Processing 2-D Data

phantom_2d_workflow

BASH

# create phantom with 2D spectral encoding
#Phantom generation
create_phantom.sh -acqfile data/acq_phantom.txt -spectfile data/Phantom_spect.txt -outfolder Phantom2D

spectEstimation.sh Phantom2D/Phantom_data.mat  Phantom2D/Phantom_mask .mat \
    Phantom2D/Phantom_spectrm_info.mat  demos/Phantom_ladmm.ini  Result/Phantom_ladmm_spect .mat

#spectrum Estimation --admm
# spectEstimation Phantom2D/Phantom_data.mat  Phantom2D/Phantom_mask .mat \
#     Phantom2D/Phantom_spectrm_info.mat  demos/Phantom_admm.ini  Result/Phantom_admm_spect .mat
# 
#spectrum Estimation --nnls
# spectEstimation Phantom2D/Phantom_data.mat  Phantom2D/Phantom_mask .mat \
#     Phantom2D/Phantom_spectrm_info.mat  demos/Phantom_nnls.ini  Result/Phantom_nnls_spect .mat

#plot Average spectra
plotAvgSpectra Result/Phantom_ladmm_spect .mat   Phantom2D/Phantom_mask .mat \
    Result/Phantom_data_ladmm_avg_spectra  png pdf

# Plot spectroscopic image
idx=1; #encoding sample chosen to show back ground MR data intensity
plotspectIm Result/Phantom_ladmm_spect.mat  Phantom2D/Phantom_data.mat $idx \
    Phantom2D/Phantom_mask .mat Result/Phantom_spectroscopic_Im  png

# Plot component Maps
plotCompMaps Result/Phantom_ladmm_spect.mat  data/spectrum_mask_inj_mouse.mat \
    data/four_color.mat  Result/Phantom_component_maps  png epsc

MATLAB

% create phantom with 2D spectral encoding
%Phantom generation
create_phantom('acqfile','data/acq_phantom.txt','spectfile','data/Phantom_spect.txt','outfolder','Phantom2D') %or create_phantom
%spectrum Estimation --ladmm
spectEstimation('Phantom2D/Phantom_data.mat', 'Phantom2D/Phantom_mask.mat', ...
    'Phantom2D/Phantom_spectrm_info.mat', 'demos/Phantom_ladmm.ini', 'Result/Phantom_ladmm_spect.mat')

%spectrum Estimation --admm
% spectEstimation('Phantom2D/Phantom_data.mat', 'Phantom2D/Phantom_mask.mat', ...
%     'Phantom2D/Phantom_spectrm_info.mat', 'demos/Phantom_admm.ini', 'Result/Phantom_admm_spect.mat')
% 
%spectrum Estimation --nnls
% spectEstimation('Phantom2D/Phantom_data.mat', 'Phantom2D/Phantom_mask.mat', ...
%     'Phantom2D/Phantom_spectrm_info.mat', 'demos/Phantom_nnls.ini', 'Result/Phantom_nnls_spect.mat')

%plot Average spectra
plotAvgSpectra('Result/Phantom_ladmm_spect.mat',  'Phantom2D/Phantom_mask.mat', ...
    'Result/Phantom_data_ladmm_avg_spectra', 'png','pdf');

% Plot spectroscopic image
idx=1;%encoding sample chosen to show back ground MR data intensity
plotspectIm('Result/Phantom_ladmm_spect.mat', 'Phantom2D/Phantom_data.mat',idx, ...
    'Phantom2D/Phantom_mask.mat','Result/Phantom_spectroscopic_Im', 'png')

% Plot component Maps
plotCompMaps('Result/Phantom_ladmm_spect.mat', 'data/spectrum_mask_inj_mouse.mat', ...
    'data/four_color.mat', 'Result/Phantom_component_maps', 'png', 'epsc');