Problem with dimensions


I have a few questions:

I went through the FSL-MRS practical with the example data and it worked perfectly. Now I am trying to use my own data (Siemens, TWIX), but I am running into an issue with the coil combination. It says:
ValueError: operands could not be broadcast together with shapes (2080,2,49,32,1,1,1) (2,32,1,1,1)
In the attatchment below is shown the info of these files and at the very last line the command I tried to use.

  1. I don’t understand why it shows in the error message that the shape of the wref_temp is only (1,1,1,32,2). Where has the value 2080 gone? Is this the problem?

  2. And also when comparing these to the example data it looks like the ‘DIM_USER_0’ and the ‘DIM_DYN’ are the wrong way around. I am guessing that the DIM_DYN is supposed to be the 2 and the ‘DIM_USER_0’ to be the 49. How can I fix this?

  3. Also I am guessing that the DIM_USER_0 is the amount of FIDs in this file. Do I need to get rid of that dimension also and if yes, how do I do that?

Thank you for your help!

Looking into it a little more I understand this better now. I still dont know what the DIM_USER_0 is, it looks just has an averaged spectra and then a spectra that is 0.

1.Not a problem, but still don’t know why it isn’t shown.
2. it is not flipped. it is as it is supposed to be
3. I am guessing, that you can get rid of the extra dimension with just averaging the dimension with:
fsl_mrs_proc average --file data/FILE --dim DIM_USER_0 --output OUTPUTFOLDER --filename NEWFILE
Just be sure to do this to both water reference and metabolite data and after that start the preprocessing accordingly.

Hi @zellavie ,

Sorry for the delay in replying. The first error arises from the water references having two averages. You can fix this by running fsl_mrs_proc average --file wref.nii.gz --dim DIM_USER_0 --output .

I should adjust the error output to be more helpful for this. The DIM_USER_0 tag is just a generic tag when spec2nii doesn’t have any information on what the dimension is used for. DIM_DYN is the number of repeats.

The empty spectrum is a bit odd. What sequence is this from?