This recon is now obsolete. Here is a better, unified offline and online recon: https://github.com/usc-mrel/PulseqGadgetronRecon

General pipeline

Siemens .dat -> MRD -> mrd2mat4mapping.m -> preproc4mapping.m -> main_XXmap.m -> NistPhantomTXROIAnalysis.m

1. Using siemens_to_ismrmrd command, raw data and noise measurements should be exported as following:

DATA_ROOT/
|- data_folder/
    |- dcm/ (if exists)
    |- raw/
        |- meas_XXXXX.dat
            .
            .
            .
        |- h5/
            |- meas_XXXXX.h5
                .
                .
                .
        |- noise/
            |- noise_meas_XXXXX.h5
                .
                .
                .

2. mrd2mat4mapping.m converts, reconstructs and shows the images using MRD acquisition and noise datasets for a given measurement.

3. Preproc4Mapping.m allows us to select the slice, extracts the vial masks and specify the vial set we are looking into (MnCl2 or NiCl2).

4. main_XXmap.m depending on the T1 T2 or B1 mapping, calculates the required map. B1 map is a dependency to T1 map.

5. NistPhantomTXROIAnalysis.m depending on T1 or T2 mapping, calculates the mean and std of individual vials, and compares them with given reference values.