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

#!/usr/bin/env perl

package App::AFNI::SiemensPhysio;
use strict; 
use warnings;
use Carp;
use List::MoreUtils qw/minmax uniq/;
use File::Basename;
use feature 'say';


=pod 

=head1 NAME
 
App::AFNI:SiemensPhysio - Physio from Siemens into format suitable for AFNI's RetroTS retroicor routine

=head1 SYNOPSIS

Get slice based respiration volume per time (RVT) regressors from physio collected on Siemens scanner

  my $p = SiemensPhysio->new({VERB=>1});
  # read MR data (get times, TR, nslices)
  #  looks at all files in this directory with "dicom_hinfo"
  $p->readMRdir('MRRaw/10824_20111108/rest_384x384.21/');

  # read pulse
  $p->readPhysio('10824/20111108/wpc4951_10824_20111108_110811.puls');
  # write card: $protocol_$sessionTime.puls.dat
  $p->writeMRPhys;

  # read card
  $p->readPhysio('10824/20111108/wpc4951_10824_20111108_110811.resp');
  # write resp: $protocol_$sessionTime.resp.dat
  $p->writeMRPhys;

  # 
  $p->retroTS('matlab')

  # we could get the raw data 
  #   in this case, card was resp was loaded last
  #   thats what will be returned)
  my @pval = $p->getMRPhys();

=head1 DESCRIPTION



=head2 Pipeline

=over

=item read Siemens physio files

=item read timing from MR DICOM files

=item snip physio files relative to MR 

=item prepare/run AFNI's RetroTS

=back


=head2 prior art


=over 

=item  https://cfn.upenn.edu/aguirre/public/exvolt/

=item https://cfn.upenn.edu/aguirre/wiki/public:pulse-oximetry_during_fmri_scanning

=back

=cut



=head2 new

initialize object

=head3 OPTIONS