Accessing Testing Data Set

Overview

The 2024 MRSI Data Processing and Quantitation Challenge will test the ability of data processing and spectral analysis pipelines to create accurate metabolite maps from a group of FID-MRSI data sets simulated using in vivo experimental data. The Challenge contains two sub-challenges:

  • Sub-Challenge 1: Perform nuisance signal removal and spectral quantification on (x,t)-space MRSI data contaminated by noise, baseline signals, spectral distortions, residual water signals, and unsuppressed lipid signals.
  • Sub-Challenge 2: Perform spectral quantification on (x,t)-space MRSI data contaminated by noise, baseline signals, and spectral distortions.

Interested groups are encouraged to participate in either or both of the challenges.

Note. You do NOT have to be attending the ISMRM MRS Workshop in October to participate in this challenge.

1. Testing Data for Sub-Challenge 1

Box folder links will be emailed to each Team as data is released. As with the Training data, the Testing data folders will contain subdirectories with the MRI/FID-MRSI data in NIfTI and NIfTI-MRS formats as well as MATLAB .mat format. There are in total five Testing datasets with different SNR levels, nuisance signal levels, and/or different baseline parameters for Sub-Challenge 1.

Image data files provided in NIfTI format, (nx, ny, nz) array:

  • xxx_mri_t1w_mpr.nii.gz - T1w image stack
  • xxx_mri_b0_map.nii.gz - B0 map (in Hz) image stack
  • xxx_brain_mask.nii.gz - Brain mask image stack

Spectral data files provided in NIfTI-MRS format array:

  • xxx_mrs_fids_si_data.nii.gz – (x,t)-space data for FID-MRSI data, which contains residual water signals, unsuppressed lipid signals, metabolite signals (along with macromolecular signals), and noise, with the same acquisition parameters as the Training data:
    • matrix = 64,64,32,384 (nx,ny,nz,nt)
    • TR/TE = 450ms/1.66 ms
    • dwell time = 0.83 ms
    • center frequency = 127.7 MHz
    • All data formats have been co-registered

The same data are also provided in an MATLAB .mat file (xxx_all.mat)

  • B0map (64x64x32) - B0 map in Hz
  • Iref (64x64x32) - T1w image at the resolution of the metabolite maps
  • brainMask (64x64x32) - Brain mask
  • xtAll (64x64x32x384) - (x,t)-space data for FID-MRSI data, which contains residual water signals, unsuppressed lipid signals, metabolite signals (along with macromolecular signals), and noise, with the same acquisition parameters as the Training data.

The .mat file includes the following additional information

  • IrefHr (128x128x64) – High-resolution T1w image
  • VtMM (10x386) – The first to the ninth row of VtMM contains the temporal basis functions of macromolecular signals for t = 0, , …, 385 , where = 0.83 ms is the dwell time. The last row contains the basis of Cr at 3.9 ppm as a reference.
  • Vt (16x386) – The temporal basis functions of the following metabolites for t = 0, , …, 385: ‘Asp’; ‘GABA’; ‘Gln’; ‘Glu’; ‘Lac’; ‘Lac41’; ‘NAA’; ‘NAAG’; ‘PE’; ‘PE40’; ‘Tau’; ‘mIns’; ‘sIno’; ‘tCho’; ‘tCr’; ‘tCr39’;
  • t (1x384) – Time domain sampling grid of the MRSI data, i.e., t = 2 , 3 , …, 385
  • hzpppm – Herz per ppm
  • ppmoff – Offset for display purpose

2. Testing Data for Sub-Challenge 2

Box folder links will be emailed to each Team as data is released. As with the Training data, the Testing data folders will contain subdirectories with the MRI/FID-MRSI data in NIfTI and NIfTI-MRS formats as well as MATLAB .mat format. There are in total three Testing datasets with different SNR levels and/or different baseline parameters for Sub-Challenge 2.

Image data files provided in NIfTI format, (nx, ny, nz) array:

  • xxx_mri_t1w_mpr.nii.gz - T1w image stack
  • xxx_mri_b0_map.nii.gz - B0 map (in Hz) image stack
  • xxx_brain_mask.nii.gz - Brain mask image stack

Spectral data files provided in NIfTI-MRS format array:

  • xxx_mrs_fids_si_data.nii.gz – (x,t)-space data for FID-MRSI data, which contains metabolite signals (along with macromolecular signals) and noise, with the same acquisition parameters as the Training data:
    • matrix = 64,64,32,384 (nx,ny,nz,nt)
    • TR/TE = 450ms/1.66 ms
    • dwell time = 0.83 ms
    • center frequency = 127.7 MHz
    • All data formats have been co-registered

The same data are also provided in an MATLAB .mat file (xxx_all.mat)

  • B0map (64x64x32) - B0 map in Hz
  • Iref (64x64x32) - T1w image at the resolution of the metabolite maps
  • brainMask (64x64x32) - Brain mask
  • xtAll (64x64x32x384) - (x,t)-space data for FID-MRSI data, which contains metabolite signals (along with macromolecular signals) and noise, with the same acquisition parameters as the Training data.

The .mat file includes the following additional information

  • IrefHr (128x128x64) – High-resolution T1w image
  • VtMM (10x386) – The first to the ninth row of VtMM contains the temporal basis functions of macromolecular signals for t = 0, , …, 385 , where = 0.83 ms is the dwell time. The last row contains the basis of Cr at 3.9 ppm as a reference.
  • Vt (16x386) – The temporal basis functions of the following metabolites for t = 0, , …, 385: ‘Asp’; ‘GABA’; ‘Gln’; ‘Glu’; ‘Lac’; ‘Lac41’; ‘NAA’; ‘NAAG’; ‘PE’; ‘PE40’; ‘Tau’; ‘mIns’; ‘sIno’; ‘tCho’; ‘tCr’; ‘tCr39’;
  • t (1x384) – Time domain sampling grid of the MRSI data, i.e., t = 2 , 3 , …, 385
  • hzpppm – Herz per ppm
  • ppmoff – Offset for display purpose

3. Miscellaneous Topics

Note that in the context of this Challenge, the area is defined as the following:

\[s(n\delta t) = \sum_{m=1}^M c_m g_m(n\delta t), n= 2, ..., 384\]

where $s(n\delta t)$ is the time-domain signal after removal of the water, lipid and baseline signal, $c_m$ is the area of the m-th metabolite or macromolecular signal, $\delta t$ denotes a signal decay function, and $g_m$ is the temporal basis function of the m-th metabolite or macromolecular signal stored in Vt and VtMM.

If you have trouble accessing the data, or other questions, please email us at fittingchallenge2024@gmail.com