Dear developers,
I would like to create a Basis set for processing my MRS data. Following the README they mention I should edit the simMRS.json file and then run the run_simulations_cloud.m.
In the original JSON file, there are many parameters mostly related to a MEGA PRESS sequence, for example, “editOn”, “editOff”, “editTP”, and “editTarget”. I am using a PRESS sequence, therefore I thought I would erase them and/or set them to 0. However, as I run the simulation, I got errors due to this editing.
Do you have any recommendations in what to set these values to, or should I leave them as they are, and the code will identify that I am using a PRESS sequence, therefore it will ignore this info for the simulations?
Below, I am copying the original JSON file input and the JSON input following my analysis.
Thank you so much in advance for your help!!
-----------> original JSON
{
“userInput”: {
“metablist”: [“Ch”,“GABA”,“Glu”,“Lac”,“mI”,“PCh”,“PCr”],
“FieldStr”: [“3T”],
“vendor”: [“Philips”],
“mega_or_hadam”: [“UnEdited”],
“localization”: [“PRESS”],
“editTarget”: [“GABA”],
“TE”: 35,
“editOn”: 1.9,
“editOff”: 7.5,
“editTp”: 20,
“spatial_points”: 101,
“tm”: 30
},
“private”: {
“metab_default”: [“Cr”,“NAA”,“H2O”,“CrCH2”],
“flipAngle”: 180,
“centreFreq”: 3.0,
“edit_flipAngle”: 180,
“excflipAngle”: 90
},
“DIRECTORY”:{
“save_dir”: “C:/Users/SHUI/Documents/MATLAB/MRSCloud/save_dir/”,
“work_dir”: “C:/Users/SHUI/Documents/MATLAB/MRSCloud”,
“outputFile”: “C:/Users/SHUI/Documents/MATLAB/MRSCloud/mrs_sim_out.zip”
}
}
-------------> edited by me
{
“userInput”: {
“metablist”: [“NAA”,“Cr”,“Ch”,“Glu”,“PCh”,“PCr”],
“FieldStr”: [“3T”],
“vendor”: [“Philips”],
“mega_or_hadam”: [“UnEdited”],
“localization”: [“PRESS”],
“editTarget”: [“GABA”],
“TE”: 36,
“editOn”: 0,
“editOff”: 0,
“editTp”: 0,
“spatial_points”: 41,
“tm”: 30
},
“private”: {
“metab_default”: [“Cr”,“NAA”,“H2O”,“CrCH2”],
“flipAngle”: 180,
“centreFreq”: 3.0,
“edit_flipAngle”: 180,
“excflipAngle”: 90
},
"DIRECTORY":{
"save_dir": "/home/juliana/Documents/klifoanae/propofolstudy/Analyses/spectroscopy/BASIS/MRSCloud/PRESS_TE35",
"work_dir": "/home/juliana/Downloads/MRSCloud",
"outputFile": "/home/juliana/Downloads/MRSCloud/mrs_sim_out.zip"
}
}