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# 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
```


## Usage

```bash
siemphysdat respfile pulsefile MRdir
```

look for new `*dat` (chopped physio) and `*slibase.1D` (RVT regressors, ready for `-ricor` in `afni_proc.py`) files

### Example/Practice
run [`./prepareForDemo.bash`](prepareForDemo.bash) and follow instructions.

works on files included in [`data/`](data/) and save output to `data/phys`

### Help
see `siemphysdat -h`, `perldoc siemphysdat`, or `./prepareForDemo.bash` 


## Install

```bash
cpanm App::AFNI::SiemensPhysio
```

Hint: get [cpanm](http://search.cpan.org/~miyagawa/App-cpanminus-1.7019/lib/App/cpanminus.pm) like `curl -L https://cpanmin.us | perl - --sudo App::cpanminus`

### From this source
with [Dist::Zilla](http://dzil.org/)
```bash
dzil build
dzil install
```


## Trouble Shooting/Dependencies
### RetroTS.m in path
You should have [afni's matlab scripts](http://afni.nimh.nih.gov/afni/download/afnimatlab/releases/latest) and they should be your [`MATLABPATH`](http://www.mathworks.com/help/matlab/ref/path.html) (e.g. `export MATLABPATH="$HOME/afni_matlab:$MATLABP...

### dicom_hinfo in path
[`dicom_hinfo`](http://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hinfo.html) from [AFNI](http://afni.nimh.nih.gov/afni/download) is used to read slice timing, TR, and MR times. This must be in `PATH`. 

See `which dicom_hinfo` to check.

## See Also/Alternatives
`exvolt` as described by the [Aguirre Lab @ UPenn](https://cfn.upenn.edu/aguirre/wiki/public:pulse-oximetry_during_fmri_scanning)
 * https://cfn.upenn.edu/aguirre/public/exvolt/
 * https://cfn.upenn.edu/aguirre/wiki/public:pulsecomplete_source
 * http://www.nitrc.org/projects/voxbo/

## Name