[MINC-users] dcm2mnc and long attribute fields

[Soren Christensen]

Thanks Andrew,
 That explains it - had not thought of the command line as the problem.
We'll work around it, thanks for the script.

Cheers
Soren

On Tue, Jun 23, 2009 at 3:55 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren
>
> >  Someone at the department here had a problem that seems to be related
> > to dcm2mnc behaviour.
> > When dcm2mnc is run on a large number of dicom files, the parsed files
> > contain attribute with all the names of the files used as argument.
> >
> > It seems minc_modify_header can have problems with long attribute fields.
> > Here's output from an mritoself on a couple of files:
>
> Yes, this certainly is a (more general) problem with long attributes
> that typically are DICOM related. Given that the root "cause" of this
> is that the size of arguments on the C/L is limited you could just
> increase the size of ncargs in your kernel to get around this.
>
> My attack plan for such things is to simply strip all the dicom bits
> out of the header before further processing using something like the
> following (perl) script that I affectionately call
> "minc_de-dicomerise".
>
> ----
> #! /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
> #
> # USE AT OWN RISK!  THIS MAY MUNGE YOUR MINC FILES HEADER!
>
> use warnings "all";
> use File::Basename;
>
> $me = &basename($0);
> if($#ARGV == -1){
>   die "\n+++WARNING: THIS SCRIPT MAY MUNGE YOUR FILE PERMANENTLY!+++\n\n".
>       "Usage: $me <file1_to_clean.mnc> [<file2.mnc> [...]]\n\n";
>   }
>
> foreach $file (@ARGV){
>   print " + Working on $file\n";
>
>   (@yukky_vars) = split(' ', `mincinfo -varnames $file`);
>
>   foreach $var (grep {/dicom/} @yukky_vars){
>      foreach (split(' ', `mincinfo -varatts $var $file`)){
>         print " | [$file] - removing $var:$_\n";
>         system('minc_modify_header', '-delete', "$var:$_", $file) == 0 or
> die;
>         }
>      }
>   }
> ----
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
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