App-AFNI-SiemensPhysio

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

 
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();

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

    $self->{$k} = $defaults{$k} unless $self and $self->{$k};
  }

  return bless $self, $class;
}

=head2 readPhysio

after intializing p, provide a file name

 $p->readPhysio('10824/20111108/wpc4951_10824_20111108_110811.puls');

=head3 input file format

 1 2 40 280 ...
 ECG  Freq Per: 0 0
 PULS Freq Per: 74 807
 RESP Freq Per: 20 2860
 EXT  Freq Per: 0 0
 ECG  Min Max Avg StdDiff: 0 0 0 0
 PULS Min Max Avg StdDiff: 527 1586 828 4

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

             $self->{physEnd},
             $#{$self->{measures}},
             $self->{PhRate} ) unless $self->{trustIdx}=~/All|Phys/i;
}


=head2 readMRdir

after intializing p, read in MR info from raw DICOM directory

  $p->readMRdir('MRRaw/10824_20111108/rest_384x384.21/');

sets 

=over

=item timing (MRstart and MRend)

=item protcol info (protocol,TR,ET,nslices,Series)

=back

=head3 Example Info

dicom header info

  dicom_hdr MRRaw/10824_20111108/rest_384x384.21/MR* |egrep 'protocol|acquisition Time|Echo Time|Repetition Time' -i
    0008 0031       14 [620     ] //                 ID Series Time//164627.359000
    0008 0032       14 [642     ] //            ID Acquisition Time//164932.315000 
    0018 0080        4 [1418    ] //            ACQ Repetition Time//1500
    0018 0081        2 [1430    ] //                  ACQ Echo Time//29
    0018 1030        4 [1612    ] //              ACQ Protocol Name//rest
    0019 100a        2 [1788    ] //                               // 29

shortend to

  dicom_hinfo -tag 0008,0032 0008,0031 0018,0080 0018,0081 0018,1030 MR*

prepareForDemo.bash  view on Meta::CPAN

   done
fi

# make an output directory to save files to
# (git wont track empty folders)
[ ! -d data/phys ] && mkdir data/phys/

# exvolt (extract voltage) is a c++ program that should do about the same thing
#    it is shifted by 340 msecs (17 samples)?
[ ! -r exvolt ] && wget https://cfn.upenn.edu/aguirre/public/exvolt/exvolt
# ./exvolt  ../App-AFNI-SiemensPhysio/data/MR ../App-AFNI-SiemensPhysio/data/wpc4951_10824_20111108_110811.resp test.dat


echo "
TRY:

  perl -Ilib lib/bin/siemphysdat -o data/phys/ data/wpc4951_10824_20111108_110811.* data/MR/

Then look in data/phys/
"

readme.mkdn  view on Meta::CPAN

# siemphysdat <img height=100 widht=100 align=right src=https://raw.githubusercontent.com/LabNeuroCogDevel/siemphysdat/master/icon.png>

Utility to chop physio measures (voltages) from Siemens Physiologic Monitoring Unit (PMU) and generate respiration volume per time (RVT) regressors for a single MR protocol with AFNI's `RetroTS.m`

This is for you if you want  `1D` inputs for `3dretroicor` or `afni_proc.py` (`ricor` block) and have physio recordings (`*.resp` and `*.puls`) files the look like [this](data/wpc4951_10824_20111108_110811.puls):

```
1 2 40 280 ...
ECG  Freq Per: 0 0
PULS Freq Per: 74 807
RESP Freq Per: 20 2860
....
6003
```