8. Phantom Data

DRSuite also provides a tool to generate synthetic multicontrast phantom data with from a known ground-truth spectroscopic image, and accommodates custom diffusion-relaxation encoding schemes. This can be useful for evaluating and comparing the performance of different acquisition protocols and spectrum estimation methods.

The numerical phantom is designed to possess interesting spectroscopic image features, and was obtained by simplifying the features observed in the mouse spinal cord injury datasets reported in the following paper (which should be cited, along with DRSuite, when using this phantom):

    1. Kim, E. K. Doyle, J. L. Wisnowski, J. H. Kim, J. P. Haldar. Diffusion-Relaxation Correlation Spectroscopic Imaging: A Multidimensional Approach for Probing Microstructure. Magnetic Resonance in Medicine 78:2236-2249, 2017. <https://dx.doi.org/10.1002/mrm.26629>

_images/true_spect_image_avg_spectra.png

Ground-truth structure of the phantom.

Phantom data can be generated using the following command:

create_phantom.sh -acqfile acqfile_name -spectfile spectfile_name -multislice tf -outfolder outfolder_name

create_phantom('acqfile','___','spectfile','___','outfolder','___','multislice','___')

8.1. Optional Inputs

  • acqfile:

    Filename of the .txt file storing combinations of (b, TE) values where MR data will be sampled.

    b is in ms/µm² and TE is in ms.

    If omitted, defaults to a built-in 7×7 grid: b = [0 200 500 1000 1500 2500 5000]*1e-3 (\(ms/ \mu m^2\)) and TE = [99 120 160 200 250 300 400] (in \(ms\)).

    The code infers data type and spectrum information automatically:

    • only TE changes → 1D T2 phantom

    • only b changes → 1D Diffusion phantom

    • both change → D–T2 phantom

    Create a text file (e.g. acq_params.txt):

    b_1,TE_1
b_2,TE_2
...
b_n,TE_n

    For 1D Diffusion data, keep TE constant:

    b_1,TE_1
b_2,TE_1
...
b_n,TE_1

    For 1D T2-Relaxation data, keep b constant:

    b_1,TE_1
b_1,TE_2
...
b_1,TE_m

    Notes:

    • This Phantom generation tool is very sensitive to this format. If given in other format, the tool wont work.

  • spectfile:

    Filename of the .txt file storing information to create spectral sampling points along D and T2 dimensions. Used to build the dictionary matrix for spectrum estimation.

    • If both acqfile and spectfile are not provided, the spectfile defaults to the example given on the below.

    • If acqfile is provided but spectfile is not omitted, then it automatically detects the datatype and uses the default values as given below. While for both the 1D and 2D spectrum, the end points and the spacing type of the spectral grid remains the same, for 1D datatype, it uses 300 spectral grid points by dafult.

    Create a text file (e.g. spect_params.txt):

    D_min=0.01;
D_max=3;
D_spacing='log';
D_num=70;
T2_min=3;
T2_max=300;
T2_spacing='log';
T2_num=70;

    Notes:

    • The above example also comprises of the default values in the spectfile.

    • This Phantom generation tool is very sensitive to the variable names used in the above example. If any other names are used, the tool won’t work.

    • D_min, D_max should be in \(ms/ \mu m^2\); T2_min, T2_max in \(ms\).

    • D_spacing and T2_spacing can only take 'linear' or 'log'.

    • For 1D phantoms, include only relevant parameters (either D or T2).

  • multislice:

    Logical flag:

    1 → Generate five 2D slices.

    0 → Generate single 2D slice.

    Default: 0.

    Example (command line):

    create_phantom.sh -multislice 1

  • outfolder:

    Folder name where the output files will be stored. Default: Phantom (created in the current directory).

    Example:

    create_phantom.sh -outfolder "Phantom_Test"

Warning

The user is recommended to provide an input corresponding to the outfolder. Not providing a folder name will rewrite the contents of the default folder named Phantom.

8.2. Outputs

The following files are saved in the folder name specified by outfolder:

  • Phantom_data.mat:

    Stores the information related to 2D/3D spatial diffusion-relaxation MR data. Same structure as here (input to spectrum estimation tool).

  • Phantom_spectrum_info.mat:

    Stores information related to the spectrum. Structure follows format here.

  • Phantom_mask.mat:

    Spatial mask file for the MR data. Structure follows format here.

  • Phantom_mask_beta_calc.mat:

    Spatial mask file for (L)ADMM parameter beta calculation. Structure follows format here.