[MINC-users] mnc2nii, orientation of nii file

[Andrew Janke]

Correct!

Of course the original Radio vs Neuro thnig only came about when a
surgeon (who we presume was a neurologist) decided to put the X-Ray
"the other way" on a viewer because they were operating from the head
of the patient! :)

a

On 3/11/07, Soren Christensen <sorench at gmail.com> wrote:
> Hi Andrew,
>  Thanks for that, will try out but I might just stick with doing the
> "radiologicalisation" in FSL to keep the MINC file correct.
>
> After some thinking I think I understand that radiological is a display issue.
> I guess there is a mapping from voxels coordinates to real world
> coordinates and then there is a mapping onto the display on top of
> that (determining if we see the data radiologically or
> neurologically). It seems the two mappings are often lumped together
> leading to a lot of confusion.
>
> Thanks for the help!
>
> Soren
>
>
> On 3/11/07, Andrew Janke <a.janke at gmail.com> wrote:
> > Hi Soren,
> >
> > <soapbox>
> > Radio vs Neuro _should_ be something that concerns display of an image only.
> > Certain other packages think differently... :)
> > </soapbox>
> >
> > MINC will never allow you to "flip" data about in a file unless you
> > specificaly transform it or do some dodgy tricks as will be
> > illustrated in the file I am attaching!
> >
> > What you are doing with the -xdirection is to flip the voxel data
> > about and _also_ flip the step direction, so the data ends up the same
> > as what it was.
> >
> > That all said, use the script below (that I call volflip) to achieve
> > what you want. (I think I turned attachments off on this list)
> >
> >
> > a
> >
> >
> > ----- cut here ----
> >
> > #! /usr/bin/env perl
> > #
> > # Andrew Janke - rotor at cmr.uq.edu.au
> > # Center for Magnetic Resonance
> > # The University of Queensland
> > # http://www.cmr.uq.edu.au/~rotor
> > #
> > # Copyright Andrew Janke, The University of Queensland.
> > # Permission to use, copy, modify, and distribute this software and its
> > # documentation for any purpose and without fee is hereby granted,
> > # provided that the above copyright notice appear in all copies.  The
> > # author and the University of Queensland make no representations about the
> > # suitability of this software for any purpose.  It is provided "as is"
> > # without express or implied warranty.
> >
> > use strict;
> > use warnings "all";
> > use Getopt::Tabular;
> > use File::Basename;
> > use File::Temp qw/ tempdir /;
> >
> > my($Help, $Usage, $me);
> > my(@opt_table, %opt, $infile, $outfile, @args, $tmpdir);
> >
> > $me = &basename($0);
> > %opt = (
> >   'verbose'   => 0,
> >   'clobber'   => 0,
> >   'fake'      => 0,
> >   'direction' => 'x',
> >   );
> >
> > $Help = <<HELP;
> > | $me flips a volume about its centre (volume not world) there
> > |    are far easier ways to flip a volume about its world centre
> > |    than this.
> > |
> > | Problems or comments should be sent to: rotor\@cmr.uq.edu.au
> > HELP
> >
> > $Usage = "Usage: $me [options] <infile.mnc> <outfile.mnc>\n".
> >         "       $me -help to list options\n\n";
> >
> > @opt_table = (
> >   ["-verbose", "boolean", 0, \$opt{verbose},
> >      "be verbose" ],
> >   ["-clobber", "boolean", 0, \$opt{clobber},
> >      "clobber existing check files" ],
> >   ["-fake", "boolean", 0, \$opt{fake},
> >      "do a dry run, (echo cmds only)" ],
> >
> >   ["-x", "const", 'x', \$opt{direction},
> >      "flip volume in x-plane (default)" ],
> >   ["-y", "const", 'y', \$opt{direction},
> >      "flip volume in y-plane" ],
> >   ["-z", "const", 'z', \$opt{direction},
> >      "flip volume in z-plane" ],
> >   );
> >
> > # check args
> > &Getopt::Tabular::SetHelp($Help, $Usage);
> > &GetOptions(\@opt_table, \@ARGV) || exit 1;
> > die $Usage if($#ARGV != 1);
> > $infile = shift(@ARGV);
> > $outfile = shift(@ARGV);
> >
> > # check for files
> > die "$me: Couldn't find input file: $infile\n" if (!-e $infile);
> > if(-e $outfile && !$opt{clobber}){
> >   die "$me: $outfile exists, -clobber to overwrite\n";
> >   }
> >
> > # make tmpdir
> > $tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );
> >
> > my($step);
> >
> > # get file start and step info
> > chomp($step = `mincinfo -attvalue $opt{direction}space:step $infile`);
> >
> > # first make sure we don't get bitten by slice normalisation
> > &do_cmd('mincreshape', '-clobber',
> >        '-normalize',
> >        $infile, "$tmpdir/nrm.mnc");
> > # reshape
> > &do_cmd('mincreshape', '-clobber',
> >        '-dimsize', "$opt{direction}space=-1",
> >        ($step > 0) ? "-$opt{direction}direction" :"+$opt{direction}direction",
> >        "$tmpdir/nrm.mnc", "$tmpdir/res.mnc");
> >
> > # create template image and copy data
> > &do_cmd('cp', '-f', "$tmpdir/nrm.mnc", $outfile);
> > &do_cmd('minccopy', "$tmpdir/res.mnc", $outfile);
> >
> >
> > sub do_cmd {
> >   print STDOUT "@_\n" if $opt{verbose};
> >   if(!$opt{fake}){
> >      system(@_) == 0 or die;
> >      }
> >   }
> >
> >
> >
> > --- fin ---
> >
> >
> > On 3/11/07, Soren Christensen <sorench at gmail.com> wrote:
> > > Hi,
> > >  I have a coronal MRI that are have re-oriented to x,y,z data-order
> > > with all posetive stepsizes as described by Andrew on
> > > http://brainbody.nottingham.ac.uk/users/wiki/pmwiki.php?n=MincUsersGroup.FAQDataFormats
> > >
> > > The directional cosines are othogonal, posetive and increasing in the
> > > size of the dimension (eg 1,0,0 for x).
> > >
> > > When I run mnc2nii the resulting nifti files comes out as neurological.
> > > I'd like it to be radiological since FSL seems to not be completely
> > > independent of the voxel data storage order.
> > >
> > > Is there something I can do to make mnc2nii output it radiologically?
> > > I thought that reshaping with -xdirection might work but it doesn't.
> > >
> > > Alternatively I guess I could change the nii file order+orienteation
> > > using the FSL tools but I'd like to understand why it does not seem
> > > possible with mnc2nii.
> > >
> > > 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 || http://a.janke.googlepages.com/)
> > Canberra->Australia    +61 (402) 700 883
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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