIC?


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

From M.Bahri at ulg.ac.be  Wed Mar 31 05:39:53 2010
From: M.Bahri at ulg.ac.be (Mohamed Ali Bahri)
Date: Wed, 31 Mar 2010 11:39:53 +0200
Subject: [MINC-users] N3 on Cygwin
In-Reply-To: <d747ed50905060528h44df7f91qe33f5ad625a5a2a0@mail.gmail.com>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be> <4A018103.3060105@ulg.ac.be>
	<d747ed50905060528h44df7f91qe33f5ad625a5a2a0@mail.gmail.com>
Message-ID: <4BB31869.9070501@ulg.ac.be>

Dear All,

I would like use the N3 package, could anyone describe to me which 
modules should I install?  I installed cygwin on my windows XP 64bit.

Many thanks in advance,

Mohamed

-- 
Mohamed Ali BAHRI, Ph.D.
Collaborateur Scientifique F.N.R.S
Cyclotron Research Centre
University of Li?ge, B?t. B30
All?e du 6 ao?t n?8
B-4000 Li?ge
Belgium
email:M.Bahri at ulg.ac.be


From delphine.ribes at epfl.ch  Wed Mar 31 05:49:11 2010
From: delphine.ribes at epfl.ch (Ribes Delphine)
Date: Wed, 31 Mar 2010 11:49:11 +0200
Subject: [MINC-users] RE :  N3 on Cygwin
In-Reply-To: <4BB31869.9070501@ulg.ac.be>
References: <200904051436.n35EajZi022585@grumio.bic.mni.mcgill.ca>
	<49D9BB0E.3040601@ulg.ac.be>
	<d747ed50904060146p326dbb2er30e03742fa68cc2a@mail.gmail.com>
	<49D9D156.7020709@ulg.ac.be> <4A018103.3060105@ulg.ac.be>
	<d747ed50905060528h44df7f91qe33f5ad625a5a2a0@mail.gmail.com>,
	<4BB31869.9070501@ulg.ac.be>
Message-ID: <D583B46872069E46ACBBA505605DFD2BB58C471BFD@rex5.intranet.epfl.ch>


http://www.ece.ubc.ca/~alberth/project.html

It worked for me couple of weeks ago.
________________________________________
De : minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] de la part de Mohamed Ali Bahri [M.Bahri at ulg.ac.be]
Date d'envoi : mercredi 31 mars 2010 11:39
? : MINC users mailing list
Objet : [MINC-users] N3 on Cygwin

Dear All,

I would like use the N3 package, could anyone describe to me which
modules should I install?  I installed cygwin on my windows XP 64bit.

Many thanks in advance,

Mohamed

--
Mohamed Ali BAHRI, Ph.D.
Collaborateur Scientifique F.N.R.S
Cyclotron Research Centre
University of Li?ge, B?t. B30
All?e du 6 ao?t n?8
B-4000 Li?ge
Belgium
email:M.Bahri at ulg.ac.be

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

From pgravel at bic.mni.mcgill.ca  Wed Mar 31 11:32:17 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 31 Mar 2010 11:32:17 -0400 (EDT)
Subject: [MINC-users] mincheader for minc2
In-Reply-To: <d747ed51003301727hf015f91j1ff7475007c78a8f@mail.gmail.com>
References: <6fe841c71003261306v5d23008bq8df467ac4de1f39@mail.gmail.com> 
	<201003271221408432484@gmail.com>
	<Pine.LNX.4.64.1003301246150.22026@grumio.bic.mni.mcgill.ca>
	<d747ed51003301727hf015f91j1ff7475007c78a8f@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1003311120500.23045@grumio.bic.mni.mcgill.ca>

Thanks Andrew, Samir, and Kevin L.!

I did get a reply from Kevin Larcher yesterday suggesting I typed:
source /data/aces/aces1/quarantines/Linux-i686/Feb-14-2008/init-sge.csh

and it solved the problem.

btw, I do run this on a BIC machine.

I also typed /usr/local/bic/bin/mincdump -h infile.mnc (before sourcing 
the init-sge.csh) and it did spit out the header!

Thanks again!

Paul


On Wed, 31 Mar 2010, Andrew Janke wrote:

> On Wed, Mar 31, 2010 at 03:48, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> Would anyone know where I could find mincheader for minc2 files?
>>
>> I have tried /usr/local/bic/bin/mincheader infile.mnc but I get the
>> following error message:
>> ncopen: filename "infile.mnc": NetCDF: Unknown file format
>> miopen: MINC package entry point
>>
>> However: /usr/local/bic/bin/mincinfo infile.mnc does work.
>
> Well this is all very strange.  What does mincdump -h return?
>
> You seem to somehow have a few versions of MINC installs mixed up.  Is
> this your own machine or one at the BIC?
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
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