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wtclarke / fsl_mrs

Mirror of the FSL-MRS gitlab repository
https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
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dimension error in philips 3T MRS data reprocessing #18

Closed karthikrrish closed 1 year ago

karthikrrish commented 1 year ago

Hi,

I am relatively new to the field of MRS analysis. I am analyzing MRS data acquired for my Ph.D.

I am running fsl_mrsproc with the following command :

fsl_mrs_proc average --file /mnt/New_Volume/Karthik_Thesis/MRS_BS/Sub-250/sub-250.nii.gz/dACC_SVS_PRESS_35_ref.nii.gz --dim DIM_DYN --output fsl_mrs_proc --filename press_wref_tmp

However, I get the following error :

image

Upon verifying, I found out that my data doesn't have the required parameter specified, as shown by the following command :

image

Help me make sense of this error. I have two doubts:

  1. Is it a problem with the a) scan acquisition parameters; b) scanner software or c) spec2nii conversion that is responsible for the dimensions data not being shown?
  2. Can I skip the steps which require the dimensions to be told to fsl_mrsproc?
wtclarke commented 1 year ago

Hi @karthikrrish,

Not all data needs all steps of the pre-processing to be run, as depending on the export pipeline from the scanner (e.g. raw data [.dat/.7/.SDAT/SPAR] vs. DICOM) different parts of the preprocessing has already been applied.

Here it looks like nearly all of the preprocessing has been applied by the scanner (this might not be optimal, but I don't know what data you have access to), so no need to repeat it in FSL.

I'd suggest you take a look at the Near et al pre-processing paper for more info. And drop by forums.mrshub.org for general help on MRS processing - there's a friendly crowd with lots of experience across scanners who can help guide you.