Chemical shift imaging pipeline

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1

Hi all,

I’m working on a project to overlay chemical shift imaging (CSI) data onto anatomical images for analysis. Both datasets are in .nii.gz format from a Siemens 3T scanner.

Anatomical Data: 256x256x176 dimensions, 1.1mm slice thickness.
CSI Data: 16x16 matrix, 15mm slab thickness.

Challenges:

  1. LCModel Compatibility: LCModel requires .rda files, but my CSI data is in .nii.gz.
  2. jMRUI Access: Unable to sign in due to account issues (working to resolve this).
  3. MATLAB Visualization: Using niftiread in MATLAB only gives a 16x16 table of numbers, and I don’t understand what they represent or how to extract spectroscopic data.

Any advice on handling .nii.gz CSI data, converting to .rda, or extracting spectroscopic data would be greatly appreciated!

Thanks in advance!

2

Why not use FSL-MRS? fsleyes can load and display both anatomical and CSI data (overlay on images, and shows spectra for each voxel).