Obtaining time dynamics from fMRS


I have fMRS data during a visual task and am using fsl_mrs to analyse it.

Pre-processing the data worked fairly straight forward as well as fitting the averaged data over time dynamics. Now I’m trying to dynamically fit the data, so I’m trying to obtain the time variables for the dynamics. I had a look and couldn’t figure it out, I was wondering if it has something to do with ‘dynamic_hdr_vals’ but couldn’t obtain anything from that.

I’m new to python and fsl_mrs so this could be a user error, but just wouldn’t to check that this is obtainable before spending more time on this.


Hi @daniel,

On pat leave at the moment, so a little slow in replying. Have you found GitHub - wtclarke/fsl_mrs_fmrs_demo: Fitting fMRS data in FSL-MRS - ISMRM 2022 yet? That should hopefully explain a lot. Currently the exact values of the time variables probably isn’t too important, so you can simply define then as a monotonically increasing vector.

Hi @wclarke thank you for responding, I hadn’t seen that I’ll take a look.


Just testing out the main_demo notebook and after cloning the repository I get the following error:ImageFileError: File /home/user/fsl_mrs_fmrs_demo/simulated_data/sub0_stim.nii.gz is not a gzip file. Any idea why this might be?

Yes, you need to install git LFS first.https://git-lfs.com/

Apologies I thought I had this already installed. Script runs now thank you

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