Noise Prewhitening

Info

Currently only implemented for use with the SPI readout module.

OpenMRF allows the easy inclusion of noise pre-whitening into your sequence. In all example sequences using the SPI readout module, this will be active per default. It requires two steps:

In the sequence creation script, add the noise pre-scans after initializing the SPI readout module and before adding any other objects to the sequence structure.
```
SPI.Nnoise = 16;
SPI_add_prescans();
```
In the reconstruction script, check for pre-scans during raw data read in and, if applicable, perform the pre-whitening operation.

Without noise pre-whiteningWith noise pre-whitening

DATA = SPI_get_rawdata(twix_obj, Nnoise);
DATA = permute(DATA, [3,1,2]);
DATA(:,:,1:adcNPad)  = [];     % adc padding

if isfield(PULSEQ.SPI, 'Nnoise')
    Nnoise = PULSEQ.SPI.Nnoise;
else
    Nnoise = 0;
end
[DATA, ~, ~, ~, NOISE] = SPI_get_rawdata(twix_obj, Nnoise);
DATA = permute(DATA, [3,1,2]); % mrf rawdata
DATA(:,:,1:adcNPad)  = [];     % adc padding

% noise pre-whitening
if ~isempty(NOISE)
    NOISE = permute(NOISE, [3,1,2]);  % permute noise prescans
    NOISE(:,:,1:adcNPad) = [];        % adc padding
    DATA = mg_noise_prewhitIening(DATA, NOISE, 'cholesky', 1);
end
clear NOISE;