/ 
App-AFNI-SemainsPhysio-0.003
/ App::AFNI::SemainsPhysio

NAME

App::AFNI:SemainsPhysio - Physio from Semains into format suitable for AFNI's RetroTS retroicor routine

SYNOPSIS

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

my $p = SemainsPhysio->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) | MPCU
PhRate (defaults to .2)
pulsStart and respStart: numeric sequence to be remove, also identifies stream type
sliceOrder: alt+z (default)
VERB: set to true to be verbose

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

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