Numpy Axis Error - FSL MRS


I am receiving the error message:

numpy.AxisError: axis 4 is out of bounds for array of dimension 4

When I simply attempt to visualise my converted raw metabolite spectra (METAB_RAW_1.nii.gz) using:

mrs_tools vis METAB_RAW_1.nii.gz

Please advise on how to fix this.


Hi Joe,

Sorry you’ve ran into an error. Could you tell me what mrs_tools info METAB_RAW_1.nii.gz gives you?

Hi Will,

Thanks for the response. Apologies I should’ve added this in the original message.

mrs_tools info METAB_RAW_1.nii.gz gives me:

Read file METAB_RAW_1.nii.gz (/Users/joephilby/Documents/NeuRA/Spec Programmes/fsl_mrs-master/PRESS_0.8x0.8x0.8-6_1-act:ref).

NIfTI-MRS version 0.7

Data shape (1, 1, 1, 1024, 1)

Dimension tags: [‘DIM_DYN’, None, None]

Spectrometer Frequency: 127.758832 MHz

Dwelltime (Bandwidth): 5.000E-04s (2000 Hz)

Nucleus: 1H

Field Strength: 3.00 T

Hi @Joe_Philby
This arises from that extra singleton dimension on the data Data shape (1, 1, 1, 1024, 1).

This is something I need to clean up, but for now there might be a work around. How are you converting the data?


Hi Will,

I am using the spec2nii tool to convert my Philips SDAT file into a .nii.gz file so I can use it in the FSL-MRS software.


Hi @Joe_Philby ,

Sorry for the delay in responding. This should be fixed in the most recent version of spec2nii (0.7.2).

This new version is up on Pypi now and will be on conda-forge shortly.

conda update -c conda-forge spec2nii