NAME

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

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();

DESCRIPTION

Pipeline

read Siemens physio files

read timing from MR DICOM files

snip physio files relative to MR

prepare/run AFNI's RetroTS

prior art

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

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

new

initialize object

OPTIONS

timetype

MDH (default) or MPCU

PhRate

Physio sample rate defaults to .2

pulsStart and respStart numeric sequence to be remove, also identifies stream type

defaults:

  pulsStart =>'1 2 40 280'
  respStart =>'1 2 20 2'

sliceOrder

alt+z (default) other options: alt-z,seq+z,seq-z,filename # slice order

VERB

set to true to be verbose, defaults false

trustIdx

don't check sample rate and index count against end-start time none=> check both MR => trust MR (TR) phys=> trust physio (PhRate as set by init) all => trust both

Note: just have to match reg exp, so MRphys is same as all

readPhysio

after intializing p, provide a file name

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

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
 RESP Min Max Avg StdDiff: 2380 6700 3477 86
 EXT  Min Max Avg StdDiff: 0 0 0 0
 NrTrig NrMP NrArr AcqWin: 0 0 0 0
 LogStartMDHTime:  66439690
 LogStopMDHTime:   71116595
 LogStartMPCUTime: 66439512
 LogStopMPCUTime:  71114802
 6003

readMRdir

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

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

sets

timing (MRstart and MRend)

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

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*

writeMRPhys

write phys during MR to file works on most recently loaded physio file

  $p->writeMRPhys

use getMRphys to get values

use writeDat to write values

retroTS

This is kludgy code hacked together and untested :) =over

use a bunch of hacks to find the matlab binary

construct a matlab call using options in self object

execute matlab or McRetroTS

move outputs to fit local naming convention

get/run command to get Resp. Vol./Time (RVT) via AFNI's retroTS a la http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715870/ MUST have already read MR and written card and resp dat files

  $p->retroTS('matlab')

how this step is handled is defined by the first argument

matlab: use RetroTS.m

McRetroTs: use compiled matlab verson of RetroTS.m

show: print commands for both matlab and McRetroTS

none: do nothing (why'd you call me then!?)

External Commands

see

http://afni.nimh.nih.gov/afni/matlab/

http://afni.nimh.nih.gov/sscc/dglen/McRetroTS

http://fieldtrip.googlecode.com/svn/trunk/external/afni/RetroTS.m

if using matlab+retroTS, the path to retroTS.m should be in your MATLABPATH export MATLABPATH="$HOME/afni_matlab/matlab/:$MATLABPATH"

cpanm App::AFNI::SiemensPhysio

perl -MCPAN -e shell
install App::AFNI::SiemensPhysio