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spec2nii website  

A program for multi-format conversion of in vivo MRS to the NIfTI-MRS format.

This program was inspired by the imaging DICOM to NIfTI converter dcm2niix developed by Chris Rorden. All MRS(I) orientations are tested with images converted using dcm2niix. I consider the combination of images converted using dcm2niix and displayed in FSLeyes the de facto standard.

Visualisation of MRS converted by spec2nii can be carried out with a recent (>0.31.0) version of FSLeyes. A FSLeyes plugin for NIfTI-MRS is in development.

Environment Modules

Run module spider spec2nii to find out what environment modules are available for this application.

System Variables

  • HPC_SPEC2NII_DIR - installation directory
  • HPC_SPEC2NII_BIN - executable directory


If you publish research that uses spec2nii you have to cite it as follows:

Some GE test data comes from the BIG GABA dataset whichw as funded by NIH grant R01 EB016089. Please see Mikkelsen M et al. Big GABA: Edited MR spectroscopy at 24 research sites. NeuroImage 2017;159:32–45. doi: 10.1016/j.neuroimage.2017.07.021 for more information.