From misssophy at gmail.com  Tue Dec  5 10:01:16 2006
From: misssophy at gmail.com (=?ISO-8859-1?Q?Sofie_S=F8rensen?=)
Date: Tue, 5 Dec 2006 10:01:16 -0500
Subject: [MINC-users] Display cannot enlarge!
Message-ID: <a1bf1cda0612050701p73b07fbbofdc685382bc79602@mail.gmail.com>

Hi jonathan!
Finally I also upgraded my Ubuntu 6.06 to  6.10 and now both Display and
register work!
Nice, thanks!

Sofie

On 11/29/06, minc-users-request at bic.mni.mcgill.ca <
minc-users-request at bic.mni.mcgill.ca> wrote:
>
> Send MINC-users mailing list submissions to
>         minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
>         minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
>         minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
>
> Today's Topics:
>
>    1. Re: Display cannot enlarge!!! (Jonathan LAU)
>    2. iv2bicobj (Jason Lerch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Nov 2006 13:28:56 -0500
> From: "Jonathan LAU" <lau at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] Display cannot enlarge!!!
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Message-ID:
>         <eb9fb4b10611281028g2c9835fjc066a423ac8f565d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Sofie,
>
> Since installing the latest version of Ubuntu (6.10, Edgy Eft), these
> problems have gone away.
>
> Hope it works out for you too.
>
> cheers,
> jonathan
>
> On 9/29/06, Sofie S?rensen <misssophy at gmail.com> wrote:
> >
> > Thanks Jonathan!
> > It seems that we got the same problem.
> > I wont be able to go online for the next to weeks, but i'm still woking
> to
> > solve the problem, and will be happy to get new clews!
> >
> > On 9/29/06, minc-users-request at bic.mni.mcgill.ca <
> > minc-users-request at bic.mni.mcgill.ca> wrote:
> > >
> > > Send MINC-users mailing list submissions to
> > >         minc-users at bic.mni.mcgill.ca
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > >         http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > or, via email, send a message with subject or body 'help' to
> > >         minc-users-request at bic.mni.mcgill.ca
> > >
> > > You can reach the person managing the list at
> > >         minc-users-owner at bic.mni.mcgill.ca
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of MINC-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Display cannot enlarge!!! ( Sofie S?rensen )
> > >    2. Re: Display cannot enlarge!!! (Jonathan LAU)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Thu, 28 Sep 2006 22:35:38 +0200
> > > From: " Sofie S?rensen " <misssophy at gmail.com>
> > > Subject: [MINC-users] Display cannot enlarge!!!
> > > To: minc-users at bic.mni.mcgill.ca
> > > Message-ID:
> > >         <a1bf1cda0609281335o56a1b638r1d5bad6163e8af46 at mail.gmail.com>
> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > >
> > > Hi,
> > >
> > > I'm running Display in Ubuntu 6.06. When running Display, I can only
> > view
> > > in
> > > a small window. When I enlarge the viewing, the pictures (3 slices)
> > > disappear. It seems, that there is only allocated space in the view
> for
> > a
> > > certain picture size, and therefore, they disappear when completely
> > > enlarged.
> > >
> > > Can anyone explain to me, what is wrong? Is there some settings in the
> > > program that can be changed?
> > >
> > > I don't get any warnings!
> > >
> > > Sofie Lykke S?rensen, student
> > > Biomedical Engineering,
> > > Aalborg University, Denmark
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Thu, 28 Sep 2006 17:50:45 -0400
> > > From: "Jonathan LAU" <lau at bic.mni.mcgill.ca>
> > > Subject: Re: [MINC-users] Display cannot enlarge!!!
> > > To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> > > Message-ID:
> > >         <eb9fb4b10609281450h3874e41dse314ce294a8bf576 at mail.gmail.com>
> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > >
> > > Hi Sofie,
> > >
> > > I have the same problem with Display on my laptop (also Ubuntu Dapper
> > > Drake)
> > > -- are you also using a widescreen?
> > > http://www.bic.mni.mcgill.ca/~lau/img/Display_clipping.jpg<
> > > http://www.bic.mni.mcgill.ca/%7Elau/img/Display_clipping.jpg>
> > >
> > > I've posted about a similar problem with register, where the 3rd view
> > > clips
> > > when maximized to full widescreen but the Display issue you raised is
> > much
> > > more severe.  For the record:
> > > http://www.bic.mni.mcgill.ca/~lau/img/register_ws_noclip.jpg<
> > > http://www.bic.mni.mcgill.ca/%7Elau/img/register_ws_noclip.jpg>
> > > http://www.bic.mni.mcgill.ca/~lau/img/register_ws_clip.jpg<
> > > http://www.bic.mni.mcgill.ca/%7Elau/img/register_ws_clip.jpg>
> > >
> > > I'm afraid to look at the code, but may try to look at it one of these
> > > days.  Anyone have any ideas?
> > >
> > > cheers,
> > > jon
> > >
> > > On 9/28/06, Sofie S?rensen <misssophy at gmail.com> wrote:
> > > >
> > > > Hi,
> > > >
> > > > I'm running Display in Ubuntu 6.06. When running Display, I can only
> > > view
> > > > in
> > > > a small window. When I enlarge the viewing, the pictures (3 slices)
> > > > disappear. It seems, that there is only allocated space in the view
> > for
> > > a
> > > > certain picture size, and therefore, they disappear when completely
> > > > enlarged.
> > > >
> > > > Can anyone explain to me, what is wrong? Is there some settings in
> the
> > > > program that can be changed?
> > > >
> > > > I don't get any warnings!
> > > >
> > > > Sofie Lykke S?rensen, student
> > > > Biomedical Engineering,
> > > > Aalborg University, Denmark
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > MINC-users mailing list
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > >
> > > End of MINC-users Digest, Vol 14, Issue 7
> > > *****************************************
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 28 Nov 2006 16:05:16 -0500
> From: Jason Lerch <jason at bic.mni.mcgill.ca>
> Subject: [MINC-users] iv2bicobj
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <456CA48C.2080001 at bic.mni.mcgill.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Greetings all,
>
> for the morbidly curious: I've added a somewhat misnamed iv2bicobj
> utility to the bicInventor library. It lets you go from inventor meshes
> back to David's obj file format. Only works for polygons/indexed face
> sets for the moment. And unless I hear people clamoring for other data
> types that's probably all that it'll work for. Has very little error
> checking at this point, so will probably give horrible segfaults if
> tried with other data types (or with some version of inventor meshes
> which violate the simplistic assumptions I've made).
>
> Why? There are a number of programs out there - such as amira - which
> can do neat things to meshes and save in the inventor format.
>
> Cheers,
>
> Jason
>
>
> ------------------------------
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> End of MINC-users Digest, Vol 16, Issue 11
> ******************************************
>

From Kent.Conover at concordia.ca  Thu Dec  7 14:44:28 2006
From: Kent.Conover at concordia.ca (conover)
Date: Thu, 7 Dec 2006 14:44:28 -0500
Subject: [MINC-users] Bug in MNI Perl routines
Message-ID: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>

Hi Everybody,

There seems to be a bug in the Perl module "AutoLoader.pm" in that it  
fails to recognize my operating system as that of Mac OS X:

Here is the code segment:

	if (defined($filename = $INC{"$pkg.pm"})) {
	    if ($is_macos) {
		$pkg =~ tr#/#:#;
		$filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg:$func.al#s;
	    } else {
		$filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/$func.al#s;
	    }

Upon evaluating  "if ($is_macos)", this routine jumps to the "else"  
condition. I suspect that I need to modify the file separators that  
define the $filename string somehow. I would appreciate your insights.

Regards,
-Kent

PS.

Here is the text of the Perl module "AutoLoader.pm" in which the bug  
resides.

package AutoLoader;

use strict;
use 5.006_001;

our($VERSION, $AUTOLOAD);

my $is_dosish;
my $is_epoc;
my $is_vms;
my $is_macos;

BEGIN {
     $is_dosish = $^O eq 'dos' || $^O eq 'os2' || $^O eq 'MSWin32' ||  
$^O eq 'NetWare';
     $is_epoc = $^O eq 'epoc';
     $is_vms = $^O eq 'VMS';
     $is_macos = $^O eq 'MacOS';
     $VERSION = '5.60';
}

AUTOLOAD {
     my $sub = $AUTOLOAD;
     my $filename;
     # Braces used to preserve $1 et al.
     {
	# Try to find the autoloaded file from the package-qualified
	# name of the sub. e.g., if the sub needed is
	# Getopt::Long::GetOptions(), then $INC{Getopt/Long.pm} is
	# something like '/usr/lib/perl5/Getopt/Long.pm', and the
	# autoload file is '/usr/lib/perl5/auto/Getopt/Long/GetOptions.al'.
	#
	# However, if @INC is a relative path, this might not work.  If,
	# for example, @INC = ('lib'), then $INC{Getopt/Long.pm} is
	# 'lib/Getopt/Long.pm', and we want to require
	# 'auto/Getopt/Long/GetOptions.al' (without the leading 'lib').
	# In this case, we simple prepend the 'auto/' and let the
	# C<require> take care of the searching for us.

	my ($pkg,$func) = ($sub =~ /(.*)::([^:]+)$/);
	$pkg =~ s#::#/#g;
	if (defined($filename = $INC{"$pkg.pm"})) {
	    if ($is_macos) {
		$pkg =~ tr#/#:#;
		$filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg:$func.al#s;
	    } else {
		$filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/$func.al#s;
	    }

	    # if the file exists, then make sure that it is a
	    # a fully anchored path (i.e either '/usr/lib/auto/foo/bar.al',
	    # or './lib/auto/foo/bar.al'.  This avoids C<require> searching
	    # (and failing) to find the 'lib/auto/foo/bar.al' because it
	    # looked for 'lib/lib/auto/foo/bar.al', given @INC = ('lib').

	    if (-r $filename) {
		unless ($filename =~ m|^/|s) {
		    if ($is_dosish) {
			unless ($filename =~ m{^([a-z]:)?[\\/]}is) {
			     if ($^O ne 'NetWare') {
					$filename = "./$filename";
				} else {
					$filename = "$filename";
				}
			}
		    }
		    elsif ($is_epoc) {
			unless ($filename =~ m{^([a-z?]:)?[\\/]}is) {
			     $filename = "./$filename";
			}
		    }
		    elsif ($is_vms) {
			# XXX todo by VMSmiths
			$filename = "./$filename";
		    }
		    elsif (!$is_macos) {
			$filename = "./$filename";
		    }
		}
	    }
	    else {
		$filename = undef;
	    }
	}
	unless (defined $filename) {
	    # let C<require> do the searching
	    $filename = "auto/$sub.al";
	    $filename =~ s#::#/#g;
	}
     }
     my $save = $@;
     local $!; # Do not munge the value.
     eval { local $SIG{__DIE__}; require $filename };
     if ($@) {
	if (substr($sub,-9) eq '::DESTROY') {
	    no strict 'refs';
	    *$sub = sub {};
	    $@ = undef;
	} elsif ($@ =~ /^Can't locate/) {
	    # The load might just have failed because the filename was too
	    # long for some old SVR3 systems which treat long names as errors.
	    # If we can successfully truncate a long name then it's worth a go.
	    # There is a slight risk that we could pick up the wrong file here
	    # but autosplit should have warned about that when splitting.
	    if ($filename =~ s/(\w{12,})\.al$/substr($1,0,11).".al"/e){
		eval { local $SIG{__DIE__}; require $filename };
	    }
	}
	if ($@){
	    $@ =~ s/ at .*\n//;
	    my $error = $@;
	    require Carp;
	    Carp::croak($error);
	}
     }
     $@ = $save;
     goto &$sub;
}

sub import {
     my $pkg = shift;
     my $callpkg = caller;

     #
     # Export symbols, but not by accident of inheritance.
     #

     if ($pkg eq 'AutoLoader') {
	no strict 'refs';
	*{ $callpkg . '::AUTOLOAD' } = \&AUTOLOAD
	    if @_ and $_[0] =~ /^&?AUTOLOAD$/;
     }

     #
     # Try to find the autosplit index file.  Eg., if the call package
     # is POSIX, then $INC{POSIX.pm} is something like
     # '/usr/local/lib/perl5/POSIX.pm', and the autosplit index file  
is in
     # '/usr/local/lib/perl5/auto/POSIX/autosplit.ix', so we require  
that.
     #
     # However, if @INC is a relative path, this might not work.  If,
     # for example, @INC = ('lib'), then
     # $INC{POSIX.pm} is 'lib/POSIX.pm', and we want to require
     # 'auto/POSIX/autosplit.ix' (without the leading 'lib').
     #

     (my $calldir = $callpkg) =~ s#::#/#g;
     my $path = $INC{$calldir . '.pm'};
     if (defined($path)) {
	# Try absolute path name.
	if ($is_macos) {
	    (my $malldir = $calldir) =~ tr#/#:#;
	    $path =~ s#^(.*)$malldir\.pm\z#$1auto:$malldir:autosplit.ix#s;
	} else {
	    $path =~ s#^(.*)$calldir\.pm\z#$1auto/$calldir/autosplit.ix#;
	}

	eval { require $path; };
	# If that failed, try relative path with normal @INC searching.
	if ($@) {
	    $path ="auto/$calldir/autosplit.ix";
	    eval { require $path; };
	}
	if ($@) {
	    my $error = $@;
	    require Carp;
	    Carp::carp($error);
	}
     }
}

sub unimport {
     my $callpkg = caller;

     no strict 'refs';
     my $symname = $callpkg . '::AUTOLOAD';
     undef *{ $symname } if \&{ $symname } == \&AUTOLOAD;
     *{ $symname } = \&{ $symname };
}

1;

__END__

=head1 NAME

AutoLoader - load subroutines only on demand

=head1 SYNOPSIS

     package Foo;
     use AutoLoader 'AUTOLOAD';   # import the default AUTOLOAD  
subroutine

     package Bar;
     use AutoLoader;              # don't import AUTOLOAD, define our  
own
     sub AUTOLOAD {
         ...
         $AutoLoader::AUTOLOAD = "...";
         goto &AutoLoader::AUTOLOAD;
     }

=head1 DESCRIPTION

The B<AutoLoader> module works with the B<AutoSplit> module and the
C<__END__> token to defer the loading of some subroutines until they are
used rather than loading them all at once.

To use B<AutoLoader>, the author of a module has to place the
definitions of subroutines to be autoloaded after an C<__END__> token.
(See L<perldata>.)  The B<AutoSplit> module can then be run manually to
extract the definitions into individual files F<auto/funcname.al>.

B<AutoLoader> implements an AUTOLOAD subroutine.  When an undefined
subroutine in is called in a client module of B<AutoLoader>,
B<AutoLoader>'s AUTOLOAD subroutine attempts to locate the subroutine  
in a
file with a name related to the location of the file from which the
client module was read.  As an example, if F<POSIX.pm> is located in
F</usr/local/lib/perl5/POSIX.pm>, B<AutoLoader> will look for perl
subroutines B<POSIX> in F</usr/local/lib/perl5/auto/POSIX/*.al>, where
the C<.al> file has the same name as the subroutine, sans package.  If
such a file exists, AUTOLOAD will read and evaluate it,
thus (presumably) defining the needed subroutine.  AUTOLOAD will then
C<goto> the newly defined subroutine.

Once this process completes for a given function, it is defined, so
future calls to the subroutine will bypass the AUTOLOAD mechanism.

=head2 Subroutine Stubs

In order for object method lookup and/or prototype checking to operate
correctly even when methods have not yet been defined it is necessary to
"forward declare" each subroutine (as in C<sub NAME;>).  See
L<perlsub/"SYNOPSIS">.  Such forward declaration creates "subroutine
stubs", which are place holders with no code.

The AutoSplit and B<AutoLoader> modules automate the creation of forward
declarations.  The AutoSplit module creates an 'index' file containing
forward declarations of all the AutoSplit subroutines.  When the
AutoLoader module is 'use'd it loads these declarations into its callers
package.

Because of this mechanism it is important that B<AutoLoader> is always
C<use>d and not C<require>d.

=head2 Using B<AutoLoader>'s AUTOLOAD Subroutine

In order to use B<AutoLoader>'s AUTOLOAD subroutine you I<must>
explicitly import it:

     use AutoLoader 'AUTOLOAD';

=head2 Overriding B<AutoLoader>'s AUTOLOAD Subroutine

Some modules, mainly extensions, provide their own AUTOLOAD subroutines.
They typically need to check for some special cases (such as constants)
and then fallback to B<AutoLoader>'s AUTOLOAD for the rest.

Such modules should I<not> import B<AutoLoader>'s AUTOLOAD subroutine.
Instead, they should define their own AUTOLOAD subroutines along these
lines:

     use AutoLoader;
     use Carp;

     sub AUTOLOAD {
         my $sub = $AUTOLOAD;
         (my $constname = $sub) =~ s/.*:://;
         my $val = constant($constname, @_ ? $_[0] : 0);
         if ($! != 0) {
             if ($! =~ /Invalid/ || $!{EINVAL}) {
                 $AutoLoader::AUTOLOAD = $sub;
                 goto &AutoLoader::AUTOLOAD;
             }
             else {
                 croak "Your vendor has not defined constant  
$constname";
             }
         }
         *$sub = sub { $val }; # same as: eval "sub $sub { $val }";
         goto &$sub;
     }

If any module's own AUTOLOAD subroutine has no need to fallback to the
AutoLoader's AUTOLOAD subroutine (because it doesn't have any AutoSplit
subroutines), then that module should not use B<AutoLoader> at all.

=head2 Package Lexicals

Package lexicals declared with C<my> in the main block of a package
using B<AutoLoader> will not be visible to auto-loaded subroutines,  
due to
the fact that the given scope ends at the C<__END__> marker.  A module
using such variables as package globals will not work properly under the
B<AutoLoader>.

The C<vars> pragma (see L<perlmod/"vars">) may be used in such
situations as an alternative to explicitly qualifying all globals with
the package namespace.  Variables pre-declared with this pragma will be
visible to any autoloaded routines (but will not be invisible outside
the package, unfortunately).

=head2 Not Using AutoLoader

You can stop using AutoLoader by simply

	no AutoLoader;

=head2 B<AutoLoader> vs. B<SelfLoader>

The B<AutoLoader> is similar in purpose to B<SelfLoader>: both delay the
loading of subroutines.

B<SelfLoader> uses the C<__DATA__> marker rather than C<__END__>.
While this avoids the use of a hierarchy of disk files and the
associated open/close for each routine loaded, B<SelfLoader> suffers a
startup speed disadvantage in the one-time parsing of the lines after
C<__DATA__>, after which routines are cached.  B<SelfLoader> can also
handle multiple packages in a file.

B<AutoLoader> only reads code as it is requested, and in many cases
should be faster, but requires a mechanism like B<AutoSplit> be used to
create the individual files.  L<ExtUtils::MakeMaker> will invoke
B<AutoSplit> automatically if B<AutoLoader> is used in a module source
file.

=head1 CAVEATS

AutoLoaders prior to Perl 5.002 had a slightly different interface.  Any
old modules which use B<AutoLoader> should be changed to the new calling
style.  Typically this just means changing a require to a use, adding
the explicit C<'AUTOLOAD'> import if needed, and removing B<AutoLoader>
from C<@ISA>.

On systems with restrictions on file name length, the file corresponding
to a subroutine may have a shorter name that the routine itself.  This
can lead to conflicting file names.  The I<AutoSplit> package warns of
these potential conflicts when used to split a module.

AutoLoader may fail to find the autosplit files (or even find the wrong
ones) in cases where C<@INC> contains relative paths, B<and> the program
does C<chdir>.

=head1 SEE ALSO

L<SelfLoader> - an autoloader that doesn't use external files.

=cut


From Michel.Audette at medizin.uni-leipzig.de  Mon Dec 11 12:09:08 2006
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Mon, 11 Dec 2006 18:09:08 +0100
Subject: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (but not
	1st...)
Message-ID: <160E3DD4FB702C4CB860C65186686E690114509F@MRZS152229.medizin.uni-leipzig.de>

Hi everyone, 

I am returning to an old dcm2mnc problem that has become urgent. I am trying to convert what appears to be Philips DICOM files to a minc file, and using the debugger and some printfs, I see the following... 

The first call to read_numa4_dicom() seems to go fine, for all dicom files, although I get warnings: 
WARNING: Can't find Philips slice count
WARNING: Can't find Philips slice index

as well as the following in the final stages of that 1st pass...
WARNING: Can't find Philips private creator ID.
 file list 1st pass... file_list[ifile] Schlossmacher_Marita/Schlossmacher_Marita_478.dcm (this is a printf statement I put in)
WARNING: calculated slice width (0.4499999490) disagrees with file's slice width (0.4499512000)

Error parsing file 'Schlossmacher_Marita/Schlossmacher_Marita_0.dcm' during 2nd pass.

In the 2nd pass, read_std_dicom() and  acr_input_group_list() return NULL, and within acr_input_group_list(), one call to acr_input_group_with_max() apparently returns status = ACR_PROTOCOL_ERROR...

Can anyone suggest the cause of this error in the 2nd pass, or a means to better pinpoint it? 
Also, can anyone suggest a workaround? Is the varying slice width the issue here? 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Philipp-Rosenthal-Strasse 55
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09


From a.janke at gmail.com  Mon Dec 11 22:33:18 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 11 Dec 2006 22:33:18 -0500
Subject: [MINC-users] Usage: minc_modify_header
In-Reply-To: <1A1740B4-7B41-471A-9C41-310E942FD83F@concordia.ca>
References: <1A1740B4-7B41-471A-9C41-310E942FD83F@concordia.ca>
Message-ID: <d747ed50612111933s508b5908k150c0f166d55174a@mail.gmail.com>

Hi Kent,

I can't remember as to whether there was a reply here, in any case here goes:

Unfortunately adjusting a dimensions length is about the only thing
you can't change with minc_modify_header as would change the image
size.

to change a files step in x to 1.2mm for example (which is ok!)

   minc_modify_header -dinsert xspace:step=1.2  input.mnc

to change a files size/length you will need to use mincreshape

   mincreshape -dimrange time=0,720 input.mnc output.mnc


a

On 11/16/06, conover <kent.conover at concordia.ca> wrote:
>         I would greatly appreciate it if some one would give me an example
> of how to specify the argument for the "minc_modify_header" routine.
> All I want to do is change the value for the length of the time
> dimension, but I am not sure of the variable and attribute names, or
> the exact syntax.
>
> Here is the command that I submit:
>
>  >minc_modify_header -dinsert time:length=720  minc_file_name
>
> Here is the response from the routine:
>
> -dinsert option requires argument <var>:<attr>=<val>
>
> Suggestions?
>
>
> Regards,
>
> -Kent
> _______________________________________________
> 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 a.janke at gmail.com  Tue Dec 12 00:47:38 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 12 Dec 2006 00:47:38 -0500
Subject: [MINC-users] Bug in MNI Perl routines
In-Reply-To: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>
References: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>
Message-ID: <d747ed50612112147k65abbaddy7495c7b13326aa1e@mail.gmail.com>

Hi Kent,

First, just checking that you realise that AutoLoader.pm is part of
the base perl distribution and has nothing to do with MINC.

I suspect that what you are seeing is a problem caused by some missing
dependency.  What was the error message that led you to this bit of
code?

a


On 12/7/06, conover <Kent.Conover at concordia.ca> wrote:
> Hi Everybody,
>
> There seems to be a bug in the Perl module "AutoLoader.pm" in that it
> fails to recognize my operating system as that of Mac OS X:
>
> Here is the code segment:
>
>         if (defined($filename = $INC{"$pkg.pm"})) {
>             if ($is_macos) {
>                 $pkg =~ tr#/#:#;
>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg:$func.al#s;
>             } else {
>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/$func.al#s;
>             }
>
> Upon evaluating  "if ($is_macos)", this routine jumps to the "else"
> condition. I suspect that I need to modify the file separators that
> define the $filename string somehow. I would appreciate your insights.
>
> Regards,
> -Kent

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

From Michel.Audette at medizin.uni-leipzig.de  Tue Dec 12 05:27:42 2006
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 12 Dec 2006 11:27:42 +0100
Subject: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (but
	not1st...)
References: <160E3DD4FB702C4CB860C65186686E690114509F@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011450A2@MRZS152229.medizin.uni-leipzig.de>

Hi again, 

sorry about the confusion, but I have downloaded the latest minc code (2.0.12), and the errors that I am seeing are somewhat different than in the previous message. 

Whether this information is relevant to anyone able to help me remains to be seen. The following text features snippets of the messages that I am seeing: 

Checking file types...
File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm appears to be DICOM (CD/Export).
WARNING: Failed to find image position
...
WARNING: Failed to find image position
Skipping file Schlossmacher_Marita/Schlossmacher_Marita_88.dcm, which is not in the expected format.
...
WARNING: Failed to find image position
Using 478 files
Sorting 478 files...   
num  filename                         studyid        serialno acq      nec  iec  ndy  idy  nsl  isl  acol rcol mrow img#  seq             
   0 arita/Schlossmacher_Marita_0.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
 477 rita/Schlossmacher_Marita_99.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
Done sorting files.
Processing files, one series at a time...
Using directory 'Schlossmacher_Marita_mnc/'
file_prefix:  [Schlossmacher_Marita_mnc/]

Series    0                                           ( 478 files):
     Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
...
     Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
WARNING: Image coordinates absent or incomplete.
WARNING: Slice location is untrustworthy.

File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
(I made the error message a little more descriptive...)
...
File Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
Not sorting Slice dimension
Not sorting Echo dimension
Not sorting Time dimension
Not sorting Phase dimension
Not sorting ChmSh dimension
Done processing files.

I should add that my Linux machine is 64-bit. Please advise. 

Best regards, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Mon 12/11/2006 6:09 PM
To: minc-users at bic.mni.mcgill.ca
Subject: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (but not1st...)
 
Hi everyone, 

I am returning to an old dcm2mnc problem that has become urgent. I am trying to convert what appears to be Philips DICOM files to a minc file, and using the debugger and some printfs, I see the following... 

The first call to read_numa4_dicom() seems to go fine, for all dicom files, although I get warnings: 
WARNING: Can't find Philips slice count
WARNING: Can't find Philips slice index

as well as the following in the final stages of that 1st pass...
WARNING: Can't find Philips private creator ID.
 file list 1st pass... file_list[ifile] Schlossmacher_Marita/Schlossmacher_Marita_478.dcm (this is a printf statement I put in)
WARNING: calculated slice width (0.4499999490) disagrees with file's slice width (0.4499512000)

Error parsing file 'Schlossmacher_Marita/Schlossmacher_Marita_0.dcm' during 2nd pass.

In the 2nd pass, read_std_dicom() and  acr_input_group_list() return NULL, and within acr_input_group_list(), one call to acr_input_group_with_max() apparently returns status = ACR_PROTOCOL_ERROR...

Can anyone suggest the cause of this error in the 2nd pass, or a means to better pinpoint it? 
Also, can anyone suggest a workaround? Is the varying slice width the issue here? 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Philipp-Rosenthal-Strasse 55
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09

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



From Kent.Conover at concordia.ca  Tue Dec 12 10:10:45 2006
From: Kent.Conover at concordia.ca (conover)
Date: Tue, 12 Dec 2006 10:10:45 -0500
Subject: [MINC-users] Bug in MNI Perl routines
In-Reply-To: <d747ed50612112147k65abbaddy7495c7b13326aa1e@mail.gmail.com>
References: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>
	<d747ed50612112147k65abbaddy7495c7b13326aa1e@mail.gmail.com>
Message-ID: <B0FC85F5-1D11-411D-85D7-243E585FFE5E@concordia.ca>

Hi Andrew,

I thank you for your reply. Here is the text of the error message:

fmr_preprocess_ver_mni.pl: couldn't find program "mincconcat"
fmr_preprocess_ver_mni.pl: couldn't find program "mincreshape"
fmr_preprocess_ver_mni.pl: couldn't find program "mincblur"
fmr_preprocess_ver_mni.pl: couldn't find program "mincresample"
fmr_preprocess_ver_mni.pl: couldn't find program "autocrop"
fmr_preprocess_ver_mni.pl: couldn't find program "minctracc"
fmr_preprocess_ver_mni.pl: couldn't find program "param2xfm"

Usage: fmr_preprocess_ver_mni.pl input.mnc -options

I strongly suspect that I am having path problems. I have tried many  
options, but to no avail.

Regards,

-Kent

On 12-Dec-06, at 12:47 AM, Andrew Janke wrote:

> Hi Kent,
>
> First, just checking that you realise that AutoLoader.pm is part of
> the base perl distribution and has nothing to do with MINC.
>
> I suspect that what you are seeing is a problem caused by some missing
> dependency.  What was the error message that led you to this bit of
> code?
>
> a
>
>
> On 12/7/06, conover <Kent.Conover at concordia.ca> wrote:
>> Hi Everybody,
>>
>> There seems to be a bug in the Perl module "AutoLoader.pm" in that it
>> fails to recognize my operating system as that of Mac OS X:
>>
>> Here is the code segment:
>>
>>         if (defined($filename = $INC{"$pkg.pm"})) {
>>             if ($is_macos) {
>>                 $pkg =~ tr#/#:#;
>>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg: 
>> $func.al#s;
>>             } else {
>>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/ 
>> $func.al#s;
>>             }
>>
>> Upon evaluating  "if ($is_macos)", this routine jumps to the "else"
>> condition. I suspect that I need to modify the file separators that
>> define the $filename string somehow. I would appreciate your  
>> insights.
>>
>> Regards,
>> -Kent
>
> -- 
> 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
>


From Michel.Audette at medizin.uni-leipzig.de  Tue Dec 12 11:16:37 2006
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 12 Dec 2006 17:16:37 +0100
Subject: [MINC-users] please disregard Philips dcm2mnc problem
References: <160E3DD4FB702C4CB860C65186686E690114509F@MRZS152229.medizin.uni-leipzig.de>
	<160E3DD4FB702C4CB860C65186686E69011450A2@MRZS152229.medizin.uni-leipzig.de>
	<160E3DD4FB702C4CB860C65186686E69011450A9@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011450AA@MRZS152229.medizin.uni-leipzig.de>

Hi gents, 

please disregard my previous messages on dcm2mnc problems with the Philips format. 

I've discovered the virtues of dicom3_to_minc, which works like a charm. 

Thanks also to Jonathan Harlap for saving my bacon. 

Cheers, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Tue 12/12/2006 11:27 AM
To: MINC users mailing list; minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (butnot1st...)
 
Hi again, 

sorry about the confusion, but I have downloaded the latest minc code (2.0.12), and the errors that I am seeing are somewhat different than in the previous message. 

Whether this information is relevant to anyone able to help me remains to be seen. The following text features snippets of the messages that I am seeing: 

Checking file types...
File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm appears to be DICOM (CD/Export).
WARNING: Failed to find image position
...
WARNING: Failed to find image position
Skipping file Schlossmacher_Marita/Schlossmacher_Marita_88.dcm, which is not in the expected format.
...
WARNING: Failed to find image position
Using 478 files
Sorting 478 files...   
num  filename                         studyid        serialno acq      nec  iec  ndy  idy  nsl  isl  acol rcol mrow img#  seq             
   0 arita/Schlossmacher_Marita_0.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
 477 rita/Schlossmacher_Marita_99.dcm       0.000000       -1        0   -1   -1   -1   -1   -1   -1   -1   -1   -1    -1                 
Done sorting files.
Processing files, one series at a time...
Using directory 'Schlossmacher_Marita_mnc/'
file_prefix:  [Schlossmacher_Marita_mnc/]

Series    0                                           ( 478 files):
     Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
...
     Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
WARNING: Image coordinates absent or incomplete.
WARNING: Slice location is untrustworthy.

File Schlossmacher_Marita/Schlossmacher_Marita_0.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
(I made the error message a little more descriptive...)
...
File Schlossmacher_Marita/Schlossmacher_Marita_99.dcm
ERROR: Needed values missing, marking invalid  nrows 0 ncolumns 0 bits_stored 0 bits_alloc 0 
Not sorting Slice dimension
Not sorting Echo dimension
Not sorting Time dimension
Not sorting Phase dimension
Not sorting ChmSh dimension
Done processing files.

I should add that my Linux machine is 64-bit. Please advise. 

Best regards, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Mon 12/11/2006 6:09 PM
To: minc-users at bic.mni.mcgill.ca
Subject: [MINC-users] dcm2mnc: "Error parsing file during 2nd pass" (but not1st...)
 
Hi everyone, 

I am returning to an old dcm2mnc problem that has become urgent. I am trying to convert what appears to be Philips DICOM files to a minc file, and using the debugger and some printfs, I see the following... 

The first call to read_numa4_dicom() seems to go fine, for all dicom files, although I get warnings: 
WARNING: Can't find Philips slice count
WARNING: Can't find Philips slice index

as well as the following in the final stages of that 1st pass...
WARNING: Can't find Philips private creator ID.
 file list 1st pass... file_list[ifile] Schlossmacher_Marita/Schlossmacher_Marita_478.dcm (this is a printf statement I put in)
WARNING: calculated slice width (0.4499999490) disagrees with file's slice width (0.4499512000)

Error parsing file 'Schlossmacher_Marita/Schlossmacher_Marita_0.dcm' during 2nd pass.

In the 2nd pass, read_std_dicom() and  acr_input_group_list() return NULL, and within acr_input_group_list(), one call to acr_input_group_with_max() apparently returns status = ACR_PROTOCOL_ERROR...

Can anyone suggest the cause of this error in the 2nd pass, or a means to better pinpoint it? 
Also, can anyone suggest a workaround? Is the varying slice width the issue here? 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Philipp-Rosenthal-Strasse 55
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09

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


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




From a.janke at gmail.com  Fri Dec 15 13:39:11 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 15 Dec 2006 13:39:11 -0500
Subject: [MINC-users] MINC benchmarking
Message-ID: <d747ed50612151039y1361e18fqf91c373a861926f7@mail.gmail.com>

Hi all,

In an effort to answer a few "which machine should I buy" for a few
people about the BIC I put this page together.

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

Others have contributed results so feel free to do the same.

Thanks

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

From kevin.casey at mail.mcgill.ca  Fri Dec 15 16:57:52 2006
From: kevin.casey at mail.mcgill.ca (Kevin Casey)
Date: Fri, 15 Dec 2006 16:57:52 -0500
Subject: [MINC-users] MINC packages entry for sources.list
Message-ID: <200612151657.52447.kevin.casey@mail.mcgill.ca>

Hi,
I'm using kubuntu 6.10, and I've mostly managed to configure the minc tools 
and various bic software by building it from source, but I'd like to switch 
over to the packages. I'm wondering what the exact line to add to my 
sources.list file is? I'd like the packages from 
http://packages.bic.mni.mcgill.ca/deb-minc2/
Thanks!
Kevin Casey




From sylvain at bic.mni.mcgill.ca  Fri Dec 15 17:02:33 2006
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Fri, 15 Dec 2006 17:02:33 -0500
Subject: [MINC-users] MINC packages entry for sources.list
In-Reply-To: <200612151657.52447.kevin.casey@mail.mcgill.ca>
References: <200612151657.52447.kevin.casey@mail.mcgill.ca>
Message-ID: <Pine.SGI.4.58.0612151700450.9941047@yorick.bic.mni.mcgill.ca>


add this:

deb http://packages.bic.mni.mcgill.ca/deb-minc2     ./

On Fri, 15 Dec 2006, Kevin Casey wrote:

> Hi,
> I'm using kubuntu 6.10, and I've mostly managed to configure the minc tools
> and various bic software by building it from source, but I'd like to switch
> over to the packages. I'm wondering what the exact line to add to my
> sources.list file is? I'd like the packages from
> http://packages.bic.mni.mcgill.ca/deb-minc2/
> Thanks!
> Kevin Casey
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4

From a.janke at gmail.com  Sat Dec 16 09:06:43 2006
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 16 Dec 2006 09:06:43 -0500
Subject: [MINC-users] Bug in MNI Perl routines
In-Reply-To: <B0FC85F5-1D11-411D-85D7-243E585FFE5E@concordia.ca>
References: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>
	<d747ed50612112147k65abbaddy7495c7b13326aa1e@mail.gmail.com>
	<B0FC85F5-1D11-411D-85D7-243E585FFE5E@concordia.ca>
Message-ID: <d747ed50612160606l4847c0c4heae0b164df66b075@mail.gmail.com>

Hi Kent,

check what "echo $PATH" gives you.  It should include /usr/local/mni/bin

If not add a line like this to your .bashrc (presuming you are using bash)

    export PATH=$PATH:/usr/local/mni/bin


a


On 12/12/06, conover <Kent.Conover at concordia.ca> wrote:
> Hi Andrew,
>
> I thank you for your reply. Here is the text of the error message:
>
> fmr_preprocess_ver_mni.pl: couldn't find program "mincconcat"
> fmr_preprocess_ver_mni.pl: couldn't find program "mincreshape"
> fmr_preprocess_ver_mni.pl: couldn't find program "mincblur"
> fmr_preprocess_ver_mni.pl: couldn't find program "mincresample"
> fmr_preprocess_ver_mni.pl: couldn't find program "autocrop"
> fmr_preprocess_ver_mni.pl: couldn't find program "minctracc"
> fmr_preprocess_ver_mni.pl: couldn't find program "param2xfm"
>
> Usage: fmr_preprocess_ver_mni.pl input.mnc -options
>
> I strongly suspect that I am having path problems. I have tried many
> options, but to no avail.
>
> Regards,
>
> -Kent
>
> On 12-Dec-06, at 12:47 AM, Andrew Janke wrote:
>
> > Hi Kent,
> >
> > First, just checking that you realise that AutoLoader.pm is part of
> > the base perl distribution and has nothing to do with MINC.
> >
> > I suspect that what you are seeing is a problem caused by some missing
> > dependency.  What was the error message that led you to this bit of
> > code?
> >
> > a
> >
> >
> > On 12/7/06, conover <Kent.Conover at concordia.ca> wrote:
> >> Hi Everybody,
> >>
> >> There seems to be a bug in the Perl module "AutoLoader.pm" in that it
> >> fails to recognize my operating system as that of Mac OS X:
> >>
> >> Here is the code segment:
> >>
> >>         if (defined($filename = $INC{"$pkg.pm"})) {
> >>             if ($is_macos) {
> >>                 $pkg =~ tr#/#:#;
> >>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg:
> >> $func.al#s;
> >>             } else {
> >>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/
> >> $func.al#s;
> >>             }
> >>
> >> Upon evaluating  "if ($is_macos)", this routine jumps to the "else"
> >> condition. I suspect that I need to modify the file separators that
> >> define the $filename string somehow. I would appreciate your
> >> insights.
> >>
> >> Regards,
> >> -Kent
> >
> > --
> > 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
> >
>
> _______________________________________________
> 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 Kent.Conover at concordia.ca  Mon Dec 18 09:33:44 2006
From: Kent.Conover at concordia.ca (conover)
Date: Mon, 18 Dec 2006 09:33:44 -0500
Subject: [MINC-users] Bug in MNI Perl routines
In-Reply-To: <d747ed50612160606l4847c0c4heae0b164df66b075@mail.gmail.com>
References: <9948B12C-C06B-4C57-A25E-CE413A7FA83B@concordia.ca>
	<d747ed50612112147k65abbaddy7495c7b13326aa1e@mail.gmail.com>
	<B0FC85F5-1D11-411D-85D7-243E585FFE5E@concordia.ca>
	<d747ed50612160606l4847c0c4heae0b164df66b075@mail.gmail.com>
Message-ID: <1331E785-F4AD-427E-BEA2-F6CCE5521ECE@concordia.ca>

Hi Andrew,

Thank you for these suggestions, I will try them soon!

-Kent

On 16-Dec-06, at 9:06 AM, Andrew Janke wrote:

> Hi Kent,
>
> check what "echo $PATH" gives you.  It should include /usr/local/ 
> mni/bin
>
> If not add a line like this to your .bashrc (presuming you are  
> using bash)
>
>     export PATH=$PATH:/usr/local/mni/bin
>
>
> a
>
>
> On 12/12/06, conover <Kent.Conover at concordia.ca> wrote:
>> Hi Andrew,
>>
>> I thank you for your reply. Here is the text of the error message:
>>
>> fmr_preprocess_ver_mni.pl: couldn't find program "mincconcat"
>> fmr_preprocess_ver_mni.pl: couldn't find program "mincreshape"
>> fmr_preprocess_ver_mni.pl: couldn't find program "mincblur"
>> fmr_preprocess_ver_mni.pl: couldn't find program "mincresample"
>> fmr_preprocess_ver_mni.pl: couldn't find program "autocrop"
>> fmr_preprocess_ver_mni.pl: couldn't find program "minctracc"
>> fmr_preprocess_ver_mni.pl: couldn't find program "param2xfm"
>>
>> Usage: fmr_preprocess_ver_mni.pl input.mnc -options
>>
>> I strongly suspect that I am having path problems. I have tried many
>> options, but to no avail.
>>
>> Regards,
>>
>> -Kent
>>
>> On 12-Dec-06, at 12:47 AM, Andrew Janke wrote:
>>
>>> Hi Kent,
>>>
>>> First, just checking that you realise that AutoLoader.pm is part of
>>> the base perl distribution and has nothing to do with MINC.
>>>
>>> I suspect that what you are seeing is a problem caused by some  
>>> missing
>>> dependency.  What was the error message that led you to this bit of
>>> code?
>>>
>>> a
>>>
>>>
>>> On 12/7/06, conover <Kent.Conover at concordia.ca> wrote:
>>>> Hi Everybody,
>>>>
>>>> There seems to be a bug in the Perl module "AutoLoader.pm" in  
>>>> that it
>>>> fails to recognize my operating system as that of Mac OS X:
>>>>
>>>> Here is the code segment:
>>>>
>>>>         if (defined($filename = $INC{"$pkg.pm"})) {
>>>>             if ($is_macos) {
>>>>                 $pkg =~ tr#/#:#;
>>>>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto:$pkg:
>>>> $func.al#s;
>>>>             } else {
>>>>                 $filename =~ s#^(.*)$pkg\.pm\z#$1auto/$pkg/
>>>> $func.al#s;
>>>>             }
>>>>
>>>> Upon evaluating  "if ($is_macos)", this routine jumps to the "else"
>>>> condition. I suspect that I need to modify the file separators that
>>>> define the $filename string somehow. I would appreciate your
>>>> insights.
>>>>
>>>> Regards,
>>>> -Kent
>>>
>>> --
>>> 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
>>>
>>
>> _______________________________________________
>> 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
>


From atsuko at bic.mni.mcgill.ca  Wed Dec 20 10:54:36 2006
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano)
Date: Wed, 20 Dec 2006 10:54:36 -0500
Subject: [MINC-users] coordinate flip
Message-ID: <16761c140612200754w31ab8c7atb06a8253ea0c2e5e@mail.gmail.com>

Hello all,

I converted images in Brain Voyager format into minc files.
The value for each voxel seems correct, but the x-y-z-coordinate is mixed.

I would like to flip [y z x] into [x y z] coordinate.
Please let me know how to do it easily.

Best Regards,

Atsuko

From sylvain at bic.mni.mcgill.ca  Wed Dec 20 14:53:08 2006
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Wed, 20 Dec 2006 14:53:08 -0500
Subject: [MINC-users] coordinate flip
In-Reply-To: <16761c140612200754w31ab8c7atb06a8253ea0c2e5e@mail.gmail.com>
References: <16761c140612200754w31ab8c7atb06a8253ea0c2e5e@mail.gmail.com>
Message-ID: <Pine.SGI.4.58.0612201451330.11094129@yorick.bic.mni.mcgill.ca>



Hello Atsuko,

use mincreshape:

type 'man mincreshape' for more info.

mincreshape old.mnc new.mnc -dimorder xspace,yspace,zspace


S


On Wed, 20 Dec 2006, Atsuko Nagano wrote:

> Hello all,
>
> I converted images in Brain Voyager format into minc files.
> The value for each voxel seems correct, but the x-y-z-coordinate is mixed.
>
> I would like to flip [y z x] into [x y z] coordinate.
> Please let me know how to do it easily.
>
> Best Regards,
>
> Atsuko
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4