From jharlap at bic.mni.mcgill.ca  Sat Apr  1 11:30:34 2006
From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP)
Date: Sat, 1 Apr 2006 11:30:34 -0500
Subject: [MINC-users] Problem compiling ray_trace
In-Reply-To: <9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com>
References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>
	<20060331174006.A17125@mrs.mni.mcgill.ca>
	<9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com>
	<20060331181131.A17807@mrs.mni.mcgill.ca>
	<9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com>
	<9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com>
Message-ID: <20060401163034.GA278351@bic.mni.mcgill.ca>

You probably want libnetbpm9-dev...

Cheers,
J



On Fri, Mar 31, 2006 at 06:50:12PM -0500, Gil Citro wrote:
> (Sorry for the last message, I sent too soon)
> 
> On 3/31/06, Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca> wrote:
> > > libppm is provided by the netpbnm and netpbm=dev packages,
> > > I belive.
> > >
> > > Alex
> > >
> >
> 
> netpbm is the newest version.  netpbm-dev is a virtual package, and
> libnetpbm10-dev  is installed to provude it.  When I pass
> --with-image-ppm to configure when compiling bicpl-1.4.2 is still says
> configure: error: cannot find required header, but if I pass
> --with-image-netpbm it configures and compiles without error.
> 
> However, when I then try to configure and compile ray_trace it
> configures without error but gives the following error when being
> compiled
> 
> undefined reference to `ppm_writeppminit`  (see below)
> 
> If I compile bicpl without --with-image-netpbm I don't get this error
> when compiling ray_trace, but then I have the original problem I
> reported.
> 
> It looks to me like I'm missing some libraries having to do with
> pixmaps, so I did apt-cache search pixmap, and apt-get install for the
> packages below, but no change.
> 
> libgd-gd2-perl
> libgd2-xpm
> libgd2-xpm-dev
> libgdchart-gd2-xpm
> libgdchart-gd2-xpm-dev
> libgd-tools
> libxpm-dev
> libxpm4
> libxpm4-dbg
> 
> Compiling bicpl with --with-image-ppm goves the same error, and
> --with-image-netpbm gives no error until I compile ray_trace.
> 
> Thanks for all the help so far.  If anyone has any other ideas I'd
> greatly appreciate it.
> 
> Gil
> 
> 
> make  all-recursive
> make[1]: Entering directory `/usr/local/mni/ray_trace-1.0'
> Making all in Graphics
> make[2]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics'
> Making all in GLUT_windows
> make[3]: Entering directory
> `/usr/local/mni/ray_trace-1.0/Graphics/GLUT_windows'make[3]: Nothing
> to be done for `all'.
> make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics/GLUT_windows'
> Making all in G_graphics
> make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics/G_graphics'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics/G_graphics'
> Making all in OpenGL_graphics
> make[3]: Entering directory
> `/usr/local/mni/ray_trace-1.0/Graphics/OpenGL_graphics'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory
> `/usr/local/mni/ray_trace-1.0/Graphics/OpenGL_graphics'
> make[3]: Entering directory `/usr/local/mni/ray_trace-1.0/Graphics'
> make[3]: Nothing to be done for `all-am'.
> make[3]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics'
> make[2]: Leaving directory `/usr/local/mni/ray_trace-1.0/Graphics'
> make[2]: Entering directory `/usr/local/mni/ray_trace-1.0'
> /bin/sh ./libtool --mode=link gcc  -g -O2   -o ray_trace  ray_trace.o
> intersect.o trace.o volume.o Graphics/libbicgl.a -lbicpl -lvolume_io
> -lminc -lnetcdf -lm
> mkdir .libs
> gcc -g -O2 -o ray_trace ray_trace.o intersect.o trace.o volume.o 
> Graphics/libbicgl.a -lbicpl /usr/lib/libvolume_io.so
> /usr/lib/libminc.so -lnetcdf -lm
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x3e): In function `input_rgb_file':
> /usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:31: undefined reference
> to `ppm_readppminit'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x4b):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:33:
> undefined reference to `pm_allocrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xa2):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:46:
> undefined reference to `ppm_readppmrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xb6):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:56:
> undefined reference to `pm_freerow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1c3): In function
> `output_rgb_file':/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:97:
> undefined reference to `ppm_writeppminit'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1d1):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:100:
> undefined reference to `pm_allocrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x20c):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:118:
> undefined reference to `ppm_writeppmrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x219):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:121:
> undefined reference to `pm_freerow'
> collect2: ld returned 1 exit status
> make[2]: *** [ray_trace] Error 1
> make[2]: Leaving directory `/usr/local/mni/ray_trace-1.0'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/usr/local/mni/ray_trace-1.0'
> make: *** [all] Error 2
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From ed.gronenschild at mi.unimaas.nl  Mon Apr  3 09:34:09 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Mon, 3 Apr 2006 15:34:09 +0200
Subject: [MINC-users] Availability minc_bet
Message-ID: <0BD7A161-E701-44CE-828E-27F7F7C75068@mi.unimaas.nl>

Hi,

Where can I find minc_bet, the derivative of BET from FSL.
I'm on a Mac OSX 10.3.9.

Regards,

Ed


From citrog at gmail.com  Mon Apr  3 13:13:39 2006
From: citrog at gmail.com (Gil Citro)
Date: Mon, 3 Apr 2006 13:13:39 -0400
Subject: [MINC-users] Problem compiling ray_trace
In-Reply-To: <20060401163034.GA278351@bic.mni.mcgill.ca>
References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>
	<20060331174006.A17125@mrs.mni.mcgill.ca>
	<9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com>
	<20060331181131.A17807@mrs.mni.mcgill.ca>
	<9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com>
	<9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com>
	<20060401163034.GA278351@bic.mni.mcgill.ca>
Message-ID: <9c80f12d0604031013n1697607cgb242f103f69b4509@mail.gmail.com>

If I install libnetbpm9-dev I can ./configure bicpl-14.2 --with-image-ppm
without errors.  However, when I then try to configure and compile
conglomerate-1.6 I get the error below when compiling.  This does not
happen if bicpl is configured without --with-image-ppm.

I hope nobody minds my sending this to the list.  I just thought it would
be useful in case anyone searches for an answer to a similar problem
in the future.  If it's too much detail for this list let me know.  Thanks.

Gil


On 4/1/06, Jonathan HARLAP <jharlap at bic.mni.mcgill.ca> wrote:
> You probably want libnetbpm9-dev...
>
> Cheers,
> J
>

/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x3e): In function `input_rgb_file':
/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:31: undefined reference
to `ppm_readppminit'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x4b):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:33:
undefined reference to `pm_allocrow'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xa2):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:46:
undefined reference to `ppm_readppmrow'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xb6):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:56:
undefined reference to `pm_freerow'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1c3): In function
`output_rgb_file':/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:97:
undefined reference to `ppm_writeppminit'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1d1):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:100:
undefined reference to `pm_allocrow'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x20c):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:118:
undefined reference to `ppm_writeppmrow'
/usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x219):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:121:
undefined reference to `pm_freerow'
collect2: ld returned 1 exit status
make[1]: *** [composite_images] Error 1
make[1]: Leaving directory `/usr/local/mni/conglomerate-1.6'
make: *** [all] Error 2


From acveilleux at mrs.mni.mcgill.ca  Mon Apr  3 13:30:28 2006
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 3 Apr 2006 13:30:28 -0400
Subject: [MINC-users] Problem compiling ray_trace
In-Reply-To: <9c80f12d0604031013n1697607cgb242f103f69b4509@mail.gmail.com>;
	from citrog@gmail.com on Mon, Apr 03, 2006 at 01:13:39PM -0400
References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>
	<20060331174006.A17125@mrs.mni.mcgill.ca>
	<9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com>
	<20060331181131.A17807@mrs.mni.mcgill.ca>
	<9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com>
	<9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com>
	<20060401163034.GA278351@bic.mni.mcgill.ca>
	<9c80f12d0604031013n1697607cgb242f103f69b4509@mail.gmail.com>
Message-ID: <20060403133028.B29759@mrs.mni.mcgill.ca>

	It's not linking with the lib, most likely. Maybe try this:

cd <conglomerate dir>
vi Makefile
/^LIBS
A
 -lppm
<escape>
:wq
make

	You could also rerun ./configure with some environment variable
set so it does the smart thing.

Alex


On Mon, Apr 03, 2006 at 01:13:39PM -0400, Gil Citro wrote:
> Date: Mon, 3 Apr 2006 13:13:39 -0400
> From: "Gil Citro" <citrog at gmail.com>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Problem compiling ray_trace
> 
> If I install libnetbpm9-dev I can ./configure bicpl-14.2 --with-image-ppm
> without errors.  However, when I then try to configure and compile
> conglomerate-1.6 I get the error below when compiling.  This does not
> happen if bicpl is configured without --with-image-ppm.
> 
> I hope nobody minds my sending this to the list.  I just thought it would
> be useful in case anyone searches for an answer to a similar problem
> in the future.  If it's too much detail for this list let me know.  Thanks.
> 
> Gil
> 
> 
> On 4/1/06, Jonathan HARLAP <jharlap at bic.mni.mcgill.ca> wrote:
> > You probably want libnetbpm9-dev...
> >
> > Cheers,
> > J
> >
> 
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x3e): In function `input_rgb_file':
> /usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:31: undefined reference
> to `ppm_readppminit'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x4b):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:33:
> undefined reference to `pm_allocrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xa2):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:46:
> undefined reference to `ppm_readppmrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0xb6):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:56:
> undefined reference to `pm_freerow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1c3): In function
> `output_rgb_file':/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:97:
> undefined reference to `ppm_writeppminit'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x1d1):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:100:
> undefined reference to `pm_allocrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x20c):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:118:
> undefined reference to `ppm_writeppmrow'
> /usr/local/lib/libbicpl.a(rgb_io.o)(.text+0x219):/usr/local/mni/bicpl-1.4.2/Images/rgb_io_ppm.c:121:
> undefined reference to `pm_freerow'
> collect2: ld returned 1 exit status
> make[1]: *** [composite_images] Error 1
> make[1]: Leaving directory `/usr/local/mni/conglomerate-1.6'
> make: *** [all] Error 2
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From citrog at gmail.com  Mon Apr  3 14:46:11 2006
From: citrog at gmail.com (Gil Citro)
Date: Mon, 3 Apr 2006 14:46:11 -0400
Subject: [MINC-users] Problem compiling ray_trace
In-Reply-To: <20060403133028.B29759@mrs.mni.mcgill.ca>
References: <9c80f12d0603311432od4aacedm383a0c8f1aede0f9@mail.gmail.com>
	<20060331174006.A17125@mrs.mni.mcgill.ca>
	<9c80f12d0603311505r281125c4x4969608430302bed@mail.gmail.com>
	<20060331181131.A17807@mrs.mni.mcgill.ca>
	<9c80f12d0603311529jdd7b3c7h526a39f578aaa3f3@mail.gmail.com>
	<9c80f12d0603311550h358d0b10k3c3bef94d8263734@mail.gmail.com>
	<20060401163034.GA278351@bic.mni.mcgill.ca>
	<9c80f12d0604031013n1697607cgb242f103f69b4509@mail.gmail.com>
	<20060403133028.B29759@mrs.mni.mcgill.ca>
Message-ID: <9c80f12d0604031146j36132feg4d82f82e7167620b@mail.gmail.com>

Thanks, that works.  I had to do the same when compiling ray_trace,
but then it also worked!


On 4/3/06, Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca> wrote:
>         It's not linking with the lib, most likely. Maybe try this:
>
> cd <conglomerate dir>
> vi Makefile
> /^LIBS
> A
>  -lppm
> <escape>
> :wq
> make
>
>         You could also rerun ./configure with some environment variable
> set so it does the smart thing.
>
> Alex
>
>


From citrog at gmail.com  Mon Apr  3 15:23:20 2006
From: citrog at gmail.com (Gil Citro)
Date: Mon, 3 Apr 2006 15:23:20 -0400
Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
	mni_perllib-0.07
Message-ID: <9c80f12d0604031223l3ee52299x8f57fe7348a05b19@mail.gmail.com>

After a couple of days of trying to install the MNI tools they seem to
be working with one last problem.  Thanks for all the help so far!

When I try to install mni_autoreg_model-1.1 I get these errors

make  all-am
make[1]: Entering directory `/usr/local/mni/mni_autoreg_model-1.1'
make_model average_305
Using base filename average_305
Note that your input volume *must* be in Talairach space for this to work
** Making average_305_pad.mnc from average_305.mnc by resampling on
2mm grid and padding by 16mm
"split_path" is not exported by the MNI::FileUtilities module
Can't continue after import errors at /usr/local/bin/autocrop line 31
BEGIN failed--compilation aborted at /usr/local/bin/autocrop line 31.
** Building 16mm data for average_305
Error: opening MINC file "average_305_pad.mnc".
Error in mincblur in file mincblur.c, line 264
problems reading `average_305_pad.mnc'.
"split_path" is not exported by the MNI::FileUtilities module
Can't continue after import errors at /usr/local/bin/autocrop line 31
BEGIN failed--compilation aborted at /usr/local/bin/autocrop line 31.
(from miopen): Unable to open file 'average_305_16_blur.mnc'
ncvarid: ncid -1: Not a netCDF id
etc...
make[1]: *** No rule to make target `average_305_16_mask.mnc', needed
by `all-am'.  Stop.
make[1]: Leaving directory `/usr/local/mni/mni_autoreg_model-1.1'
make: *** [all] Error 2

It says that there's a problem with MNI::FileUtilities, and in fact
when I installed mni_perllib-0.07 I did get many errors on make test,
but the README suggests this may be due to overly strict tests, so I
ignored the failed tests at first.  Here are the results I got from
make test.  If anyone can suggest how to solve this last problem I'd
appreciate it.  Thanks again.

Gil

PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/batch-0........ok
t/batch-1......../usr/bin/at: invalid option -- J
Usage: at [-V] [-q x] [-f file] [-m] time
       atq [-V] [-q x]
       atrm [-V] [-q x] job ...
       batch [-V] [-f file] [-m]
t/batch-1........dubious
        Test returned status 0 (wstat 13, 0xd)
DIED. FAILED tests 1-21
        Failed 21/21 tests, 0.00% okay
t/batch-2......../usr/bin/at: invalid option -- J
Usage: at [-V] [-q x] [-f file] [-m] time
       atq [-V] [-q x]
       atrm [-V] [-q x] job ...
       batch [-V] [-f file] [-m]
Error closing pipe to batch:
 at t/batch-2.t line 53
`batch' exited with non-zero status code: 256
 at t/batch-2.t line 53
/usr/bin/at: invalid option -- J
Usage: at [-V] [-q x] [-f file] [-m] time
       atq [-V] [-q x]
       atrm [-V] [-q x] job ...
       batch [-V] [-f file] [-m]
t/batch-2........dubious
        Test returned status 0 (wstat 13, 0xd)
DIED. FAILED tests 1-3
        Failed 3/3 tests, 0.00% okay
t/checkdirs......Error in distribution -- t not writeable
Compilation failed in require at t/checkdirs.t line 19.
t/checkdirs......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-42
        Failed 42/42 tests, 0.00% okay
t/checkfiles.....Error in distribution -- t not writeable
Compilation failed in require at t/checkfiles.t line 18.
t/checkfiles.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-41
        Failed 41/41 tests, 0.00% okay
t/datadir........ok
t/mincutil.......ok 6/22cp: cannot create regular file
`t/testcopy.mnc': Permission denied
cp failed at t/mincutil.t line 86.
t/mincutil.......dubious
        Test returned status 1 (wstat 256, 0x100)
DIED. FAILED tests 7-22
        Failed 16/22 tests, 27.27% okay
t/miscutil.......ok
t/numutil........ok
t/pathutil.......ok
t/searchfiles....Error in distribution -- t not writeable
Compilation failed in require at t/searchfiles.t line 19.
t/searchfiles....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-19
        Failed 19/19 tests, 0.00% okay
t/spawn..........ok 44/56couldn't create "ls": Permission denied
t/spawn..........FAILED tests 45-56
        Failed 12/56 tests, 78.57% okay
t/startup........ok 18/26couldn't open log: No such file or directory
t/startup........FAILED tests 10-16, 19-26
        Failed 15/26 tests, 42.31% okay
t/tagset..........tag4127-1.tag : Permission denied
 at t/tagset.t line 70
        (in cleanup) .tag4127-1.tag : Permission denied
 at t/tagset.t line 0
t/tagset.........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 7-10
        Failed 4/10 tests, 60.00% okay
Failed Test     Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/batch-1.t        0    13    21   42 200.00%  1-21
t/batch-2.t        0    13     3    6 200.00%  1-3
t/checkdirs.t    255 65280    42   84 200.00%  1-42
t/checkfiles.t   255 65280    41   82 200.00%  1-41
t/mincutil.t       1   256    22   32 145.45%  7-22
t/searchfiles.t  255 65280    19   38 200.00%  1-19
t/spawn.t                     56   12  21.43%  45-56
t/startup.t                   26   15  57.69%  10-16 19-26
t/tagset.t       255 65280    10    8  80.00%  7-10
Failed 9/14 test scripts, 35.71% okay. 173/381 subtests failed, 54.59% okay.
make: *** [test_dynamic] Error 255


From acveilleux at mrs.mni.mcgill.ca  Mon Apr  3 15:52:09 2006
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 3 Apr 2006 15:52:09 -0400
Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
	mni_perllib-0.07
In-Reply-To: <9c80f12d0604031223l3ee52299x8f57fe7348a05b19@mail.gmail.com>;
	from citrog@gmail.com on Mon, Apr 03, 2006 at 03:23:20PM -0400
References: <9c80f12d0604031223l3ee52299x8f57fe7348a05b19@mail.gmail.com>
Message-ID: <20060403155209.D29759@mrs.mni.mcgill.ca>

	split_path is exported by MNI::PathUtilities, at least on
my systems (I'm using an ancient version). Sounds like you have some
bugs in autocrop to me. I know there's been some changes in the
autoreg perl libs lately (they used to use a very ancient version of
the MNI:: stuff that was kept separate from the main perl libs.)

	Over here, MNI::Spawn.pm imports split_path:

MNI/Spawn.pm:use MNI::PathUtilities qw(split_path);

	If it is imported from MNI::FileUtilities, it is wrong. Or
maybe someone's been playing in the perl (Andrew?)

Alex

On Mon, Apr 03, 2006 at 03:23:20PM -0400, Gil Citro wrote:
> Date: Mon, 3 Apr 2006 15:23:20 -0400
> From: "Gil Citro" <citrog at gmail.com>
> To: "MINC Users List" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
> 	mni_perllib-0.07
> 
> After a couple of days of trying to install the MNI tools they seem to
> be working with one last problem.  Thanks for all the help so far!
> 
> When I try to install mni_autoreg_model-1.1 I get these errors
[snip]

From a.janke at gmail.com  Mon Apr  3 16:52:35 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 3 Apr 2006 16:52:35 -0400
Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
	mni_perllib-0.07
In-Reply-To: <20060403155209.D29759@mrs.mni.mcgill.ca>
References: <9c80f12d0604031223l3ee52299x8f57fe7348a05b19@mail.gmail.com>
	<20060403155209.D29759@mrs.mni.mcgill.ca>
Message-ID: <d747ed50604031352v1a547691lcf62822695bed89b@mail.gmail.com>

Correct, There have been a few lingering bugs in the later releases of
mni_autoreg. The latest point release (0.99.1) resolves this issue.

   http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.99.1.tar.gz

There are no binary packages for this release yet.


a


On 4/3/06, Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca> wrote:
>         split_path is exported by MNI::PathUtilities, at least on
> my systems (I'm using an ancient version). Sounds like you have some
> bugs in autocrop to me. I know there's been some changes in the
> autoreg perl libs lately (they used to use a very ancient version of
> the MNI:: stuff that was kept separate from the main perl libs.)
>
>         Over here, MNI::Spawn.pm imports split_path:
>
> MNI/Spawn.pm:use MNI::PathUtilities qw(split_path);
>
>         If it is imported from MNI::FileUtilities, it is wrong. Or
> maybe someone's been playing in the perl (Andrew?)
>
> Alex
>
> On Mon, Apr 03, 2006 at 03:23:20PM -0400, Gil Citro wrote:
> > Date: Mon, 3 Apr 2006 15:23:20 -0400
> > From: "Gil Citro" <citrog at gmail.com>
> > To: "MINC Users List" <minc-users at bic.mni.mcgill.ca>
> > Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
> >       mni_perllib-0.07
> >
> > After a couple of days of trying to install the MNI tools they seem to
> > be working with one last problem.  Thanks for all the help so far!
> >
> > When I try to install mni_autoreg_model-1.1 I get these errors
> [snip]
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From citrog at gmail.com  Mon Apr  3 17:40:42 2006
From: citrog at gmail.com (Gil Citro)
Date: Mon, 3 Apr 2006 17:40:42 -0400
Subject: [MINC-users] Problem Installing mni_autoreg_model-1.1 with
	mni_perllib-0.07
In-Reply-To: <d747ed50604031352v1a547691lcf62822695bed89b@mail.gmail.com>
References: <9c80f12d0604031223l3ee52299x8f57fe7348a05b19@mail.gmail.com>
	<20060403155209.D29759@mrs.mni.mcgill.ca>
	<d747ed50604031352v1a547691lcf62822695bed89b@mail.gmail.com>
Message-ID: <9c80f12d0604031440m6a62da33wa3799449ed825731@mail.gmail.com>

Great, it's all working now.  Thanks!
Gil

On 4/3/06, Andrew Janke <a.janke at gmail.com> wrote:
> Correct, There have been a few lingering bugs in the later releases of
> mni_autoreg. The latest point release (0.99.1) resolves this issue.
>
>    http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.99.1.tar.gz
>
> There are no binary packages for this release yet.
>
>
> a


From Paul.Rasser at newcastle.edu.au  Mon Apr  3 19:03:31 2006
From: Paul.Rasser at newcastle.edu.au (Paul Rasser)
Date: Tue, 04 Apr 2006 09:03:31 +1000
Subject: [MINC-users] MacOS packages faulty?
Message-ID: <s432366c.056@MC-GWDOM2.newcastle.edu.au>

Just wondering how things are progressing regarding the Mac OS packages?

Paul.




>>> Paul.Rasser at newcastle.edu.au 03/07/06 4:33 PM >>>
Both the packages below failed to install on 10.4.4

http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz


Paul.

>>> dale at bic.mni.mcgill.ca 02/25/06 1:47 PM >>>
Hello,
    I am displease to inform you all that I believe the packages listed 
below to be faulty...    Since I do not have a 10.4 system I will need 
a volunteer.  Someone with a MacOS 10.4 system;  download and install 
anyone of them  if it fails there are all probably broken.

Please be careful to read the error message at the end!!!

http://packages.bic.mni.mcgill.ca/osx/classify-1.0.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/glim-image-1.1.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/inormalize-0.99.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/mincblob-1.2.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98s.pkg.tar.gz
http://packages.bic.mni.mcgill.ca/osx/register-1.3.6.pkg.tar.gz


NOTE:  It looks like they have been broken for a while.  Even the ones 
on my backup from a month-ago are bad.   They look to have been 
corrupted in the transfer.


I am sorry for the pain this may have cause.  I will try to have it 
rectified shortly.


PS:  My last official day is Tuesday :)
Cheers!
dale

_______________________________________________
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 ed.gronenschild at mi.unimaas.nl  Tue Apr  4 03:26:58 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Tue, 4 Apr 2006 09:26:58 +0200
Subject: [MINC-users] Left-right convention in Display
Message-ID: <ff3f500bef97be80acbe8a30967a0a4c@mi.unimaas.nl>

Hi,

I'm not sure about the left-right convention used in Display:
is it the neuroscience convention where left on the screen is also the 
left side
of the patient or just the opposite (radiological) convention?

Regards,

Ed


From U951678 at STUDMED.AU.DK  Tue Apr  4 04:11:42 2006
From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=)
Date: Tue, 4 Apr 2006 10:11:42 +0200
Subject: [MINC-users] MINC install
Message-ID: <FB47ED393635794CB4523F0C52A3D1C2F0A144@urd.svf.au.dk>

Hi,
 I am trying to compile MINC 1.4 after compiling and installing NetCDF.
However, I get the following error during make:

if /bin/sh ./libtool --mode=compile gcc32 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema    -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF "$depbase.Tpo" -c -o volume_io/Prog_utils/time.lo volume_io/Prog_utils/time.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
gcc32 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF volume_io/Prog_utils/.deps/time.Tpo -c volume_io/Prog_utils/time.c -o volume_io/Prog_utils/time.o
volume_io/Prog_utils/time.c: In function `get_clock_ticks_per_second':
volume_io/Prog_utils/time.c:59: `CLK_TCK' undeclared (first use in this function)
volume_io/Prog_utils/time.c:59: (Each undeclared identifier is reported only once
volume_io/Prog_utils/time.c:59: for each function it appears in.)
make[2]: *** [volume_io/Prog_utils/time.lo] Error 1
make[2]: Leaving directory `/home/soren/minc-1.4'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soren/minc-1.4'
make: *** [all] Error 2

I saw on the group that someone had a similar problem a while ago, but he solved it using gcc in stead of c99.
I use gcc32 on Fedora core 5. Some words of advice are appreciated!


Thanks 
Soren


From a.janke at gmail.com  Tue Apr  4 06:51:56 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 4 Apr 2006 06:51:56 -0400
Subject: [MINC-users] Left-right convention in Display
In-Reply-To: <ff3f500bef97be80acbe8a30967a0a4c@mi.unimaas.nl>
References: <ff3f500bef97be80acbe8a30967a0a4c@mi.unimaas.nl>
Message-ID: <d747ed50604040351m134aae61x2a63f57ba5c1934d@mail.gmail.com>

Neurological.

Left is left.


a

On 4/4/06, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi,
>
> I'm not sure about the left-right convention used in Display:
> is it the neuroscience convention where left on the screen is also the
> left side
> of the patient or just the opposite (radiological) convention?
>
> Regards,
>
> Ed
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Tue Apr  4 09:29:04 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 4 Apr 2006 09:29:04 -0400
Subject: [MINC-users] MINC install
In-Reply-To: <FB47ED393635794CB4523F0C52A3D1C2F0A144@urd.svf.au.dk>
References: <FB47ED393635794CB4523F0C52A3D1C2F0A144@urd.svf.au.dk>
Message-ID: <d747ed50604040629s5c9e83datd4cc25337f75231b@mail.gmail.com>

This is a difference in the timing libraries. Thus it is more a
difference in libc.  What version of gcc are you using?


a

On 4/4/06, S?ren Christensen <U951678 at studmed.au.dk> wrote:
> Hi,
>  I am trying to compile MINC 1.4 after compiling and installing NetCDF.
> However, I get the following error during make:
>
> if /bin/sh ./libtool --mode=compile gcc32 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema    -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF "$depbase.Tpo" -c -o volume_io/Prog_utils/time.lo volume_io/Prog_utils/time.c; \
> then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
> gcc32 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF volume_io/Prog_utils/.deps/time.Tpo -c volume_io/Prog_utils/time.c -o volume_io/Prog_utils/time.o
> volume_io/Prog_utils/time.c: In function `get_clock_ticks_per_second':
> volume_io/Prog_utils/time.c:59: `CLK_TCK' undeclared (first use in this function)
> volume_io/Prog_utils/time.c:59: (Each undeclared identifier is reported only once
> volume_io/Prog_utils/time.c:59: for each function it appears in.)
> make[2]: *** [volume_io/Prog_utils/time.lo] Error 1
> make[2]: Leaving directory `/home/soren/minc-1.4'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/soren/minc-1.4'
> make: *** [all] Error 2
>
> I saw on the group that someone had a similar problem a while ago, but he solved it using gcc in stead of c99.
> I use gcc32 on Fedora core 5. Some words of advice are appreciated!
>
>
> Thanks
> 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 || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Wed Apr  5 08:11:14 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 5 Apr 2006 08:11:14 -0400
Subject: [MINC-users] MacOS packages faulty?
In-Reply-To: <s432366c.056@MC-GWDOM2.newcastle.edu.au>
References: <s432366c.056@MC-GWDOM2.newcastle.edu.au>
Message-ID: <d747ed50604050511j536cd1fh27b9bf611cf0dbc0@mail.gmail.com>

Hi Paul (and others)

I recompiled a bunch of them last night under 10.4 there were a few
small tweaks that were needed for POSIX compliance but by en large
things progressed smoothly.  For the packages that require external
libraries (bicpl and netpbm for example) I have used the fink
versions.  In the future I may use darwinports as it seems a bit
"cleaner" but at the moment I am unconvinced either way.

Could those who use tiger please test the new packages here:

   http://packages.bic.mni.mcgill.ca/osx-10.4/

Note that this is not a complete list (some failed for various reasons
that I will try to rectify over the next few days).


Andrew


On 4/3/06, Paul Rasser <Paul.Rasser at newcastle.edu.au> wrote:
> Just wondering how things are progressing regarding the Mac OS packages?
>
> Paul.
>
>
>
>
> >>> Paul.Rasser at newcastle.edu.au 03/07/06 4:33 PM >>>
> Both the packages below failed to install on 10.4.4
>
> http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz
>
>
> Paul.
>
> >>> dale at bic.mni.mcgill.ca 02/25/06 1:47 PM >>>
> Hello,
>     I am displease to inform you all that I believe the packages listed
> below to be faulty...    Since I do not have a 10.4 system I will need
> a volunteer.  Someone with a MacOS 10.4 system;  download and install
> anyone of them  if it fails there are all probably broken.
>
> Please be careful to read the error message at the end!!!
>
> http://packages.bic.mni.mcgill.ca/osx/classify-1.0.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/glim-image-1.1.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/inormalize-0.99.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/mincblob-1.2.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98s.pkg.tar.gz
> http://packages.bic.mni.mcgill.ca/osx/register-1.3.6.pkg.tar.gz
>
>
> NOTE:  It looks like they have been broken for a while.  Even the ones
> on my backup from a month-ago are bad.   They look to have been
> corrupted in the transfer.
>
> I am sorry for the pain this may have cause.  I will try to have it
> rectified shortly.

--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From Kent.Conover at concordia.ca  Wed Apr  5 09:52:57 2006
From: Kent.Conover at concordia.ca (conover)
Date: Wed, 5 Apr 2006 09:52:57 -0400
Subject: [MINC-users] MacOS packages faulty?
In-Reply-To: <d747ed50604050511j536cd1fh27b9bf611cf0dbc0@mail.gmail.com>
References: <s432366c.056@MC-GWDOM2.newcastle.edu.au>
	<d747ed50604050511j536cd1fh27b9bf611cf0dbc0@mail.gmail.com>
Message-ID: <305FFFA3-DCC2-4689-8313-89873992076C@concordia.ca>

Hi Andrew,

I successfully installed all the OS 10.4 packages that you posted on  
5-Apr-06. Do you know where I can get EMMA binaries for OS 10.4? I am  
trying to work through the example analysis script provided by Keith  
Wosley, and it requires EMMA routines that I do not have.

Regards,

Kent

On 5-Apr-06, at 8:11 AM, Andrew Janke wrote:

> Hi Paul (and others)
>
> I recompiled a bunch of them last night under 10.4 there were a few
> small tweaks that were needed for POSIX compliance but by en large
> things progressed smoothly.  For the packages that require external
> libraries (bicpl and netpbm for example) I have used the fink
> versions.  In the future I may use darwinports as it seems a bit
> "cleaner" but at the moment I am unconvinced either way.
>
> Could those who use tiger please test the new packages here:
>
>    http://packages.bic.mni.mcgill.ca/osx-10.4/
>
> Note that this is not a complete list (some failed for various reasons
> that I will try to rectify over the next few days).
>
>
> Andrew
>
>
> On 4/3/06, Paul Rasser <Paul.Rasser at newcastle.edu.au> wrote:
>> Just wondering how things are progressing regarding the Mac OS  
>> packages?
>>
>> Paul.
>>
>>
>>
>>
>>>>> Paul.Rasser at newcastle.edu.au 03/07/06 4:33 PM >>>
>> Both the packages below failed to install on 10.4.4
>>
>> http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz
>>
>>
>> Paul.
>>
>>>>> dale at bic.mni.mcgill.ca 02/25/06 1:47 PM >>>
>> Hello,
>>     I am displease to inform you all that I believe the packages  
>> listed
>> below to be faulty...    Since I do not have a 10.4 system I will  
>> need
>> a volunteer.  Someone with a MacOS 10.4 system;  download and install
>> anyone of them  if it fails there are all probably broken.
>>
>> Please be careful to read the error message at the end!!!
>>
>> http://packages.bic.mni.mcgill.ca/osx/classify-1.0.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/glim-image-1.1.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/inormalize-0.99.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/mincblob-1.2.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98s.pkg.tar.gz
>> http://packages.bic.mni.mcgill.ca/osx/register-1.3.6.pkg.tar.gz
>>
>>
>> NOTE:  It looks like they have been broken for a while.  Even the  
>> ones
>> on my backup from a month-ago are bad.   They look to have been
>> corrupted in the transfer.
>>
>> I am sorry for the pain this may have cause.  I will try to have it
>> rectified shortly.
>
> --
> Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> Canada->Montreal                                   Cell: +1 (514)  
> 924 2012
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From sean at rogue-research.com  Wed Apr  5 10:33:53 2006
From: sean at rogue-research.com (Sean McBride)
Date: Wed, 5 Apr 2006 10:33:53 -0400
Subject: [MINC-users] MacOS packages faulty?
In-Reply-To: <305FFFA3-DCC2-4689-8313-89873992076C@concordia.ca>
References: <s432366c.056@MC-GWDOM2.newcastle.edu.au>
	<d747ed50604050511j536cd1fh27b9bf611cf0dbc0@mail.gmail.com>
	<305FFFA3-DCC2-4689-8313-89873992076C@concordia.ca>
Message-ID: <20060405143353.21551@smtp1.sympatico.ca>

On 2006-04-05 09:52, conover said:

>I successfully installed all the OS 10.4 packages that you posted on  
>5-Apr-06. Do you know where I can get EMMA binaries for OS 10.4? I am  
>trying to work through the example analysis script provided by Keith  
>Wosley, and it requires EMMA routines that I do not have.

Version 0.9.7 is available here:
<http://packages.bic.mni.mcgill.ca/tgz/>

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




From ed.gronenschild at mi.unimaas.nl  Wed Apr  5 11:23:51 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Wed, 5 Apr 2006 17:23:51 +0200
Subject: [MINC-users] Problem with building application on Mac
Message-ID: <DD7541E4-5D91-4C06-8A86-3A3169D97222@mi.unimaas.nl>

Hi,

I'm trying to make use of the BIC Volume IO Library in a Mac OSX  
application,
for instance to import a MINC volume. I'm using XCode and the problem  
is that
in one of the include files, namely geom_structs.h, the data type  
Point is declared
which conflicts with the same name of a data type declared in the Mac  
Toolbox.
Does anybody know how to solve this?

Ed

From sean at rogue-research.com  Wed Apr  5 11:45:44 2006
From: sean at rogue-research.com (Sean McBride)
Date: Wed, 5 Apr 2006 11:45:44 -0400
Subject: [MINC-users] Problem with building application on Mac
In-Reply-To: <DD7541E4-5D91-4C06-8A86-3A3169D97222@mi.unimaas.nl>
References: <DD7541E4-5D91-4C06-8A86-3A3169D97222@mi.unimaas.nl>
Message-ID: <20060405154544.15480@smtp1.sympatico.ca>

On 2006-04-05 17:23, Ed Gronenschild said:

>I'm trying to make use of the BIC Volume IO Library in a Mac OSX  
>application,
>for instance to import a MINC volume. I'm using XCode and the problem  
>is that
>in one of the include files, namely geom_structs.h, the data type  
>Point is declared
>which conflicts with the same name of a data type declared in the Mac  
>Toolbox.
>Does anybody know how to solve this?

What version of MINC are you using?  In 1.4, all your questions are
answered in geom_structs.h itself.  Basically, use VIO_Point, not Point.

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




From a.janke at gmail.com  Wed Apr  5 13:30:54 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 5 Apr 2006 13:30:54 -0400
Subject: [MINC-users] Problem with building application on Mac
In-Reply-To: <20060405154544.15480@smtp1.sympatico.ca>
References: <DD7541E4-5D91-4C06-8A86-3A3169D97222@mi.unimaas.nl>
	<20060405154544.15480@smtp1.sympatico.ca>
Message-ID: <d747ed50604051030u70ee5e3xb83341e679d0827e@mail.gmail.com>

Correct, there has been a recent effort to make sure that volume_io
(and thus MINC) does not do so much name space pollution as in the
past.

In order to make full use of this (And in a new application) be sure to

  #define DISABLE_DEPRECATED

Somewhere and the older style decs, (Point, X, Y, etc) are done away with.


a

On 4/5/06, Sean McBride <sean at rogue-research.com> wrote:
> On 2006-04-05 17:23, Ed Gronenschild said:
>
> >I'm trying to make use of the BIC Volume IO Library in a Mac OSX
> >application,
> >for instance to import a MINC volume. I'm using XCode and the problem
> >is that
> >in one of the include files, namely geom_structs.h, the data type
> >Point is declared
> >which conflicts with the same name of a data type declared in the Mac
> >Toolbox.
> >Does anybody know how to solve this?
>
> What version of MINC are you using?  In 1.4, all your questions are
> answered in geom_structs.h itself.  Basically, use VIO_Point, not Point.
>
> --
> ____________________________________________________________
> 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 || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Wed Apr  5 16:13:48 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 5 Apr 2006 16:13:48 -0400
Subject: [MINC-users] Bug in mni_autoreg-0.98v ?
In-Reply-To: <44182CFA.6020709@hst.aau.dk>
References: <mailman.3.1142355609.1237548.minc-users@bic.mni.mcgill.ca>
	<4416FA32.8000404@fz-juelich.de>
	<d747ed50603141410sc3ebf61k47cec6f0827c5fdc@mail.gmail.com>
	<44182CFA.6020709@hst.aau.dk>
Message-ID: <d747ed50604051313u4f918ceauff751b418961fde5@mail.gmail.com>

On 3/15/06, Simon Fristed Eskildsen <se at hst.aau.dk> wrote:
> Since we're correcting the perl scripts, I'm slightly annoyed by the way
> mritotal handles logging. Somewhere after version 0.98r mritotal has
> considered stdout as an open filehandle for logging, which means that it
> is not possible to pipe stdout from mritotal:
>     mritotal mri.mnc mri.xfm > test.log
>     self_announce: if supplied, $log must be an open filehandle at
> /gruppe/ad_mri/Opteron/pack/bin/mritotal line 571
> Removing the following from mritotal solves the problem:
>     &self_announce("STDOUT") if $Verbose && ! -t "STDOUT";
> I realize that the filehandle check is in the self_announce function,
> but i am reluctant to change anything in the mni_perllib.

As am I.  (changing things in mni_perllib)  In short after a bit of
digging into this and a holiday inbetween, I have come to the
conclusion that much of mni_perllib is no longer needed.  A lot of the
functionality it provided is now included in perl by default.

So my fix to this would be as such in mritotal:

diff -u -b -B -r1.18 mritotal.in
--- mritotal.in 7 Dec 2005 03:19:13 -0000       1.18
+++ mritotal.in 5 Apr 2006 19:59:15 -0000
@@ -565,10 +565,8 @@

    $, = ' ';     # set output field separator

-   # First, announce ourselves to stdout (for ease in later dissection
-   # of log files) -- unless STDOUT is a tty.
-
-   &self_announce("STDOUT") if $Verbose && ! -t "STDOUT";
+   # First, announce ourselves
+   &self_announce if $Verbose;

    # Set defaults for the global variables.  These can be overridden by
    # the configuration file or the command line.

This will fix the problem and should retain most of the old behaviour
(rather than just removing the offending line).

Thoughts?

I will make the change for 0.99.2

> Maybe a commandline option to mritotal for handling logging would be in
> order?

I'm adverse to adding such functionality to a perl program.  This
should be handled by a simple '>' on the command line! :)

Sorry about the delay with the reply.


a


From a.janke at gmail.com  Wed Apr  5 16:50:01 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 5 Apr 2006 16:50:01 -0400
Subject: [MINC-users] Problem with building application on Mac
In-Reply-To: <d747ed50604051030u70ee5e3xb83341e679d0827e@mail.gmail.com>
References: <DD7541E4-5D91-4C06-8A86-3A3169D97222@mi.unimaas.nl>
	<20060405154544.15480@smtp1.sympatico.ca>
	<d747ed50604051030u70ee5e3xb83341e679d0827e@mail.gmail.com>
Message-ID: <d747ed50604051350x4dca5d1aw16a775b55fb75ab2@mail.gmail.com>

Actually, make that:

#define VIO_PREFIX_NAMES 1

I had GTK on my brain.

a

On 4/5/06, Andrew Janke <a.janke at gmail.com> wrote:
> Correct, there has been a recent effort to make sure that volume_io
> (and thus MINC) does not do so much name space pollution as in the
> past.
>
> In order to make full use of this (And in a new application) be sure to
>
>   #define DISABLE_DEPRECATED
>
> Somewhere and the older style decs, (Point, X, Y, etc) are done away with.
>
>
> a
>
> On 4/5/06, Sean McBride <sean at rogue-research.com> wrote:
> > On 2006-04-05 17:23, Ed Gronenschild said:
> >
> > >I'm trying to make use of the BIC Volume IO Library in a Mac OSX
> > >application,
> > >for instance to import a MINC volume. I'm using XCode and the problem
> > >is that
> > >in one of the include files, namely geom_structs.h, the data type
> > >Point is declared
> > >which conflicts with the same name of a data type declared in the Mac
> > >Toolbox.
> > >Does anybody know how to solve this?
> >
> > What version of MINC are you using?  In 1.4, all your questions are
> > answered in geom_structs.h itself.  Basically, use VIO_Point, not Point.
> >
> > --
> > ____________________________________________________________
> > 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 || www.cmr.uq.edu.au/~rotor)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Thu Apr  6 07:04:03 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 6 Apr 2006 07:04:03 -0400
Subject: [MINC-users] MacOS packages faulty?
In-Reply-To: <20060405143353.21551@smtp1.sympatico.ca>
References: <s432366c.056@MC-GWDOM2.newcastle.edu.au>
	<d747ed50604050511j536cd1fh27b9bf611cf0dbc0@mail.gmail.com>
	<305FFFA3-DCC2-4689-8313-89873992076C@concordia.ca>
	<20060405143353.21551@smtp1.sympatico.ca>
Message-ID: <d747ed50604060404w184b5c8cnf6fd0edc1b4dde73@mail.gmail.com>

On 4/5/06, Sean McBride <sean at rogue-research.com> wrote:
> On 2006-04-05 09:52, conover said:
>
> >I successfully installed all the OS 10.4 packages that you posted on
> >5-Apr-06. Do you know where I can get EMMA binaries for OS 10.4? I am
> >trying to work through the example analysis script provided by Keith
> >Wosley, and it requires EMMA routines that I do not have.
>
> Version 0.9.7 is available here:
> <http://packages.bic.mni.mcgill.ca/tgz/>

As Sean has mentioned, there are source versions available. 
Unfortunately I dont have plans to release a binary version of emma as
of yet as I don't have a matlab licence for my little 12" Powerbook! 
I use it to do all of the 10.4 binary builds.


Andrew


From ed.gronenschild at mi.unimaas.nl  Thu Apr  6 09:16:33 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Thu, 6 Apr 2006 15:16:33 +0200
Subject: [MINC-users] How to use insect properly?
Message-ID: <4cea1dae9c67badd380c811293fa8f38@mi.unimaas.nl>

Hi,

I've used insect to do the classification into WM, GM and CSF. I 
noticed, however,
that the background gets the same class label (=1) as CSF, so I'm not 
able
to distinguish CSF from the background. (WM gets label 3 and GM label 
2).

The command was insect input_volume.mnc, where the volume was a T1 
coronal stack.

Have I done something wrong?

The version of insect is from the classify-1.0 package and I' m on a 
Mac OSX 10.3.9.

Ed


From alex at bic.mni.mcgill.ca  Thu Apr  6 13:07:15 2006
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Thu, 06 Apr 2006 13:07:15 -0400
Subject: [MINC-users] case/hyphenation issues in deb pkgs?
Message-ID: <20060406170715.GA4205@bic.mni.mcgill.ca>

Hello,

I'm trying to install the Debian mni packages, but I'm running in some
odd dependency problems which at first glance appear to be related to
case/hyphenation inconsistencies. For example:

  splat:~# apt-get -s install classify ebtks
  Reading Package Lists... Done
  Building Dependency Tree... Done
  ebtks is already the newest version.
  Some packages could not be installed. This may mean that you have
  requested an impossible situation or if you are using the unstable
  distribution that some required packages have not yet been created
  or been moved out of Incoming.
  The following information may help to resolve the situation:

  The following packages have unmet dependencies:
    classify: Depends: EBTKS but it is not installable
  E: Broken packages

So ebtks is installed, but classify won't install because it depends
on EBTKS?

Then also:

  dpkg: dependency problems prevent configuration of mni-autoreg-model:
   mni-autoreg-model depends on mni_autoreg; however:
    Package mni_autoreg is not installed.
  # dpkg -l | grep autoreg
  ii  mni-autoreg    0.98v          mni-autoreg

So it appears that mni-autoreg-model depends on mni_autoreg, while
mni-autoreg (note hyphen vs. underscore) is actually installed.

Am I missing something?

-- A

From a.janke at gmail.com  Thu Apr  6 16:12:55 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 6 Apr 2006 16:12:55 -0400
Subject: [MINC-users] Bug in mni_autoreg-0.98v ?
In-Reply-To: <d747ed50604051313u4f918ceauff751b418961fde5@mail.gmail.com>
References: <mailman.3.1142355609.1237548.minc-users@bic.mni.mcgill.ca>
	<4416FA32.8000404@fz-juelich.de>
	<d747ed50603141410sc3ebf61k47cec6f0827c5fdc@mail.gmail.com>
	<44182CFA.6020709@hst.aau.dk>
	<d747ed50604051313u4f918ceauff751b418961fde5@mail.gmail.com>
Message-ID: <d747ed50604061312u555d23bdlb81d455893ac0570@mail.gmail.com>

The keen eyed will note that mni_autoreg-0.99.2 has made it to packages here:

   http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.99.2.tar.gz

This includes the self_announce bugfix for those who run
mritotal/mritoself in scripts.

A binary package will follow shortly.

--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Mon Apr 10 02:51:05 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 10 Apr 2006 02:51:05 -0400
Subject: [MINC-users] case/hyphenation issues in deb pkgs?
In-Reply-To: <20060406170715.GA4205@bic.mni.mcgill.ca>
References: <20060406170715.GA4205@bic.mni.mcgill.ca>
Message-ID: <d747ed50604092351n23a5b183n2e5d31ba90dfd93a@mail.gmail.com>

No,

These were a few errors that slipped through with early versions of
the debian packages that I am yet to fix, you can force the
installation of these packages with no worry.

In short they came about because debian does not allow Capitols in
package names nor underscores.


Andrew

On 4/6/06, Alex ZIJDENBOS <alex at bic.mni.mcgill.ca> wrote:
> Hello,
>
> I'm trying to install the Debian mni packages, but I'm running in some
> odd dependency problems which at first glance appear to be related to
> case/hyphenation inconsistencies. For example:
>
>  splat:~# apt-get -s install classify ebtks
>  Reading Package Lists... Done
>  Building Dependency Tree... Done
>  ebtks is already the newest version.
>  Some packages could not be installed. This may mean that you have
>  requested an impossible situation or if you are using the unstable
>  distribution that some required packages have not yet been created
>  or been moved out of Incoming.
>  The following information may help to resolve the situation:
>
>  The following packages have unmet dependencies:
>    classify: Depends: EBTKS but it is not installable
>  E: Broken packages
>
> So ebtks is installed, but classify won't install because it depends
> on EBTKS?
>
> Then also:
>
>  dpkg: dependency problems prevent configuration of mni-autoreg-model:
>   mni-autoreg-model depends on mni_autoreg; however:
>    Package mni_autoreg is not installed.
>  # dpkg -l | grep autoreg
>  ii  mni-autoreg    0.98v          mni-autoreg
>
> So it appears that mni-autoreg-model depends on mni_autoreg, while
> mni-autoreg (note hyphen vs. underscore) is actually installed.
>
> Am I missing something?
>
> -- A
> _______________________________________________
> 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/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From mathieu.dehaes at polymtl.ca  Mon Apr 10 14:16:52 2006
From: mathieu.dehaes at polymtl.ca (Mathieu Dehaes)
Date: Mon, 10 Apr 2006 14:16:52 -0400
Subject: [MINC-users] Problems with Emma in newimage.m
Message-ID: <1144693012.443aa1149664f@www.imp.polymtl.ca>

Hi,

I try to use Emma 0.9.7 on Mac OS X 10.4 and I have 2 problems with the
newimage.m function.

1- I just want to create a minc file with the command :

>> handle = newimage('new.mnc', [0 1 31 49]);

and Matlab gives me the error :

Command: micreateimage new.mnc -size 0 1 31 49 -type byte -valid_range 0 255
-orientation transverse
 Output: 
??? Error using ==> newimage
Error running micreateimage to create file new.mnc

I resolved this problem by changing the newimage.m file on line 253-255 :

if (Parent == -1)
   execstr = sprintf ('micreateimage %s -size %d %d %d %d -type %s -valid_range
%.20g %.20g -orientation %s', ...
    	      NewFile, DimSizes, ImageType, ValidRange, Orientation);

by these lines :

   execstr = sprintf ('/usr/local/emma/bin/micreateimage %s -size %d %d %d %d -
type %s -orientation %s', ...
		      NewFile, DimSizes, ImageType, Orientation);

i.e. by giving the whole path to the micreateimage program. Does anyone know how
to use newimage.m without changing the file?

2- If you check the changed lines above, there is another change. I removed the
error associated with the "ValidRange", because Matlab gave me

Command: /usr/local/emma/bin/micreateimage new.mnc -size 0 1 31 49 -type byte
-valid_range 0 255 -orientation transverse
 Output: 

??? Error using ==> newimage
Error running micreateimage to create file new.mnc

This is the reason I had removed the ValidRange parameter. Does anyone know how 
to use newimage.m with the default parameter without changing the file?  Why is
0-255 not valid for a byte type image?

Thank you.

Mathieu and Sean

From a.janke at gmail.com  Thu Apr 13 01:41:39 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 13 Apr 2006 01:41:39 -0400
Subject: [MINC-users] Availability minc_bet
In-Reply-To: <0BD7A161-E701-44CE-828E-27F7F7C75068@mi.unimaas.nl>
References: <0BD7A161-E701-44CE-828E-27F7F7C75068@mi.unimaas.nl>
Message-ID: <d747ed50604122241p508418f2kf9d30b23eed852f1@mail.gmail.com>

Hi Ed,

In short, mincbet was a dirty hack I perpetrated a while back upon a
version of FSL that I happened to have. (For the technically inclined
I modified libss to read MINC directly).  It seems to now have taken
on a life of its own. :)

Unfortunately I am sure that Steve Smith and Co would not be too
impressed if I started distributing my own hacked up versions of FSL
and thus I am somewhat reticent about it.

I could provide the extra bits of code I did add to FSL and then you
could add them in yourself. Your mileage will definitely vary here as
I suspect FSL has changed somewhat since I did this. So I suspect that
your best bet would be to simply use the nifti-1 conversion tools that
are now part of MINC 1.4

ie:

   mnc2nii infile.mnc tmp.hdr
   bet tmp.hdr....  out.hdr
   nii2mnc out.hdr outfile.mnc

This is somewhat convoluted but will work!


a


On 4/3/06, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi,
>
> Where can I find minc_bet, the derivative of BET from FSL.
> I'm on a Mac OSX 10.3.9.
>
> Regards,
>
> Ed
>
> _______________________________________________
> 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/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From ed.gronenschild at mi.unimaas.nl  Thu Apr 13 09:53:36 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Thu, 13 Apr 2006 15:53:36 +0200
Subject: [MINC-users] Once again: how to use insect properly?
Message-ID: <FDB018D9-8847-447C-8875-EAD2AD41F71F@mi.unimaas.nl>

Hi,

I posted this a week ago and until now I didn't get an answer.
So once more:

I've used insect to do the classification into WM, GM and CSF. I  
noticed, however,
that the background gets the same class label (=1) as CSF, so I'm not  
able
to distinguish CSF from the background. (WM gets label 3 and GM label  
2).

The command was insect input_volume.mnc, where the volume was a T1  
coronal stack.

Have I done something wrong?

The version of insect is from the classify-1.0 package and I' m on a  
Mac OSX 10.3.9.

Ed


From jason at bic.mni.mcgill.ca  Thu Apr 13 12:40:16 2006
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 13 Apr 2006 12:40:16 -0400
Subject: [MINC-users] Once again: how to use insect properly?
In-Reply-To: <FDB018D9-8847-447C-8875-EAD2AD41F71F@mi.unimaas.nl>
References: <FDB018D9-8847-447C-8875-EAD2AD41F71F@mi.unimaas.nl>
Message-ID: <443E7EF0.8080208@bic.mni.mcgill.ca>

Ed Gronenschild wrote:

>Hi,
>
>I posted this a week ago and until now I didn't get an answer.
>So once more:
>
>I've used insect to do the classification into WM, GM and CSF. I  
>noticed, however,
>that the background gets the same class label (=1) as CSF, so I'm not  
>able
>to distinguish CSF from the background. (WM gets label 3 and GM label  
>2).
>
>The command was insect input_volume.mnc, where the volume was a T1  
>coronal stack.
>
>  
>
Can you try using classify_clean -clean_tags on its own on a file in 
stereotaxic space? And, should that not work, can you provide a listing 
of your (prefix)/share/classify directory, where prefix is the package 
installation location?

Cheers,

Jason

>Have I done something wrong?
>
>The version of insect is from the classify-1.0 package and I' m on a  
>Mac OSX 10.3.9.
>
>Ed
>
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  
>


From pvcorrection at yahoo.com  Mon Apr 17 17:58:50 2006
From: pvcorrection at yahoo.com (Olivier Rousset)
Date: Mon, 17 Apr 2006 14:58:50 -0700 (PDT)
Subject: [MINC-users] spatially-variant mincblur?
Message-ID: <20060417215850.93305.qmail@web37204.mail.mud.yahoo.com>

I was wondering whether a non-stationary kernel can be
specified with mincblur (apparently not in the current
version), or if alternatively there would be a program
that could do that? I am thinking that maybe
stationary kernels could be used on parts of the
images [where spatial resolution is assumed constant]
and then combine the resulting blurred images [since
these operations can be considered as linear]; this
would involve masking of the image with appropriate
masks defined using "resolution isocontours". Well
before I go that route, I would like to know if any of
you is aware of anything that could solve my problem.
Thanks in advance for your input,

- Olivier

Olivier G. Rousset, Ph.D.
Johns Hopkins Medical Institutions
Radiology Department JHOC 3243
601 N. Caroline Str.
Baltimore, MD 21287
U.S.A.
tel. +1-410-955-2900
fax +1-410-955-0696
e-mail: olivier at OlivierRousset.com

From a.janke at gmail.com  Tue Apr 18 08:44:34 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 18 Apr 2006 08:44:34 -0400
Subject: [MINC-users] spatially-variant mincblur?
In-Reply-To: <20060417215850.93305.qmail@web37204.mail.mud.yahoo.com>
References: <20060417215850.93305.qmail@web37204.mail.mud.yahoo.com>
Message-ID: <d747ed50604180544ybc26d0et9942e42489a68d25@mail.gmail.com>

Oliver,

I do know that Robert Vincent was working on a version of mincblur
that would handle a non-isotropic blurring kernel.  I dont know
whether he finished it or not, Perhaps you could contact him directly.

a

On 4/17/06, Olivier Rousset <pvcorrection at yahoo.com> wrote:
> I was wondering whether a non-stationary kernel can be
> specified with mincblur (apparently not in the current
> version), or if alternatively there would be a program
> that could do that? I am thinking that maybe
> stationary kernels could be used on parts of the
> images [where spatial resolution is assumed constant]
> and then combine the resulting blurred images [since
> these operations can be considered as linear]; this
> would involve masking of the image with appropriate
> masks defined using "resolution isocontours". Well
> before I go that route, I would like to know if any of
> you is aware of anything that could solve my problem.
> Thanks in advance for your input,
>
> - Olivier
>
> Olivier G. Rousset, Ph.D.
> Johns Hopkins Medical Institutions
> Radiology Department JHOC 3243
> 601 N. Caroline Str.
> Baltimore, MD 21287
> U.S.A.
> tel. +1-410-955-2900
> fax +1-410-955-0696
> e-mail: olivier at OlivierRousset.com
> _______________________________________________
> 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/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From ed.gronenschild at mi.unimaas.nl  Tue Apr 18 10:11:50 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Tue, 18 Apr 2006 16:11:50 +0200
Subject: [MINC-users] Building OSX application with MINC libraries
Message-ID: <5385CA6E-3DA5-4777-80B4-6B2884AC0761@mi.unimaas.nl>

Hi Andrew (Janke),

A few weeks ago I dropped a question about using the MINC
libraries in building a native Mac OSX application. To get rid of
conflicting errors you adviced me to set VIO_PREFIX_NAMES
to 1. When I do so the application runs without errors, so your
suggestion worked. However, I noticed that a lot of symbols are
not defined anymore, like "FREE" (see alloc.h) and "for_less"
(see basic.h). I'm using the minc 1.4 package.
Is there any particular reason why these symbols are not defined
and thus can't be used only because of setting
VIO_PREFIX_NAMES to 1 instead of 0.

Regards,

Ed


From jharlap at bic.mni.mcgill.ca  Tue Apr 18 10:28:24 2006
From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP)
Date: Tue, 18 Apr 2006 10:28:24 -0400
Subject: [MINC-users] Building OSX application with MINC libraries
In-Reply-To: <5385CA6E-3DA5-4777-80B4-6B2884AC0761@mi.unimaas.nl>
References: <5385CA6E-3DA5-4777-80B4-6B2884AC0761@mi.unimaas.nl>
Message-ID: <4444F788.50207@bic.mni.mcgill.ca>

Hi Ed,

AFAIK, VIO_PREFIX_NAMES=1 basically gets rid of a bunch of macros that 
either are named in a way that invites conflicts (such as X) or are 
trivial/unnecessary (such as for_less).  There's really no reason a C 
programmer would make a macro for_less(X,i) = for(X=0;X<i;++X) as all it 
accomplishes is less readable code and poorer compiler optimization - so 
coders are discouraged from using the macros which are controlled by 
VIO_PREFIX_NAMES.  Unfortunately, many common minc programs use these 
macros, so it will be some work before they can really be nuked.

Cheers,
J


Ed Gronenschild wrote:
> Hi Andrew (Janke),
> 
> A few weeks ago I dropped a question about using the MINC
> libraries in building a native Mac OSX application. To get rid of
> conflicting errors you adviced me to set VIO_PREFIX_NAMES
> to 1. When I do so the application runs without errors, so your
> suggestion worked. However, I noticed that a lot of symbols are
> not defined anymore, like "FREE" (see alloc.h) and "for_less"
> (see basic.h). I'm using the minc 1.4 package.
> Is there any particular reason why these symbols are not defined
> and thus can't be used only because of setting
> VIO_PREFIX_NAMES to 1 instead of 0.
> 
> Regards,
> 
> Ed
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From kent.conover at concordia.ca  Tue Apr 18 17:15:09 2006
From: kent.conover at concordia.ca (conover)
Date: Tue, 18 Apr 2006 17:15:09 -0400
Subject: [MINC-users] Setting up MINC tools in OS X
Message-ID: <D8A1DC2E-145D-4028-8EA8-235489B988FF@concordia.ca>

To OS X users,

It turns out that I need some basic information on how to compile mex  
files. At this point, I cannot get Matlab to compile it's simple test  
program "yprime.c". I need to learn how to install the GCC 3.3  
compiler for my machine. I would appreciate any pointers that you can  
offer.

Regards,

Kent Conover,

Research Associate,
Centre for Studies in Behavioural Neurobiology,
Concordia University,
Montreal, Quebec
Canada 

From ed.gronenschild at mi.unimaas.nl  Wed Apr 19 03:21:08 2006
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Wed, 19 Apr 2006 09:21:08 +0200
Subject: [MINC-users] Once again: how to use insect properly?
In-Reply-To: <mailman.3.1145030407.1248471.minc-users@bic.mni.mcgill.ca>
References: <mailman.3.1145030407.1248471.minc-users@bic.mni.mcgill.ca>
Message-ID: <40974E0E-1FEB-409F-B5D2-BD8CAFEA2117@mi.unimaas.nl>

Hi Jason,

I have done like you proposed and got a correct classification,
or better, CSF was labeled differently from the background.
However, I noticed that the classification in general was different
from that without the option -clean_tags. So two questions remain:
1. which option should I use?
2. how to implement the option -clean_tags in the insect Perl
	script? Should I do this myself or do you have a proposal?

Cheers,

Ed

On 14 Apr 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:

> Message: 1
> Date: Thu, 13 Apr 2006 12:40:16 -0400
> From: Jason Lerch <jason at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Once again: how to use insect properly?
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <443E7EF0.8080208 at bic.mni.mcgill.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Ed Gronenschild wrote:
>
>> Hi,
>>
>> I posted this a week ago and until now I didn't get an answer.
>> So once more:
>>
>> I've used insect to do the classification into WM, GM and CSF. I
>> noticed, however,
>> that the background gets the same class label (=1) as CSF, so I'm not
>> able
>> to distinguish CSF from the background. (WM gets label 3 and GM label
>> 2).
>>
>> The command was insect input_volume.mnc, where the volume was a T1
>> coronal stack.
>>
>>
>>
> Can you try using classify_clean -clean_tags on its own on a file in
> stereotaxic space? And, should that not work, can you provide a  
> listing
> of your (prefix)/share/classify directory, where prefix is the package
> installation location?
>
> Cheers,
>
> Jason
>
>> Have I done something wrong?
>>
>> The version of insect is from the classify-1.0 package and I' m on a
>> Mac OSX 10.3.9.
>>
>> Ed


From jason at bic.mni.mcgill.ca  Wed Apr 19 09:36:29 2006
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 19 Apr 2006 09:36:29 -0400
Subject: [MINC-users] Once again: how to use insect properly?
In-Reply-To: <40974E0E-1FEB-409F-B5D2-BD8CAFEA2117@mi.unimaas.nl>
References: <mailman.3.1145030407.1248471.minc-users@bic.mni.mcgill.ca>
	<40974E0E-1FEB-409F-B5D2-BD8CAFEA2117@mi.unimaas.nl>
Message-ID: <44463CDD.7000307@bic.mni.mcgill.ca>

The easy change is to edit the script, replacing this line

Spawn(['classify_clean', $TAL, $CLA]);

with

Spawn(['classify_clean', '-clean_tags', $TAL, $CLA]);

I would recommend using tag cleaning in your classification. The default 
behaviour has been changed multiple times as we argue amongst ourselves 
what the default should be. I vote tag cleaning by default. Anyone else? 
Alex?

Jason


Ed Gronenschild wrote:

>Hi Jason,
>
>I have done like you proposed and got a correct classification,
>or better, CSF was labeled differently from the background.
>However, I noticed that the classification in general was different
>from that without the option -clean_tags. So two questions remain:
>1. which option should I use?
>2. how to implement the option -clean_tags in the insect Perl
>	script? Should I do this myself or do you have a proposal?
>
>Cheers,
>
>Ed
>
>On 14 Apr 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:
>
>  
>
>>Message: 1
>>Date: Thu, 13 Apr 2006 12:40:16 -0400
>>From: Jason Lerch <jason at bic.mni.mcgill.ca>
>>Subject: Re: [MINC-users] Once again: how to use insect properly?
>>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>>Message-ID: <443E7EF0.8080208 at bic.mni.mcgill.ca>
>>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>Ed Gronenschild wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>I posted this a week ago and until now I didn't get an answer.
>>>So once more:
>>>
>>>I've used insect to do the classification into WM, GM and CSF. I
>>>noticed, however,
>>>that the background gets the same class label (=1) as CSF, so I'm not
>>>able
>>>to distinguish CSF from the background. (WM gets label 3 and GM label
>>>2).
>>>
>>>The command was insect input_volume.mnc, where the volume was a T1
>>>coronal stack.
>>>
>>>
>>>
>>>      
>>>
>>Can you try using classify_clean -clean_tags on its own on a file in
>>stereotaxic space? And, should that not work, can you provide a  
>>listing
>>of your (prefix)/share/classify directory, where prefix is the package
>>installation location?
>>
>>Cheers,
>>
>>Jason
>>
>>    
>>
>>>Have I done something wrong?
>>>
>>>The version of insect is from the classify-1.0 package and I' m on a
>>>Mac OSX 10.3.9.
>>>
>>>Ed
>>>      
>>>
>
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  
>


From a.janke at gmail.com  Wed Apr 19 10:03:01 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 19 Apr 2006 10:03:01 -0400
Subject: [MINC-users] Once again: how to use insect properly?
In-Reply-To: <44463CDD.7000307@bic.mni.mcgill.ca>
References: <mailman.3.1145030407.1248471.minc-users@bic.mni.mcgill.ca>
	<40974E0E-1FEB-409F-B5D2-BD8CAFEA2117@mi.unimaas.nl>
	<44463CDD.7000307@bic.mni.mcgill.ca>
Message-ID: <d747ed50604190703x3c858e6fje1430382f85ea36c@mail.gmail.com>

Myself I always run classify with -clean_tags


a

On 4/19/06, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> The easy change is to edit the script, replacing this line
>
> Spawn(['classify_clean', $TAL, $CLA]);
>
> with
>
> Spawn(['classify_clean', '-clean_tags', $TAL, $CLA]);
>
> I would recommend using tag cleaning in your classification. The default
> behaviour has been changed multiple times as we argue amongst ourselves
> what the default should be. I vote tag cleaning by default. Anyone else?
> Alex?
>
> Jason
>
>
> Ed Gronenschild wrote:
>
> >Hi Jason,
> >
> >I have done like you proposed and got a correct classification,
> >or better, CSF was labeled differently from the background.
> >However, I noticed that the classification in general was different
> >from that without the option -clean_tags. So two questions remain:
> >1. which option should I use?
> >2. how to implement the option -clean_tags in the insect Perl
> >       script? Should I do this myself or do you have a proposal?
> >
> >Cheers,
> >
> >Ed
> >
> >On 14 Apr 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:
> >
> >
> >
> >>Message: 1
> >>Date: Thu, 13 Apr 2006 12:40:16 -0400
> >>From: Jason Lerch <jason at bic.mni.mcgill.ca>
> >>Subject: Re: [MINC-users] Once again: how to use insect properly?
> >>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >>Message-ID: <443E7EF0.8080208 at bic.mni.mcgill.ca>
> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >>Ed Gronenschild wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>
> >>>I posted this a week ago and until now I didn't get an answer.
> >>>So once more:
> >>>
> >>>I've used insect to do the classification into WM, GM and CSF. I
> >>>noticed, however,
> >>>that the background gets the same class label (=1) as CSF, so I'm not
> >>>able
> >>>to distinguish CSF from the background. (WM gets label 3 and GM label
> >>>2).
> >>>
> >>>The command was insect input_volume.mnc, where the volume was a T1
> >>>coronal stack.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>Can you try using classify_clean -clean_tags on its own on a file in
> >>stereotaxic space? And, should that not work, can you provide a
> >>listing
> >>of your (prefix)/share/classify directory, where prefix is the package
> >>installation location?
> >>
> >>Cheers,
> >>
> >>Jason
> >>
> >>
> >>
> >>>Have I done something wrong?
> >>>
> >>>The version of insect is from the classify-1.0 package and I' m on a
> >>>Mac OSX 10.3.9.
> >>>
> >>>Ed
> >>>
> >>>
> >
> >_______________________________________________
> >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
>


--
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From alex at bic.mni.mcgill.ca  Wed Apr 19 10:31:16 2006
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Wed, 19 Apr 2006 10:31:16 -0400
Subject: [MINC-users] Once again: how to use insect properly?
In-Reply-To: <d747ed50604190703x3c858e6fje1430382f85ea36c@mail.gmail.com>
References: <mailman.3.1145030407.1248471.minc-users@bic.mni.mcgill.ca>
	<40974E0E-1FEB-409F-B5D2-BD8CAFEA2117@mi.unimaas.nl>
	<44463CDD.7000307@bic.mni.mcgill.ca>
	<d747ed50604190703x3c858e6fje1430382f85ea36c@mail.gmail.com>
Message-ID: <20060419143116.GC1537322@bic.mni.mcgill.ca>

I'd say that the fact that BG and CSF are considered one class is not
(or shouldn't be) related to the tag cleaning stage. I assume that
classify_clean without -clean_tags doesn't use the (separate) BG tag
file, which I would consider a bug.

The reason why clean_tags was removed as a default was because its
performance was never objectively validated. But I suppose we could
change the default back to -clean_tags (sigh), since the overall
consensus appears to be that it improves things...

-- A

On Wed, Apr 19, 2006 at 10:03:01AM -0400, Andrew Janke wrote:
> Myself I always run classify with -clean_tags
> 
> 
> a
> 
> On 4/19/06, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> > The easy change is to edit the script, replacing this line
> >
> > Spawn(['classify_clean', $TAL, $CLA]);
> >
> > with
> >
> > Spawn(['classify_clean', '-clean_tags', $TAL, $CLA]);
> >
> > I would recommend using tag cleaning in your classification. The default
> > behaviour has been changed multiple times as we argue amongst ourselves
> > what the default should be. I vote tag cleaning by default. Anyone else?
> > Alex?
> >
> > Jason
> >
> >
> > Ed Gronenschild wrote:
> >
> > >Hi Jason,
> > >
> > >I have done like you proposed and got a correct classification,
> > >or better, CSF was labeled differently from the background.
> > >However, I noticed that the classification in general was different
> > >from that without the option -clean_tags. So two questions remain:
> > >1. which option should I use?
> > >2. how to implement the option -clean_tags in the insect Perl
> > >       script? Should I do this myself or do you have a proposal?
> > >
> > >Cheers,
> > >
> > >Ed
> > >
> > >On 14 Apr 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:
> > >
> > >
> > >
> > >>Message: 1
> > >>Date: Thu, 13 Apr 2006 12:40:16 -0400
> > >>From: Jason Lerch <jason at bic.mni.mcgill.ca>
> > >>Subject: Re: [MINC-users] Once again: how to use insect properly?
> > >>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >>Message-ID: <443E7EF0.8080208 at bic.mni.mcgill.ca>
> > >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > >>
> > >>Ed Gronenschild wrote:
> > >>
> > >>
> > >>
> > >>>Hi,
> > >>>
> > >>>I posted this a week ago and until now I didn't get an answer.
> > >>>So once more:
> > >>>
> > >>>I've used insect to do the classification into WM, GM and CSF. I
> > >>>noticed, however,
> > >>>that the background gets the same class label (=1) as CSF, so I'm not
> > >>>able
> > >>>to distinguish CSF from the background. (WM gets label 3 and GM label
> > >>>2).
> > >>>
> > >>>The command was insect input_volume.mnc, where the volume was a T1
> > >>>coronal stack.
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>Can you try using classify_clean -clean_tags on its own on a file in
> > >>stereotaxic space? And, should that not work, can you provide a
> > >>listing
> > >>of your (prefix)/share/classify directory, where prefix is the package
> > >>installation location?
> > >>
> > >>Cheers,
> > >>
> > >>Jason
> > >>
> > >>
> > >>
> > >>>Have I done something wrong?
> > >>>
> > >>>The version of insect is from the classify-1.0 package and I' m on a
> > >>>Mac OSX 10.3.9.
> > >>>
> > >>>Ed
> > >>>
> > >>>
> > >
> > >_______________________________________________
> > >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
> >
> 
> 
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-- 
=========================================================================
| Alex P. Zijdenbos, Ph.D.        |                                     |
| McConnell Brain Imaging Centre  |  Phone: [+1] 514 398-5220  (office) |
| Montreal Neurological Institute |         [+1] 514 398-1996   (dept.) |
| 3801 University St., WB-208     |    Fax: [+1] 514 398-8952  (office) |
| Montreal, Quebec, H3A 2B4       |         [+1] 708 810-3309 (private) | 
| CANADA                          | E-mail:      alex at bic.mni.mcgill.ca |
=========================================================================


From tpb1 at ualberta.ca  Wed Apr 19 17:37:50 2006
From: tpb1 at ualberta.ca (tpb1@ualberta.ca)
Date: Wed, 19 Apr 2006 15:37:50 -0600
Subject: [MINC-users] Faces on objects
Message-ID: <20060419153750.717hatna8gkcwswg@webmail.ualberta.ca>

I've noticed that when I import objects created in Display into 
Blender, their faces (when zoomed in enough in Blender) are not all the 
same shape.  Some faces are four sided, while others are three-sided. I 
have not seen a function in Display that would control the shape of the 
faces of an object, but I wanted to know if anyone else has found a way 
to control them.

Thanks so much,
Thomas

From jason at bic.mni.mcgill.ca  Wed Apr 19 18:06:33 2006
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 19 Apr 2006 18:06:33 -0400
Subject: [MINC-users] Faces on objects
In-Reply-To: <20060419153750.717hatna8gkcwswg@webmail.ualberta.ca>
References: <20060419153750.717hatna8gkcwswg@webmail.ualberta.ca>
Message-ID: <FA5704CA-F4B9-418C-B06D-64361E494E81@bic.mni.mcgill.ca>

I have no idea what Blender is, but the program triangulate_polygons  
inside conglomerate might do what you want.

Jason

On 19-Apr-06, at 5:37 PM, tpb1 at ualberta.ca wrote:

> I've noticed that when I import objects created in Display into
> Blender, their faces (when zoomed in enough in Blender) are not all  
> the
> same shape.  Some faces are four sided, while others are three- 
> sided. I
> have not seen a function in Display that would control the shape of  
> the
> faces of an object, but I wanted to know if anyone else has found a  
> way
> to control them.
>
> Thanks so much,
> Thomas
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From viking13 at eyou.com  Fri Apr 21 23:13:15 2006
From: viking13 at eyou.com (lv)
Date: Sat, 22 Apr 2006 11:13:15 +0800
Subject: [MINC-users] about  installing netcdf before minc
Message-ID: <345675598.17145@eyou.com>

An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: http://www.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20060421/0e0b9dc4/attachment.ksh

From viking13 at eyou.com  Fri Apr 21 23:13:45 2006
From: viking13 at eyou.com (lv)
Date: Sat, 22 Apr 2006 11:13:45 +0800
Subject: [MINC-users] about  installing netcdf before minc
Message-ID: <345675628.76144@eyou.com>

An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: http://www.bic.mni.mcgill.ca/pipermail/minc-users/attachments/20060421/db7a101d/attachment.ksh

From steven.robbins at videotron.ca  Sat Apr 22 14:50:59 2006
From: steven.robbins at videotron.ca (Steve M. Robbins)
Date: Sat, 22 Apr 2006 14:50:59 -0400
Subject: [MINC-users] spatially-variant mincblur?
In-Reply-To: <20060417215850.93305.qmail@web37204.mail.mud.yahoo.com>
References: <20060417215850.93305.qmail@web37204.mail.mud.yahoo.com>
Message-ID: <20060422185058.GN16244@nyongwa.montreal.qc.ca>

On Mon, Apr 17, 2006 at 02:58:50PM -0700, Olivier Rousset wrote:
> I was wondering whether a non-stationary kernel can be
> specified with mincblur (apparently not in the current
> version), or if alternatively there would be a program
> that could do that? I am thinking that maybe
> stationary kernels could be used on parts of the
> images [where spatial resolution is assumed constant]
> and then combine the resulting blurred images [since
> these operations can be considered as linear]; this
> would involve masking of the image with appropriate
> masks defined using "resolution isocontours".

It sounds like you are after a non-stationary isotropic smoothing --
as opposed to a non-isotropic ("don't blur across edges") smoothing.

Just out of curiousity: what sort of data requires that treatment?

-Steve


From pvcorrection at yahoo.com  Sat Apr 22 17:23:34 2006
From: pvcorrection at yahoo.com (Olivier Rousset)
Date: Sat, 22 Apr 2006 14:23:34 -0700 (PDT)
Subject: [MINC-users] spatially-variant mincblur?
In-Reply-To: <20060422185058.GN16244@nyongwa.montreal.qc.ca>
Message-ID: <20060422212334.85059.qmail@web37214.mail.mud.yahoo.com>

Steve,
What I am in search of is a non-stationary version of
mincblur, which currently supports anisotropic
blurring kernels, but provides no spatial variation
encoding. I would like to create simulated PET data,
for which I need a spatially-variant point-spread
function (PSF) that would be more realistic than a
stationary PSF.

- Olivier 

--- "Steve M. Robbins" <steven.robbins at videotron.ca>
wrote:

> On Mon, Apr 17, 2006 at 02:58:50PM -0700, Olivier
> Rousset wrote:
> > I was wondering whether a non-stationary kernel
> can be
> > specified with mincblur (apparently not in the
> current
> > version), or if alternatively there would be a
> program
> > that could do that? I am thinking that maybe
> > stationary kernels could be used on parts of the
> > images [where spatial resolution is assumed
> constant]
> > and then combine the resulting blurred images
> [since
> > these operations can be considered as linear];
> this
> > would involve masking of the image with
> appropriate
> > masks defined using "resolution isocontours".
> 
> It sounds like you are after a non-stationary
> isotropic smoothing --
> as opposed to a non-isotropic ("don't blur across
> edges") smoothing.
> 
> Just out of curiousity: what sort of data requires
> that treatment?
> 
> -Steve
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
>
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


From louis.collins at mcgill.ca  Sat Apr 22 19:13:39 2006
From: louis.collins at mcgill.ca (D. Louis Collins)
Date: Sat, 22 Apr 2006 19:13:39 -0400
Subject: [MINC-users] spatially-variant mincblur?
In-Reply-To: <20060422212334.85059.qmail@web37214.mail.mud.yahoo.com>
References: <20060422212334.85059.qmail@web37214.mail.mud.yahoo.com>
Message-ID: <8bb6fa2525298c3722265e4c7d495932@mcgill.ca>

Salut Olivier,

I think that it would be possible to create (or at least fake) 
non-stationary blurring for simulation of pet data.

I would use masks that define the regions that correspond to a 
particular spatial resolution.  Suppose that you define 3 concentric 
regions, with res=5mm at the center, then 6mm and 7mm for the two 
concentric rings. (note that the ROIs don't have to be spherical, but 
should actually correspond to the measured resolution field).

I would then blur the simulated PET data with 3 kernels (fwhm=5,6 and 
7mm) to yield three blurred volumes.  Now mask these volumes with the 
ROIs defined above and then add the results together.  Voila, the 
resulting volume will have spatially varying resolution.

But wait you say, there will be harsh discontinuities at the borders of 
these ROIs.  Right you are.  So, blur the masks with a small (say 
fwhm=3mm) spatial blurring kernel.  Normalize them, so that when added 
together, all voxels sum to 1.0.

Now, multiple the 3 blurred PET volumes with the 3 masks and add them 
together and you'll have cheap, continuous, spatially-variant 
resolution for your simulated PET volume.

While this is a hack, I think that it would go a long way for system 
evaluation.  You can probably define 5-7 concentric regions and you'd 
get even better results.  (and recoding mincblur for spatially varying 
kernel is a no-go since it uses Fourier Transforms to achieve blurring. 
  You'd have to completely rewrite it to do convolution in the spatial 
domain - which is not unlike what I describe above!)

Good luck!

-Louis


On Apr 22, 2006, at 5:23 PM, Olivier Rousset wrote:

> Steve,
> What I am in search of is a non-stationary version of
> mincblur, which currently supports anisotropic
> blurring kernels, but provides no spatial variation
> encoding. I would like to create simulated PET data,
> for which I need a spatially-variant point-spread
> function (PSF) that would be more realistic than a
> stationary PSF.
>
> - Olivier
>
> --- "Steve M. Robbins" <steven.robbins at videotron.ca>
> wrote:
>
>> On Mon, Apr 17, 2006 at 02:58:50PM -0700, Olivier
>> Rousset wrote:
>>> I was wondering whether a non-stationary kernel
>> can be
>>> specified with mincblur (apparently not in the
>> current
>>> version), or if alternatively there would be a
>> program
>>> that could do that? I am thinking that maybe
>>> stationary kernels could be used on parts of the
>>> images [where spatial resolution is assumed
>> constant]
>>> and then combine the resulting blurred images
>> [since
>>> these operations can be considered as linear];
>> this
>>> would involve masking of the image with
>> appropriate
>>> masks defined using "resolution isocontours".
>>
>> It sounds like you are after a non-stationary
>> isotropic smoothing --
>> as opposed to a non-isotropic ("don't blur across
>> edges") smoothing.
>>
>> Just out of curiousity: what sort of data requires
>> that treatment?
>>
>> -Steve
>>
>> _______________________________________________
>> 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 yalingy at usc.edu  Tue Apr 25 20:06:53 2006
From: yalingy at usc.edu (yaling yang)
Date: Tue, 25 Apr 2006 17:06:53 -0700
Subject: [MINC-users] converting .16u to minc
Message-ID: <75e1317a386590021d40f117ed02a345@usc.edu>


Dear Subscribers and experts,

Our group is working on some old structural MRI data recently and are 
trying to re-segment them using Display. However, some of the cases, 
instead of the usual dicom format, are in a format called *.16u. We are 
having trouble figuring out how to convert this type to minc (or 
analyze format such as .img). Any suggestion would be greatly 
appreciated.

Thank you very much.

Yours,
yaling


From sorench at gmail.com  Tue Apr 25 20:25:43 2006
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 26 Apr 2006 10:25:43 +1000
Subject: [MINC-users] converting .16u to minc
In-Reply-To: <75e1317a386590021d40f117ed02a345@usc.edu>
References: <75e1317a386590021d40f117ed02a345@usc.edu>
Message-ID: <d6e2d6550604251725t40d6e44ay303541ca0a61cd5c@mail.gmail.com>

Hi Yaling,
 Could it be 16 bit unsigned integers?  What is the file size and the
x,y,z resolution of your scan (if available)?

Best regards
Soren



On 4/26/06, yaling yang <yalingy at usc.edu> wrote:
>
> Dear Subscribers and experts,
>
> Our group is working on some old structural MRI data recently and are
> trying to re-segment them using Display. However, some of the cases,
> instead of the usual dicom format, are in a format called *.16u. We are
> having trouble figuring out how to convert this type to minc (or
> analyze format such as .img). Any suggestion would be greatly
> appreciated.
>
> Thank you very much.
>
> Yours,
> yaling
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From mssp02 at miba.auc.dk  Wed Apr 26 15:45:46 2006
From: mssp02 at miba.auc.dk (mssp02@miba.auc.dk)
Date: Wed, 26 Apr 2006 21:45:46 +0200
Subject: [MINC-users] ANIMAL
Message-ID: <1146080746.444fcdea2286a@www.hst.aau.dk>

Hi,

I have a question about MNI_ANIMAL as I?m not sure how to perform this 
operation. Is it basically to perform a mni_autoreg? It is not obvious to me 
from the tutorial.
 
Thanks in advance


/Morten
Email: mssp02 at miba.auc.dk




-------------------------------------------------
This mail sent through IMP: http://horde.org/imp/

From howard.chou at loni.ucla.edu  Wed Apr 26 18:55:06 2006
From: howard.chou at loni.ucla.edu (Howard Chou)
Date: Wed, 26 Apr 2006 15:55:06 -0700
Subject: [MINC-users] minc tool on intel core mac
Message-ID: <6E624D9CA72AA148932674B863E08FD1427EEC@enson.loni.ucla.edu>


To whom it may concern,
  I am trying to install minc tools on the new intel core mac, i am running into problem with x11.  This is the error i am recieving.

X Error of failed request:  BadRequest (invalid request code or no such operation)
  Major opcode of failed request:  129 (Apple-DRI)
  Minor opcode of failed request:  1 ()
  Serial number of failed request:  15
  Current serial number in output stream:  15

is it because of the intel core?

Thanks for your help
Howard

From a.janke at gmail.com  Wed Apr 26 22:05:50 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 26 Apr 2006 22:05:50 -0400
Subject: [MINC-users] minc tool on intel core mac
In-Reply-To: <6E624D9CA72AA148932674B863E08FD1427EEC@enson.loni.ucla.edu>
References: <6E624D9CA72AA148932674B863E08FD1427EEC@enson.loni.ucla.edu>
Message-ID: <d747ed50604261905k1ab4533clf57ca895643a364a@mail.gmail.com>

Hi Howard,

Which particular program are you trying to run?  I suspect Display or
register. And if so, did you compile it yourself or are you using a
static binary? (OSX package)


Andrew

On 4/26/06, Howard Chou <howard.chou at loni.ucla.edu> wrote:
>
> To whom it may concern,
>   I am trying to install minc tools on the new intel core mac, i am running into problem with x11.  This is the error i am recieving.
>
> X Error of failed request:  BadRequest (invalid request code or no such operation)
>   Major opcode of failed request:  129 (Apple-DRI)
>   Minor opcode of failed request:  1 ()
>   Serial number of failed request:  15
>   Current serial number in output stream:  15
>
> is it because of the intel core?
>
> Thanks for your help
> Howard
> _______________________________________________
> 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/)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From pvcorrection at yahoo.com  Fri Apr 28 15:47:19 2006
From: pvcorrection at yahoo.com (Olivier Rousset)
Date: Fri, 28 Apr 2006 12:47:19 -0700 (PDT)
Subject: [MINC-users] spatially-variant mincblur?
In-Reply-To: <8bb6fa2525298c3722265e4c7d495932@mcgill.ca>
Message-ID: <20060428194719.25646.qmail@web37213.mail.mud.yahoo.com>

Salut Louis,

Well I have to say that we are thinking along the same
lines here... great! I will try that -got carried away
by other things lately- and it sounds that this should
work. BTW, are you going to HBM'06 in Italy? I forgot
to let you know that our abstract "PET quantification
using an MRI-based Brain Atlas: Effect of ROI 
definition on Dopamine Binding Potential with and
without Partial Volume correction"  Olivier G.
Rousset1, D. Louis Collins2, Hiroto Kuwabara1, Andrew
H. Crabb1, Dean F. Wong1" was accepted for poster
presentation. Hope to see you there!!

Will keep you posted on the progress on the
non-stationnary PSF. 

Bien ? toi, et bonne fin de semaine (bon week-end
quoi).

- Olivier

--- "D. Louis Collins" <louis.collins at mcgill.ca>
wrote:

> Salut Olivier,
> 
> I think that it would be possible to create (or at
> least fake) 
> non-stationary blurring for simulation of pet data.
> 
> I would use masks that define the regions that
> correspond to a 
> particular spatial resolution.  Suppose that you
> define 3 concentric 
> regions, with res=5mm at the center, then 6mm and
> 7mm for the two 
> concentric rings. (note that the ROIs don't have to
> be spherical, but 
> should actually correspond to the measured
> resolution field).
> 
> I would then blur the simulated PET data with 3
> kernels (fwhm=5,6 and 
> 7mm) to yield three blurred volumes.  Now mask these
> volumes with the 
> ROIs defined above and then add the results
> together.  Voila, the 
> resulting volume will have spatially varying
> resolution.
> 
> But wait you say, there will be harsh
> discontinuities at the borders of 
> these ROIs.  Right you are.  So, blur the masks with
> a small (say 
> fwhm=3mm) spatial blurring kernel.  Normalize them,
> so that when added 
> together, all voxels sum to 1.0.
> 
> Now, multiple the 3 blurred PET volumes with the 3
> masks and add them 
> together and you'll have cheap, continuous,
> spatially-variant 
> resolution for your simulated PET volume.
> 
> While this is a hack, I think that it would go a
> long way for system 
> evaluation.  You can probably define 5-7 concentric
> regions and you'd 
> get even better results.  (and recoding mincblur for
> spatially varying 
> kernel is a no-go since it uses Fourier Transforms
> to achieve blurring. 
>   You'd have to completely rewrite it to do
> convolution in the spatial 
> domain - which is not unlike what I describe above!)
> 
> Good luck!
> 
> -Louis
> 
> 
> On Apr 22, 2006, at 5:23 PM, Olivier Rousset wrote:
> 
> > Steve,
> > What I am in search of is a non-stationary version
> of
> > mincblur, which currently supports anisotropic
> > blurring kernels, but provides no spatial
> variation
> > encoding. I would like to create simulated PET
> data,
> > for which I need a spatially-variant point-spread
> > function (PSF) that would be more realistic than a
> > stationary PSF.
> >
> > - Olivier
> >
> > --- "Steve M. Robbins"
> <steven.robbins at videotron.ca>
> > wrote:
> >
> >> On Mon, Apr 17, 2006 at 02:58:50PM -0700, Olivier
> >> Rousset wrote:
> >>> I was wondering whether a non-stationary kernel
> >> can be
> >>> specified with mincblur (apparently not in the
> >> current
> >>> version), or if alternatively there would be a
> >> program
> >>> that could do that? I am thinking that maybe
> >>> stationary kernels could be used on parts of the
> >>> images [where spatial resolution is assumed
> >> constant]
> >>> and then combine the resulting blurred images
> >> [since
> >>> these operations can be considered as linear];
> >> this
> >>> would involve masking of the image with
> >> appropriate
> >>> masks defined using "resolution isocontours".
> >>
> >> It sounds like you are after a non-stationary
> >> isotropic smoothing --
> >> as opposed to a non-isotropic ("don't blur across
> >> edges") smoothing.
> >>
> >> Just out of curiousity: what sort of data
> requires
> >> that treatment?
> >>
> >> -Steve
> >>
> >> _______________________________________________
> >> 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
>