From sean at rogue-research.com  Fri Jun  1 12:05:54 2007
From: sean at rogue-research.com (Sean McBride)
Date: Fri, 1 Jun 2007 12:05:54 -0400
Subject: [MINC-users] Web page error: MINC 1.5 vs 1.5.1
Message-ID: <20070601160554.1245928971@smtp1.sympatico.ca>

Hi all,

Does MINC 1.5.1 exist?  This page:

<http://www.bic.mni.mcgill.ca/software/minc/>

Has links to 1.5 and 1.5.1, but they BOTH link to
<http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.tar.gz>

This seems wrong.

-- 
____________________________________________________________
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  Sat Jun  2 12:15:00 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Sat, 2 Jun 2007 12:15:00 -0400
Subject: [MINC-users] small bug in autocrop
Message-ID: <ea3878950706020915y71e48484kdf62fb3f5667a13f@mail.gmail.com>

Hello,

sometimes it reports error:
set_options: must supply even number of args (option/value pairs) at
/home/vfonov/bin/autocrop line 681

See attached diff file for fix.

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

From a.janke at gmail.com  Wed Jun  6 10:31:15 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 7 Jun 2007 00:31:15 +1000
Subject: [MINC-users] Web page error: MINC 1.5 vs 1.5.1
In-Reply-To: <20070601160554.1245928971@smtp1.sympatico.ca>
References: <20070601160554.1245928971@smtp1.sympatico.ca>
Message-ID: <d747ed50706060731w1906a74dk2a1bfb831fe83ad4@mail.gmail.com>

Interesting,

Yes it does exist:

   http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.1.tar.gz

but the link does need fixing!.


a

On 6/2/07, Sean McBride <sean at rogue-research.com> wrote:
> Hi all,
>
> Does MINC 1.5.1 exist?  This page:
>
> <http://www.bic.mni.mcgill.ca/software/minc/>
>
> Has links to 1.5 and 1.5.1, but they BOTH link to
> <http://packages.bic.mni.mcgill.ca/tgz/minc-1.5.tar.gz>
>
> This seems wrong.
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng                 sean at rogue-research.com
> Rogue Research                        www.rogue-research.com
> Mac Software Developer              Montr?al, Qu?bec, Canada
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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


From se at hst.aau.dk  Tue Jun 19 11:49:55 2007
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Tue, 19 Jun 2007 17:49:55 +0200
Subject: [MINC-users] Filling with mincreshape
In-Reply-To: <455897DC.6060104@hst.aau.dk>
References: <4554CBCE.5040803@hst.aau.dk>	<d747ed50611130013y2227b098qf59dfc046a8729f9@mail.gmail.com>
	<455897DC.6060104@hst.aau.dk>
Message-ID: <4677FB23.9000408@hst.aau.dk>

Hi all,

I never resolved the issue with mincreshape, and now I have stumbled 
upon a similar problem. If I do

mincreshape -rowsize 256 -colsize 256 test.mnc test_reshaped.mnc

and test.mnc is signed short (and standard mni space size) mincreshape 
fills the "new" voxels with what seems to be the maximum value in that 
particular slice. However, if I do

mincreshape -unsigned test.mnc test_usign.mnc
mincreshape -rowsize 256 -colsize 256 test_usign.mnc test_reshaped.mnc

everything seems ok. But if I look closely, also this volume has 
non-zero filling. Three individual slices are uniformly filled.

It seems that mincreshape uses uninitialized mem.

Simon

Simon Fristed Eskildsen wrote:
> Andrew Janke wrote:
>> First, the -fill and -fillvalue options are mutually exclusive of each
>> other. Meaning choose one of -nofill -fill and -fillvalue.  in this
>> case, I think you want to skip the -fill option.
>>
>> Try this again without the -fill option.  Also check out -pixfillvalue
>> it might be closer to what you want.
>>
> 
> I think I have tried all combinations of -fill, -fillvalue, -pixfill, 
> and -pixfillvalue all with the same result. A rudimentary investigation 
> of the source code reveals that mincreshape decides that there is no 
> need to fill anything. Specifically, the variable 
> reshape_info->need_fillvalue is set to false. Maybe I am doing the 
> extrapolation wrong?
> 
> Simon
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From Jean-Francois.Malouin at bic.mni.mcgill.ca  Thu Jun 21 14:04:52 2007
From: Jean-Francois.Malouin at bic.mni.mcgill.ca (Jean-Francois Malouin)
Date: Thu, 21 Jun 2007 14:04:52 -0400
Subject: [MINC-users] (forw) Register problem
Message-ID: <20070621180452.GB25385336@yorick.bic.mni.mcgill.ca>

Anyone can help the poor soul?
(I've taken the liberty of editing the original message)
jf

----- Forwarded message from Gilles Plourde <gilles.plourde at mcgill.ca> -----

From: Gilles Plourde <gilles.plourde at mcgill.ca>
To: Trinity <trinity at bic.mni.mcgill.ca>
Subject: Register problem
Date: Thu, 21 Jun 2007 13:54:02 -0400
Message-ID: <C2A0337A.2528%gilles.plourde at mcgill.ca>
User-Agent: Microsoft-Entourage/11.2.5.060620

***********************
I get the following error message:

[Gilles-Plourdes-Computer:/mni/bin] gillespl% GLUT: Fatal Error in
no_program_name: visual with necessary capabilities not found.


when invoking register on X Window X11 1.1.3 (XFree86.4.4.0) on my Mac
running OS 10.4 . Register was running well before and I do not know what
has been changed. In the attempts to solve the problem with X windows which,
as was discovered after a few weeks, were caused by my BIC  account being
over quota, some settings of X Window X11 1.1.3 (XFree86.4.4.0) on my Mac
may have been changed.


Interestingly, register still runs ok on my Mac laptop.

Thank you!

Gilles


 
Gilles Plourde

Dept. of anesthesia, Montreal Neurological Hospital
3801 University St., Montreal, QC, H3A 2B4
Phone: 514-398-1917 Fax: 514-398-1352
Pager: 514-406-0484
*******************
D?part. d'anesth?sie, H?p. Neurologique de Montr?al
3801 rue Universit?, Montreal, QC, H3A 2B4
T?l.: 514-398-1917; T?l?cop.: 514-398-1352
T?l?-avertisseur: 514-406-0484--




----- End forwarded message -----

-- 
<? ><

From sorench at gmail.com  Thu Jun 21 21:15:54 2007
From: sorench at gmail.com (Soren Christensen)
Date: Fri, 22 Jun 2007 11:15:54 +1000
Subject: [MINC-users] Display graphics on fedora 7
Message-ID: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>

Hi,
 I have trouble with hardware rendering (I assume) in Display compiled on
Fedora 7.
The slice/cursor navigation seems slow as if software rendering is in
effect, but glxinfo | grep direct:   direct rendering: Yes, and Display also
does not give warnings except this one every time it is started:
Try R300_SPAN_DISABLE_LOCKING env var if this hangs.

Any suggestions as to what might cause this?

Also, if Desktop effects are enabled Display seems to crash - but this is
less of a problem.

Regards
Soren

From a.janke at gmail.com  Thu Jun 21 21:46:50 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Jun 2007 11:46:50 +1000
Subject: [MINC-users] Display graphics on fedora 7
In-Reply-To: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>
References: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>
Message-ID: <d747ed50706211846w49420a30uaa1341167f589a30@mail.gmail.com>

Interesting,

I certainly have no trouble with beryl/compiz under Ubutu Feisty.
This is with a Nvidia GeForce 8600GT running Dual 1600x1200 DVI.

Although I do know there is a problem with some of the nvidia cards /
drivers in register if you set to many tag points.  Sylvain has
investigated this at length and it appears that it is a combination of
certain cards and certain hardware.

My guess in all this is that Dave when he wrote these all those years
ago used a few parts of GLUT that are not all that well supported.

Is your hardware ATI or NVIDIA?  and what does glxinfo return?

If ATI, I have had more success with the fglrx (proprietary) drivers.

I also have spend much more time debugging register/Display under
nvidia than ATI, so if others are considering a new machine I would
suggest NVIDIA.


a

On 6/22/07, Soren Christensen <sorench at gmail.com> wrote:
> Hi,
>  I have trouble with hardware rendering (I assume) in Display compiled on
> Fedora 7.
> The slice/cursor navigation seems slow as if software rendering is in
> effect, but glxinfo | grep direct:   direct rendering: Yes, and Display also
> does not give warnings except this one every time it is started:
> Try R300_SPAN_DISABLE_LOCKING env var if this hangs.
>
> Any suggestions as to what might cause this?
>
> Also, if Desktop effects are enabled Display seems to crash - but this is
> less of a problem.
>
> Regards
> Soren
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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

From a.janke at gmail.com  Thu Jun 21 21:52:28 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Jun 2007 11:52:28 +1000
Subject: [MINC-users] (forw) Register problem
In-Reply-To: <20070621180452.GB25385336@yorick.bic.mni.mcgill.ca>
References: <20070621180452.GB25385336@yorick.bic.mni.mcgill.ca>
Message-ID: <d747ed50706211852q58bf8b0fw8b71cf10737810ba@mail.gmail.com>

Hi Gilles,

Is this the only message?  If so are you running register from one of
the packages on packages.bic.mni.mcgill.ca/osx or did you compile it
yourself?  What I am trying to ascertain is whether you are using the
X11 implementation of GLUT or the OSX version.

a



On 6/22/07, Jean-Francois Malouin
<Jean-Francois.Malouin at bic.mni.mcgill.ca> wrote:
> Anyone can help the poor soul?
> (I've taken the liberty of editing the original message)
> jf
>
> ----- Forwarded message from Gilles Plourde <gilles.plourde at mcgill.ca> -----
>
> From: Gilles Plourde <gilles.plourde at mcgill.ca>
> To: Trinity <trinity at bic.mni.mcgill.ca>
> Subject: Register problem
> Date: Thu, 21 Jun 2007 13:54:02 -0400
> Message-ID: <C2A0337A.2528%gilles.plourde at mcgill.ca>
> User-Agent: Microsoft-Entourage/11.2.5.060620
>
> ***********************
> I get the following error message:
>
> [Gilles-Plourdes-Computer:/mni/bin] gillespl% GLUT: Fatal Error in
> no_program_name: visual with necessary capabilities not found.
>
>
> when invoking register on X Window X11 1.1.3 (XFree86.4.4.0) on my Mac
> running OS 10.4 . Register was running well before and I do not know what
> has been changed. In the attempts to solve the problem with X windows which,
> as was discovered after a few weeks, were caused by my BIC  account being
> over quota, some settings of X Window X11 1.1.3 (XFree86.4.4.0) on my Mac
> may have been changed.
>
>
> Interestingly, register still runs ok on my Mac laptop.
>
> Thank you!
>
> Gilles
>
>
>
> Gilles Plourde
>
> Dept. of anesthesia, Montreal Neurological Hospital
> 3801 University St., Montreal, QC, H3A 2B4
> Phone: 514-398-1917 Fax: 514-398-1352
> Pager: 514-406-0484
> *******************
> D?part. d'anesth?sie, H?p. Neurologique de Montr?al
> 3801 rue Universit?, Montreal, QC, H3A 2B4
> T?l.: 514-398-1917; T?l?cop.: 514-398-1352
> T?l?-avertisseur: 514-406-0484--
>
>
>
>
> ----- End forwarded message -----
>
> --
> <? ><
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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


From sorench at gmail.com  Thu Jun 21 22:10:22 2007
From: sorench at gmail.com (Soren Christensen)
Date: Fri, 22 Jun 2007 12:10:22 +1000
Subject: [MINC-users] Display graphics on fedora 7
In-Reply-To: <d747ed50706211846w49420a30uaa1341167f589a30@mail.gmail.com>
References: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>
	<d747ed50706211846w49420a30uaa1341167f589a30@mail.gmail.com>
Message-ID: <d6e2d6550706211910j22e890dft4373cd97b0f65a47@mail.gmail.com>

Thanks!
 I have ATI - but a new DELL is on the way wirth an NVidia card in it
(for the reasons you mention - NVidia seems to be easier to trouble
shoot on Linux) - so I'll try again with Nvidia and take it from
there.

Cheers
Soren





Btw, glxifno says:
name of display: :0.0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: SGI
server glx version string: 1.2
server glx extensions:
    GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_texture_from_pixmap,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_copy_sub_buffer,
    GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGI_swap_control,
    GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_visual_select_group
client glx vendor string: SGI
client glx version string: 1.4
client glx extensions:
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory,
    GLX_MESA_copy_sub_buffer, GLX_MESA_swap_control,
    GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control,
    GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync,
    GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
    GLX_SGIX_visual_select_group, GLX_EXT_texture_from_pixmap
GLX version: 1.2
GLX extensions:
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_copy_sub_buffer,
    GLX_MESA_swap_control, GLX_MESA_swap_frame_usage, GLX_OML_swap_method,
    GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync,
    GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_visual_select_group
OpenGL vendor string: Tungsten Graphics, Inc.
OpenGL renderer string: Mesa DRI R300 20060815 AGP 1x x86/MMX/SSE2 TCL
OpenGL version string: 1.3 Mesa 6.5.2
OpenGL extensions:
    GL_ARB_fragment_program, GL_ARB_imaging, GL_ARB_multisample,
    GL_ARB_multitexture, GL_ARB_texture_border_clamp,
    GL_ARB_texture_compression, GL_ARB_texture_cube_map,
    GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
    GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3,
    GL_MESAX_texture_float, GL_ARB_texture_mirrored_repeat,
    GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
    GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_window_pos,
    GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
    GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate,
    GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
    GL_EXT_compiled_vertex_array, GL_EXT_convolution, GL_EXT_copy_texture,
    GL_EXT_draw_range_elements, GL_EXT_gpu_program_parameters,
    GL_EXT_histogram, GL_EXT_packed_pixels, GL_EXT_polygon_offset,
    GL_EXT_rescale_normal, GL_EXT_secondary_color,
    GL_EXT_separate_specular_color, GL_EXT_stencil_wrap, GL_EXT_subtexture,
    GL_EXT_texture, GL_EXT_texture3D, GL_EXT_texture_edge_clamp,
    GL_EXT_texture_env_add, GL_EXT_texture_env_combine,
    GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic,
    GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp,
    GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array,
    GL_APPLE_packed_pixels, GL_ATI_blend_equation_separate,
    GL_ATI_texture_env_combine3, GL_ATI_texture_mirror_once,
    GL_IBM_rasterpos_clip, GL_IBM_texture_mirrored_repeat,
    GL_INGR_blend_func_separate, GL_MESA_pack_invert, GL_MESA_ycbcr_texture,
    GL_MESA_window_pos, GL_NV_blend_square, GL_NV_light_max_exponent,
    GL_NV_texture_rectangle, GL_NV_texgen_reflection, GL_NV_vertex_program,
    GL_OES_read_format, GL_SGI_color_matrix, GL_SGI_color_table,
    GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp,
    GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod

   visual  x  bf lv rg d st colorbuffer ax dp st accumbuffer  ms  cav
 id dep cl sp sz l  ci b ro  r  g  b  a bf th cl  r  g  b  a ns b eat
----------------------------------------------------------------------
0x23 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
0x24 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  0  0  0  0  0  0 0 None
0x25 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
0x26 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  0 16 16 16 16  0 0 Slow
0x27 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
0x28 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  0  0  0  0  0  0 0 None
0x29 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
0x2a 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  0 16 16 16 16  0 0 Slow
0x2b 24 dc  0 32  0 r  y  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
0x2c 24 dc  0 32  0 r  y  .  8  8  8  8  0 24  0  0  0  0  0  0 0 None
0x2d 24 dc  0 32  0 r  y  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
0x2e 24 dc  0 32  0 r  y  .  8  8  8  8  0 24  0 16 16 16 16  0 0 Slow
0x2f 24 dc  0 32  0 r  .  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
0x30 24 dc  0 32  0 r  .  .  8  8  8  8  0 24  0  0  0  0  0  0 0 None
0x31 24 dc  0 32  0 r  .  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
0x32 24 dc  0 32  0 r  .  .  8  8  8  8  0 24  0 16 16 16 16  0 0 Slow
0x4b 32 tc  0 32  0 r  .  .  8  8  8  8  0  0  0  0  0  0  0  0 0 Ncon

On 6/22/07, Andrew Janke <a.janke at gmail.com> wrote:
> Interesting,
>
> I certainly have no trouble with beryl/compiz under Ubutu Feisty.
> This is with a Nvidia GeForce 8600GT running Dual 1600x1200 DVI.
>
> Although I do know there is a problem with some of the nvidia cards /
> drivers in register if you set to many tag points.  Sylvain has
> investigated this at length and it appears that it is a combination of
> certain cards and certain hardware.
>
> My guess in all this is that Dave when he wrote these all those years
> ago used a few parts of GLUT that are not all that well supported.
>
> Is your hardware ATI or NVIDIA?  and what does glxinfo return?
>
> If ATI, I have had more success with the fglrx (proprietary) drivers.
>
> I also have spend much more time debugging register/Display under
> nvidia than ATI, so if others are considering a new machine I would
> suggest NVIDIA.
>
>
> a
>
> On 6/22/07, Soren Christensen <sorench at gmail.com> wrote:
> > Hi,
> >  I have trouble with hardware rendering (I assume) in Display compiled on
> > Fedora 7.
> > The slice/cursor navigation seems slow as if software rendering is in
> > effect, but glxinfo | grep direct:   direct rendering: Yes, and Display also
> > does not give warnings except this one every time it is started:
> > Try R300_SPAN_DISABLE_LOCKING env var if this hangs.
> >
> > Any suggestions as to what might cause this?
> >
> > Also, if Desktop effects are enabled Display seems to crash - but this is
> > less of a problem.
> >
> > Regards
> > Soren
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> 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  Fri Jun 22 11:49:12 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 23 Jun 2007 01:49:12 +1000
Subject: [MINC-users] Display graphics on fedora 7
In-Reply-To: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>
References: <d6e2d6550706211815m435c32bfv872338e1851f5ba2@mail.gmail.com>
Message-ID: <d747ed50706220849k45039ef2h8804ad74a162e418@mail.gmail.com>

On 6/22/07, Soren Christensen <sorench at gmail.com> wrote:
> Hi,
>  I have trouble with hardware rendering (I assume) in Display compiled on
> Fedora 7.
> The slice/cursor navigation seems slow as if software rendering is in
> effect, but glxinfo | grep direct:   direct rendering: Yes, and Display also
> does not give warnings except this one every time it is started:
> Try R300_SPAN_DISABLE_LOCKING env var if this hangs.

Hi again Soren,

Seems I can get this error too.. I have an ATI in my T42 thinkpad
(Radeon 9600 series). In my case I can get this identical error if I
use a combination of the radeon drivers and beryl.

It doesnt happen with fglrx or ati athough I couldn't get beryl
working under fglrx + Xgl so gave up.

What this means is that I would bet that you are out of video memory
or the likes, a good way to check this is to go back to using the ati
driver in xorg.conf instead of fglrx/radeon.

So the question is does Fedora use fglrx or radeon?

And like you say, the simple solution is to stick to a nvidia card! :)


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

From najma at bic.mni.mcgill.ca  Mon Jun 25 18:56:14 2007
From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.)
Date: Mon, 25 Jun 2007 18:56:14 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
Message-ID: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>



Hi, I need to generate a surface object in order to use it with
ray_trace. As I am interested in showing subcortical markers, I
need the object file to be semi-transparent, preferably with
wireframe representation.

I'd appreciate any suggestions.
Naj


From jason at bic.mni.mcgill.ca  Mon Jun 25 19:07:32 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Mon, 25 Jun 2007 19:07:32 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
Message-ID: <725C4834-0AE3-456A-B7F3-4755ABD9506E@bic.mni.mcgill.ca>

Display can do it - Open the obj file in Display, then (E) for 3D  
Render, then (A) for Mode.

I don't know of a way to get wireframe rendering using ray_trace -  
but you can get objects to be semi-transparent by setting the opacity  
using set_object_opacity.

Jason

On 25-Jun-07, at 6:56 PM, Najmeh Khalili M. wrote:

>
>
> Hi, I need to generate a surface object in order to use it with
> ray_trace. As I am interested in showing subcortical markers, I
> need the object file to be semi-transparent, preferably with
> wireframe representation.
>
> I'd appreciate any suggestions.
> Naj
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From najma at bic.mni.mcgill.ca  Mon Jun 25 19:15:13 2007
From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.)
Date: Mon, 25 Jun 2007 19:15:13 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <725C4834-0AE3-456A-B7F3-4755ABD9506E@bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<725C4834-0AE3-456A-B7F3-4755ABD9506E@bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.58.0706251911470.26580649@yorick.bic.mni.mcgill.ca>


Thanks Jason.

If I am to use display, then would you know how to open/display
tags in display? I have three sets of tags. I want to be able to
set the color of the marker (with lighting on) for each set. (I
am sure there is a magic key combination that I missed, as I
tried all possible permutations ;) )

Thanks
Naj



On Mon, 25 Jun 2007, Jason Lerch wrote:

> Display can do it - Open the obj file in Display, then (E) for 3D
> Render, then (A) for Mode.
>
> I don't know of a way to get wireframe rendering using ray_trace -
> but you can get objects to be semi-transparent by setting the opacity
> using set_object_opacity.
>
> Jason
>
> On 25-Jun-07, at 6:56 PM, Najmeh Khalili M. wrote:
>
> >
> >
> > Hi, I need to generate a surface object in order to use it with
> > ray_trace. As I am interested in showing subcortical markers, I
> > need the object file to be semi-transparent, preferably with
> > wireframe representation.
> >
> > I'd appreciate any suggestions.
> > Naj
> >
> > _______________________________________________
> > 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 jason at bic.mni.mcgill.ca  Mon Jun 25 20:06:05 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Mon, 25 Jun 2007 20:06:05 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <Pine.SGI.4.58.0706251911470.26580649@yorick.bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<725C4834-0AE3-456A-B7F3-4755ABD9506E@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0706251911470.26580649@yorick.bic.mni.mcgill.ca>
Message-ID: <6B1C6098-1241-484A-8010-209051F7AC76@bic.mni.mcgill.ca>

tags_to_spheres should, in theory, be able to do this. Combine that  
with set_object_colour and you should be all set.

(For some reason it segfaults on my linux box and bus errors on my  
mac - but the version installed on the IRIX machines does work).

Jason

On 25-Jun-07, at 7:15 PM, Najmeh Khalili M. wrote:

>
> Thanks Jason.
>
> If I am to use display, then would you know how to open/display
> tags in display? I have three sets of tags. I want to be able to
> set the color of the marker (with lighting on) for each set. (I
> am sure there is a magic key combination that I missed, as I
> tried all possible permutations ;) )
>
> Thanks
> Naj
>
>
>
> On Mon, 25 Jun 2007, Jason Lerch wrote:
>
>> Display can do it - Open the obj file in Display, then (E) for 3D
>> Render, then (A) for Mode.
>>
>> I don't know of a way to get wireframe rendering using ray_trace -
>> but you can get objects to be semi-transparent by setting the opacity
>> using set_object_opacity.
>>
>> Jason
>>
>> On 25-Jun-07, at 6:56 PM, Najmeh Khalili M. wrote:
>>
>>>
>>>
>>> Hi, I need to generate a surface object in order to use it with
>>> ray_trace. As I am interested in showing subcortical markers, I
>>> need the object file to be semi-transparent, preferably with
>>> wireframe representation.
>>>
>>> I'd appreciate any suggestions.
>>> Naj
>>>
>>> _______________________________________________
>>> 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 lasse at hst.aau.dk  Tue Jun 26 04:15:04 2007
From: lasse at hst.aau.dk (=?ISO-8859-1?Q?Lasse_Riis_=D8stergaard?=)
Date: Tue, 26 Jun 2007 10:15:04 +0200
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
Message-ID: <4680CB08.9050500@hst.aau.dk>

I don't think ray_trace allows wireframe rendering. Instead you can do 
the following:

Step 1 - polygons_to_lines polygon.obj poly_lines.obj
Step 2 - ray_trace -output image.rgb poly_lines.obj -bg white -size 350 
350 -top -crop

Lasse

Najmeh Khalili M. wrote:
> Hi, I need to generate a surface object in order to use it with
> ray_trace. As I am interested in showing subcortical markers, I
> need the object file to be semi-transparent, preferably with
> wireframe representation.
>
> I'd appreciate any suggestions.
> Naj
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From najma at bic.mni.mcgill.ca  Tue Jun 26 09:49:01 2007
From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.)
Date: Tue, 26 Jun 2007 09:49:01 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <4680CB08.9050500@hst.aau.dk>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<4680CB08.9050500@hst.aau.dk>
Message-ID: <Pine.SGI.4.58.0706260932350.26960880@yorick.bic.mni.mcgill.ca>


Thanks Lasse, Jason.

I couldn't get the tags_to_spheres produce pretty markers, but
reducing the surface opacity allowed me to ray_trace subcortical
objects.

The plygons_to_lines works well. (Is there a way to subsample
the polygons? I tried "smooth_lines" on the polygon.obj,
but it doesn't seem to change anything. I tried it with
distance 0.2 and 100!!)

Cheers
Naj

On Tue, 26 Jun 2007, [ISO-8859-1] Lasse Riis Østergaard wrote:

> I don't think ray_trace allows wireframe rendering. Instead you can do
> the following:
>
> Step 1 - polygons_to_lines polygon.obj poly_lines.obj
> Step 2 - ray_trace -output image.rgb poly_lines.obj -bg white -size 350
> 350 -top -crop
>
> Lasse
>
> Najmeh Khalili M. wrote:
> > Hi, I need to generate a surface object in order to use it with
> > ray_trace. As I am interested in showing subcortical markers, I
> > need the object file to be semi-transparent, preferably with
> > wireframe representation.
> >
> > I'd appreciate any suggestions.
> > Naj
> >
> > _______________________________________________
> > 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 acveilleux at mrs.mni.mcgill.ca  Tue Jun 26 11:29:53 2007
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Tue, 26 Jun 2007 11:29:53 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <Pine.SGI.4.58.0706260932350.26960880@yorick.bic.mni.mcgill.ca>;
	from najma@bic.mni.mcgill.ca on Tue, Jun 26, 2007 at 09:49:01AM
	-0400
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<4680CB08.9050500@hst.aau.dk>
	<Pine.SGI.4.58.0706260932350.26960880@yorick.bic.mni.mcgill.ca>
Message-ID: <20070626112953.B1663@mrs.mni.mcgill.ca>

On Tue, Jun 26, 2007 at 09:49:01AM -0400, Najmeh Khalili M. wrote:
> 
> I couldn't get the tags_to_spheres produce pretty markers, but
> reducing the surface opacity allowed me to ray_trace subcortical
> objects.
> 
> The plygons_to_lines works well. (Is there a way to subsample
> the polygons? I tried "smooth_lines" on the polygon.obj,
> but it doesn't seem to change anything. I tried it with
> distance 0.2 and 100!!)

Couple of things about ray_trace:

	* It can't render well meshes that contain anything but
	  triangles. There's a command to convert polygons to
	  triangles to do that. (Something like triangulate_polygons
	  from memory but I'd have to check.)
	
	* -one_hit tends to produce nicer looks with semi-opaque
	  surfaces. The effect may or may not be desirable to you.

	* ray_trace has tons of undocumented switches such as
	  -marker_sphere, -marker_size, -marker_colour and so on.

	* Dave MacDonald's tutorial is fairly good (but incomplete):
	  http://www.bic.mni.mcgill.ca/~david/Ray_trace/ray_trace_tutorial.html

Alex

> 
> Cheers
> Naj
> 
> On Tue, 26 Jun 2007, [ISO-8859-1] Lasse Riis ?stergaard wrote:
> 
> > I don't think ray_trace allows wireframe rendering. Instead you can do
> > the following:
> >
> > Step 1 - polygons_to_lines polygon.obj poly_lines.obj
> > Step 2 - ray_trace -output image.rgb poly_lines.obj -bg white -size 350
> > 350 -top -crop
> >
> > Lasse
> >
> > Najmeh Khalili M. wrote:
> > > Hi, I need to generate a surface object in order to use it with
> > > ray_trace. As I am interested in showing subcortical markers, I
> > > need the object file to be semi-transparent, preferably with
> > > wireframe representation.
> > >
> > > I'd appreciate any suggestions.
> > > Naj
> > >
> > > _______________________________________________
> > > 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 najma at bic.mni.mcgill.ca  Tue Jun 26 11:42:01 2007
From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.)
Date: Tue, 26 Jun 2007 11:42:01 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <20070626112953.B1663@mrs.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<4680CB08.9050500@hst.aau.dk>
	<Pine.SGI.4.58.0706260932350.26960880@yorick.bic.mni.mcgill.ca>
	<20070626112953.B1663@mrs.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.58.0706261136570.26950402@yorick.bic.mni.mcgill.ca>


Thanks Alex,

I am planning to wikify all these comments to bring raytrace
out of obscurity :) It's a great tool for people who prefer to
script their image (re)production and not bother with Display!

Can you please tell me where/what -one_hit is/does?

Yes, semi-opaque surfaces look better than grid ones.

Best
Naj

On Tue, 26 Jun 2007, Alexandre CARMEL-VEILLEUX wrote:

> On Tue, Jun 26, 2007 at 09:49:01AM -0400, Najmeh Khalili M. wrote:
> >
> > I couldn't get the tags_to_spheres produce pretty markers, but
> > reducing the surface opacity allowed me to ray_trace subcortical
> > objects.
> >
> > The plygons_to_lines works well. (Is there a way to subsample
> > the polygons? I tried "smooth_lines" on the polygon.obj,
> > but it doesn't seem to change anything. I tried it with
> > distance 0.2 and 100!!)
>
> Couple of things about ray_trace:
>
> 	* It can't render well meshes that contain anything but
> 	  triangles. There's a command to convert polygons to
> 	  triangles to do that. (Something like triangulate_polygons
> 	  from memory but I'd have to check.)
>
> 	* -one_hit tends to produce nicer looks with semi-opaque
> 	  surfaces. The effect may or may not be desirable to you.
>
> 	* ray_trace has tons of undocumented switches such as
> 	  -marker_sphere, -marker_size, -marker_colour and so on.
>
> 	* Dave MacDonald's tutorial is fairly good (but incomplete):
> 	  http://www.bic.mni.mcgill.ca/~david/Ray_trace/ray_trace_tutorial.html
>
> Alex
>
> >
> > Cheers
> > Naj
> >
> > On Tue, 26 Jun 2007, [ISO-8859-1] Lasse Riis ?stergaard wrote:
> >
> > > I don't think ray_trace allows wireframe rendering. Instead you can do
> > > the following:
> > >
> > > Step 1 - polygons_to_lines polygon.obj poly_lines.obj
> > > Step 2 - ray_trace -output image.rgb poly_lines.obj -bg white -size 350
> > > 350 -top -crop
> > >
> > > Lasse
> > >
> > > Najmeh Khalili M. wrote:
> > > > Hi, I need to generate a surface object in order to use it with
> > > > ray_trace. As I am interested in showing subcortical markers, I
> > > > need the object file to be semi-transparent, preferably with
> > > > wireframe representation.
> > > >
> > > > I'd appreciate any suggestions.
> > > > Naj
> > > >
> > > > _______________________________________________
> > > > 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
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>




From acveilleux at mrs.mni.mcgill.ca  Tue Jun 26 11:53:43 2007
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Tue, 26 Jun 2007 11:53:43 -0400
Subject: [MINC-users] How to create a "wireframe" surface object?
In-Reply-To: <Pine.SGI.4.58.0706261136570.26950402@yorick.bic.mni.mcgill.ca>;
	from najma@bic.mni.mcgill.ca on Tue, Jun 26, 2007 at 11:42:01AM
	-0400
References: <Pine.SGI.4.58.0706251836140.26889408@yorick.bic.mni.mcgill.ca>
	<4680CB08.9050500@hst.aau.dk>
	<Pine.SGI.4.58.0706260932350.26960880@yorick.bic.mni.mcgill.ca>
	<20070626112953.B1663@mrs.mni.mcgill.ca>
	<Pine.SGI.4.58.0706261136570.26950402@yorick.bic.mni.mcgill.ca>
Message-ID: <20070626115343.F32218@mrs.mni.mcgill.ca>

On Tue, Jun 26, 2007 at 11:42:01AM -0400, Najmeh Khalili M. wrote:
> 
> Can you please tell me where/what -one_hit is/does?

	The ray will only hit once on the same object. So if a ray
would have say, gone through a sulcus and out and then back into another
one again, ray_trace will not render both surfaces if they're part of the
same .obj (I only used .obj with a single object in them I have no idea
how it would behave with multiple disconnected surfaces in a single .obj
file.)

	This is only an issue if the surface is not opaque obviously.
However with -one_hit ray_trace will render the surface of the first hit
on every different objects it encounters, like your markers.

	It's best to experiment with this.

	I hope I make sense ;-)

Alex

> 
> Yes, semi-opaque surfaces look better than grid ones.
> 
> Best
> Naj
> 
> On Tue, 26 Jun 2007, Alexandre CARMEL-VEILLEUX wrote:
> 
> > On Tue, Jun 26, 2007 at 09:49:01AM -0400, Najmeh Khalili M. wrote:
> > >
> > > I couldn't get the tags_to_spheres produce pretty markers, but
> > > reducing the surface opacity allowed me to ray_trace subcortical
> > > objects.
> > >
> > > The plygons_to_lines works well. (Is there a way to subsample
> > > the polygons? I tried "smooth_lines" on the polygon.obj,
> > > but it doesn't seem to change anything. I tried it with
> > > distance 0.2 and 100!!)
> >
> > Couple of things about ray_trace:
> >
> > 	* It can't render well meshes that contain anything but
> > 	  triangles. There's a command to convert polygons to
> > 	  triangles to do that. (Something like triangulate_polygons
> > 	  from memory but I'd have to check.)
> >
> > 	* -one_hit tends to produce nicer looks with semi-opaque
> > 	  surfaces. The effect may or may not be desirable to you.
> >
> > 	* ray_trace has tons of undocumented switches such as
> > 	  -marker_sphere, -marker_size, -marker_colour and so on.
> >
> > 	* Dave MacDonald's tutorial is fairly good (but incomplete):
> > 	  http://www.bic.mni.mcgill.ca/~david/Ray_trace/ray_trace_tutorial.html
> >
> > Alex
> >
> > >
> > > Cheers
> > > Naj
> > >
> > > On Tue, 26 Jun 2007, [ISO-8859-1] Lasse Riis ?stergaard wrote:
> > >
> > > > I don't think ray_trace allows wireframe rendering. Instead you can do
> > > > the following:
> > > >
> > > > Step 1 - polygons_to_lines polygon.obj poly_lines.obj
> > > > Step 2 - ray_trace -output image.rgb poly_lines.obj -bg white -size 350
> > > > 350 -top -crop
> > > >
> > > > Lasse
> > > >
> > > > Najmeh Khalili M. wrote:
> > > > > Hi, I need to generate a surface object in order to use it with
> > > > > ray_trace. As I am interested in showing subcortical markers, I
> > > > > need the object file to be semi-transparent, preferably with
> > > > > wireframe representation.
> > > > >
> > > > > I'd appreciate any suggestions.
> > > > > Naj
> > > > >
> > > > > _______________________________________________
> > > > > 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
> >
> > _______________________________________________
> > 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 a.janke at gmail.com  Wed Jun 27 12:10:16 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 Jun 2007 02:10:16 +1000
Subject: [MINC-users] Ubuntu MINC packages
Message-ID: <d747ed50706270910w5e8d5149n1a43f0112f979f9@mail.gmail.com>

Hi all,

Given that Ubuntu seems to be gaining in popularity, I have compiled a
number of the MINC packages here for feisty

   http://packages.bic.mni.mcgill.ca/ubuntu/

These are in both in i386 and amd64 flavor. Note that on some of the
newer CPU's the "amd64" or X86_64 kernels are returning some
impressive speeds.  (if you have a Xeon, Core 2 Duo or Core 2 Quad you
should be using a 64 bit kernel).  See here for a quick comparison:

   http://wiki.bic.mni.mcgill.ca/index.php/MincBenchmarking

Note the difference in the two results for the same machine (ben --
the last entry) with both a server-bigiron kernel (for 4GB or RAM) and
with an amd64 kernel and native compile of the MINC tools to suit.

You will note that I have removed a few dependencies in these packages
if only because the naming scheme in Ubuntu is slightly different for
some packages. You should install the following to make these work:

   sudo apt-get install libnetpbm9-dev libgsl0-dev netcdfg-dev
libhdf5-serial-dev

As usual I am interested to know if these work well for you.




-- 
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 Jun 27 12:11:43 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 Jun 2007 02:11:43 +1000
Subject: [MINC-users] Ubuntu MINC packages
In-Reply-To: <d747ed50706270910w5e8d5149n1a43f0112f979f9@mail.gmail.com>
References: <d747ed50706270910w5e8d5149n1a43f0112f979f9@mail.gmail.com>
Message-ID: <d747ed50706270911m2bed2c50t39f48330f336a214@mail.gmail.com>

PS forgot to mention one other *slightly* important thing...

These are MINC2 packages and thus will install in /usr/local/bic as
opposed to /usr/local/mni

a

On 6/28/07, Andrew Janke <a.janke at gmail.com> wrote:
> Hi all,
>
> Given that Ubuntu seems to be gaining in popularity, I have compiled a
> number of the MINC packages here for feisty
>
>    http://packages.bic.mni.mcgill.ca/ubuntu/
>
> These are in both in i386 and amd64 flavor. Note that on some of the
> newer CPU's the "amd64" or X86_64 kernels are returning some
> impressive speeds.  (if you have a Xeon, Core 2 Duo or Core 2 Quad you
> should be using a 64 bit kernel).  See here for a quick comparison:
>
>    http://wiki.bic.mni.mcgill.ca/index.php/MincBenchmarking
>
> Note the difference in the two results for the same machine (ben --
> the last entry) with both a server-bigiron kernel (for 4GB or RAM) and
> with an amd64 kernel and native compile of the MINC tools to suit.
>
> You will note that I have removed a few dependencies in these packages
> if only because the naming scheme in Ubuntu is slightly different for
> some packages. You should install the following to make these work:
>
>    sudo apt-get install libnetpbm9-dev libgsl0-dev netcdfg-dev
> libhdf5-serial-dev
>
> As usual I am interested to know if these work well for you.
>
>
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>


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

From vanerp at LifeSci.UCLA.EDU  Fri Jun 29 12:36:32 2007
From: vanerp at LifeSci.UCLA.EDU (Theo van Erp)
Date: Fri, 29 Jun 2007 09:36:32 -0700
Subject: [MINC-users] Intel mac Display-1.4.2 not loading binary .surface
	obj files
Message-ID: <C2AA8320.1B68B%vanerp@zetapup.lifesci.ucla.edu>

Hi all,

I have both downloaded the binary versions of Display-1.4.1 and
Display-1.4.2 for intel mac, and have also installed both from source.

In both cases I am able to start Display, and load .mnc and ascii versions
of surface .obj files, but not binary versions of surface .obj files.

When I try to load binary versions of .obj files I get the following error:

/usr/local/Display-1.4.1/Display  003_nu_4400_L.obj
Inputting 003_nu_4400_L.obj.
Error inputting binary data.
     (305839 out of 33554688 items of size 12).
System message: No such file or directory
Error loading 003_nu_4400_L.obj

We have the same problem on a version of Display installed on some linux
machines.

Can anyone tell me where this error may stem from?

Thanks, Theo

_____________________________________________________________
Theo G.M. van Erp, PhD

Clinical Neuroscience Lab
Department of Psychology                vanerp at psych.ucla.edu
University of California Los Angeles    voice (310) 794-9673
1285 Franz Hall, room 5556              fax (310) 794-9740
Los Angeles, California,  90095-1563
http://www.bol.ucla.edu/~vanerp
_____________________________________________________________





From jason at bic.mni.mcgill.ca  Fri Jun 29 12:40:52 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Fri, 29 Jun 2007 12:40:52 -0400
Subject: [MINC-users] Intel mac Display-1.4.2 not loading binary
	.surface obj files
In-Reply-To: <C2AA8320.1B68B%vanerp@zetapup.lifesci.ucla.edu>
References: <C2AA8320.1B68B%vanerp@zetapup.lifesci.ucla.edu>
Message-ID: <46853614.2050307@bic.mni.mcgill.ca>

The binary versions of obj files are endian dependent - so if they were 
created on a different endian machine (say a MIPS processor IRIX machine 
creates them and then a i386 linux box tries to read them) you'll get 
that error. Convert the files to ascii (using ascii_binary) on the 
machine that created the surfaces and you'll be all set.

Jason

Theo van Erp wrote:
> Hi all,
>
> I have both downloaded the binary versions of Display-1.4.1 and
> Display-1.4.2 for intel mac, and have also installed both from source.
>
> In both cases I am able to start Display, and load .mnc and ascii versions
> of surface .obj files, but not binary versions of surface .obj files.
>
> When I try to load binary versions of .obj files I get the following error:
>
> /usr/local/Display-1.4.1/Display  003_nu_4400_L.obj
> Inputting 003_nu_4400_L.obj.
> Error inputting binary data.
>      (305839 out of 33554688 items of size 12).
> System message: No such file or directory
> Error loading 003_nu_4400_L.obj
>
> We have the same problem on a version of Display installed on some linux
> machines.
>
> Can anyone tell me where this error may stem from?
>
> Thanks, Theo
>
> _____________________________________________________________
> Theo G.M. van Erp, PhD
>
> Clinical Neuroscience Lab
> Department of Psychology                vanerp at psych.ucla.edu
> University of California Los Angeles    voice (310) 794-9673
> 1285 Franz Hall, room 5556              fax (310) 794-9740
> Los Angeles, California,  90095-1563
> http://www.bol.ucla.edu/~vanerp
> _____________________________________________________________
>
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From a.janke at gmail.com  Fri Jun 29 12:42:54 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 30 Jun 2007 02:42:54 +1000
Subject: [MINC-users] Intel mac Display-1.4.2 not loading binary
	.surface obj files
In-Reply-To: <C2AA8320.1B68B%vanerp@zetapup.lifesci.ucla.edu>
References: <C2AA8320.1B68B%vanerp@zetapup.lifesci.ucla.edu>
Message-ID: <d747ed50706290942r612e973q17555e58038f4efe@mail.gmail.com>

Hi Theo,

This may be an interesting "feature" of the OSX GLUT implementation
biting you.  I would be interested to know if this works if you give
the full .obj file name.  ie: /home/theo/blah/bue/foo.obj

If so then start Display by itself with no filename and then under
File->Preferences set the Current working Directory option and then
Quit using the file menu.

Then try again with a relative path.


a

On 6/30/07, Theo van Erp <vanerp at lifesci.ucla.edu> wrote:
> Hi all,
>
> I have both downloaded the binary versions of Display-1.4.1 and
> Display-1.4.2 for intel mac, and have also installed both from source.
>
> In both cases I am able to start Display, and load .mnc and ascii versions
> of surface .obj files, but not binary versions of surface .obj files.
>
> When I try to load binary versions of .obj files I get the following error:
>
> /usr/local/Display-1.4.1/Display  003_nu_4400_L.obj
> Inputting 003_nu_4400_L.obj.
> Error inputting binary data.
>      (305839 out of 33554688 items of size 12).
> System message: No such file or directory
> Error loading 003_nu_4400_L.obj
>
> We have the same problem on a version of Display installed on some linux
> machines.
>
> Can anyone tell me where this error may stem from?
>
> Thanks, Theo
>
> _____________________________________________________________
> Theo G.M. van Erp, PhD
>
> Clinical Neuroscience Lab
> Department of Psychology                vanerp at psych.ucla.edu
> University of California Los Angeles    voice (310) 794-9673
> 1285 Franz Hall, room 5556              fax (310) 794-9740
> Los Angeles, California,  90095-1563
> http://www.bol.ucla.edu/~vanerp
> _____________________________________________________________
>
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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

From pgravel at bic.mni.mcgill.ca  Fri Jun 29 18:21:24 2007
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Fri, 29 Jun 2007 18:21:24 -0400
Subject: [MINC-users] MINC Images - Center of Mass and/or Gravity
Message-ID: <Pine.SGI.4.58.0706291819260.29771282@yorick.bic.mni.mcgill.ca>

Dear All,

Would anyone have the algorithm or a reference to an article explaining
how mincstats or minctracc calculates the center of mass or center of
gravity of a minc image?

Best,

Paul

From lau at bic.mni.mcgill.ca  Sat Jun 30 13:34:20 2007
From: lau at bic.mni.mcgill.ca (Jonathan LAU)
Date: Sat, 30 Jun 2007 13:34:20 -0400
Subject: [MINC-users] MINC Images - Center of Mass and/or Gravity
In-Reply-To: <Pine.SGI.4.58.0706291819260.29771282@yorick.bic.mni.mcgill.ca>
References: <Pine.SGI.4.58.0706291819260.29771282@yorick.bic.mni.mcgill.ca>
Message-ID: <eb9fb4b10706301034q4de0aba8gd6dcfbca94f3678e@mail.gmail.com>

Hey Paul,

Taking a look at the mincstats code, it looks like CoM calculates the voxel
and world coordinates for the centre by summing each image voxel's
coordinates weighted by its image intensity. This is, I think, just the
geometric centre if the input was binary. The results also depends on
whether you have applied a mask or not to the input image.

This might be what minctracc does, but I'm not familiar enough with the code
to comment.

hope that helps!
jon

2007/6/29, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>:
>
> Dear All,
>
> Would anyone have the algorithm or a reference to an article explaining
> how mincstats or minctracc calculates the center of mass or center of
> gravity of a minc image?
>
> Best,
>
> Paul
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>