Issue with outputting bad averages for fMRS data using FSL-MRS

MRS Software Other
1

Hi!

I’m currently analysing my fMRS data using FSL-MRS. For the analysis, I would like to create an output of the bad averages using fsl_mrs_proc unlike, which I can subsequently use to create a subject-specific design matrix (similar to fMRI analysis). However, when trying to run the following command (removed the overall folder structure to increase readability):

fsl_mrs_proc unlike --file ~/fMRS_metab.nii.gz --outputbad --output ~/derivatives/badaverages --generateReport --verbose

I receive this error:
Traceback (most recent call last):
File “/home/deboucherie/.conda/envs/fsl_mrs/bin/fsl_mrs_proc”, line 10, in
sys.exit(main())
File “/home/deboucherie/.conda/envs/fsl_mrs/lib/python3.8/site-packages/fsl_mrs/scripts/fsl_mrs_proc.py”, line 428, in main
dataout = args.func(dataList, vars(args))
File “/home/deboucherie/.conda/envs/fsl_mrs/lib/python3.8/site-packages/fsl_mrs/scripts/fsl_mrs_proc.py”, line 746, in unlike
good, bad = preproc.shift_to_reference(dataobj.data,
TypeError: shift_to_reference() got an unexpected keyword argument ‘ppmlim’

Looking at the FSL-MRS documentation, it should be optional to provide a ppmlim for fsl_mrs_proc unlike, so I’m not sure how this error arises and how to work around it. I have also tried to provide a ppm window, but this also yields errors. Does anyone have experience with this error and/or ways to solve it?
Thanks in advance!

Best,
Daphne

2

Hi @dboucherie,

On a quick inspection that looks like a bad bug from me, also lacking a test case to catch it. I’ll try to get a fix out today. For now you could make a small python script and call the function directly (using the API defined in the code. Something like:

from fsl_mrs.utils import mrs_io
from fsl_mrs.utils.preproc import nifti_mrs_proc as nproc
data = mrs_io.read_FID('/path/to/file.nii.gz')

good_avg, bad_avg = nproc.remove_unlike(data, ppmlim=None, sdlimit=1.96, niter=2, figure=False, report=None)

good_avg.save('/path/to/good.nii.gz')
bad_avg.save('/path/to/bad.nii.gz')
3

@dboucherie This should now be fixed in 2.1.11

4

Amazing! Thank you @wclarke, will give it another go today

5

@wclarke No luck unfortunately - it seems the output folder specified is not identified for --outputbad maybe?

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6

Ugh, that’s my fault for not writing a code test exploring all the command line options. I’ll make a fix for it tomorrow. Sorry

1 Like
7

@dboucherie V2.1.12 is now live and I hope is a final fix

8

@wclarke it works now, thank you! Do you maybe know if there is a way to additionally output the FID numbers of the bad averages?

9

There isn’t at the moment. Let me think of the best way to do that.

Will

10

@dboucherie 2.1.13 now inserts the indices kept/removed as a NIfTI-MRS header key in the respective outputs.