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lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

 say $matlabwrap if $runtype !~ /matlab|McRetroTs/i;
 # eg
 # matlab -nodisplay -r "try; Opts.Cardfile='rest_164627.359000.puls.dat'; Opts.VolTR=1.5; Opts.Nslices=29; Opts.SliceOrder='alt+z'; Opts.PhysFS=50.0074711455304; Opts.Respfile='rest_164627.359000.resp.dat'; rts = RetroTS(Opts); catch; exit(666); end...

 # with either command, the original output name will be "oba.slibase.1D"
 # change that to our basename (assume resp and puls have same basename, use one from resp)
 my $outputname = $self->{dat}->{resp};
 $outputname =~ s/.resp.dat$/.slibase.1D/;
 
 # or rename to specified input
 #my $outputname=shift if $#_;
 
 
 my $runcmd="";
 if($runtype =~ /matlab/i){
  $runcmd=$matlabwrap
 }elsif($runtype =~ /McRetroTs/i){
  $runcmd=$mccmd;
 }

 system($runcmd) if $runcmd;

 if( $runcmd && ! -e "oba.slibase.1D" ){
   croak "failed to run $runcmd";
 } else {
   # move file to output name if told to
   rename "oba.slibase.1D", $outputname if $outputname;
 }
}



#################
#### helpers ####
#################