Cat12 poor bias rating

Hi Everyone,

I’m running a VBM analysis with the cat12 toolbox. After preprocessing for most images, the cat12 automated report has poor ratings for the bias under “Image and Processing Quality.” The ratings are typically around 65-70% with a grade of D+, which shows up in an ominous red color.

But I can’t find any guidance on 1) how this rating is determined 2) any specific steps I can take to improve it 3) whether the results are still valid

I’m new to neuroimaging in general, so I may be missing something very basic.
Any help would be greatly appreciated!

Greg

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Hi Greg,

The bias of the image is related to the hardware (B1+ and B1- field, emitting and receiving coils) and also the filters applied to your images by the scanner (for instance with Siemens: use of normalize or Prescan Normalize filters). So to better understand your question, could you feed us with the magnetic field you are working at, the type of scanner and coils that were used to acquire those images?

Thanks for your response, we are using a Skyra 3T scanner with 32 channel coil.
It looks like the normalize and prescan normalize filters were off.

Also I am using spm12 version 7771 with cat12 version 12.7
Please let me know if any other info would be useful.
Thanks again!

Ok, I will have to check with our data, we use a 3T Prisma with 64channel coil and I think both 32ch and 64ch have similar receive field with a pretty strong receive bias. Using the Prescan Normalize filter would give you images with a better score. Of note post-precessing bias correction steps such as N4 (Ants) but also FSL, Freesurfer work very well also. CAT12, is using a bias correction step also to estimate the bias of the images and to correct for it during its segmentation process). Such post processing steps would work very well also and you don’t necessarily need to have a bias corrected image as input of standard post-processing pipelines as their bias correction routines work well. But again, I will check if we get a D score also for our raw images with no Prescan normalize filter.

I just checked on our data: the bias score of CAT12 (with prescan normalize) on our anatomical images with the 64CH at 3T range from B to C. I can totally understand that you would get D+ with no filter activated on a 32 CH coil. But despite from the strong bias, this 32CH is very good because it gives you a strong signal and many capabilities for acceleration. So,to get a better bias score you could :

  • use the prescan normalize filter
  • use other postprecessing bias corrective steps before evaluation
  • use an other sequence such as MP2RAGE for instance.

Internally, about how the rating is determined, my guess would be that it is something related to the variance measured in the bias field extracted by the CAT12 procedure.
To me it seems like the results are consistent, especially with no filter applied to your images.

Thanks for checking on this!
It sounds like this bias rating is not such a big issue. As you suggested, it’s based on the pre-bias-corrected image and the cat12 bias correction is quite good, so it should not be a problem

FWIW here is more detail on how the cat12 reports are generated:
http://www.neuro.uni-jena.de/cat12-html/cat_methods_QA.html

And for anyone with a similar issue, I was able to get a response from Christian Gaser (CAT12 creator) here:
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2103&L=SPM&D=0&P=171437

Thanks again Julien! Very inspiring to receive such useful help so quickly on this

You are welcome Greg! Thank you for sharing this ressource on how the rating is calculated with CAT12, very useful.