Hello, this is a general question for the community, but could possibly eventually be done in Brainstorm.
Does anyone have tips on pre-processing T1 MRIs? The reason I ask is that a lot of scans I'm currently working with have increased noise in the inferior region, especially near the chin.
This makes it more complicated to extract a good head surface. When Matlab downsamples the surface, a lot of vertices are used to attempt to preserve the complex "beard" shape.
The current Brainstorm default for getting the head shape smooths a lot and I loose too much detail on the ears, which I want to QC fiducial placement.
Are there existing (ideally Matlab) MRI tools that automatically detect and smooth such noise without blurring the rest of the volume? Or perhaps more generally, some that do edge-preserving volume smoothing?
Brainstorm has plugin tools that extract tissues and surfaces. Maybe some of them would already do this? I tried CAT12 and FSL but the former did not create a head surface and the latter ended up cutting into the mouth/chin region quite a bit.
Thanks!
Marc
This T1 hypersignal around the chin is indeed a common problem. It is usually not really bothering for any computation we're doing with Brainstorm. But it looks bad...
If you process this MRI with FreeSurfer/BrainVISA/BrainSuite and check the bias-corrected image: does it look any better?
This is a question you should ask to the experts directly: on the FreeSurfer mailing list, the BrainSuite forum (@Anand_Joshi), and maybe @CGaser here.
Thanks. I'll keep looking later.
I found this that seems promising: https://sites.google.com/site/pierrickcoupe/softwares/denoising/mri-denoising/mri-denoising-software
I also think CAT12 mentions denoising in it's initial steps, possibly a similar method. I'll check if I could use that.
To clarify, I'm trying to improve the details around the ears by not denoising with erode/dilate operations. This works, but I have to keep many more vertices because of this complex "beard". So it would be nice to denoise it first. It doesn't really matter if the chin looks weird, as long as it's smoother.
Hi;
you can also try the FSL (implemented recently in Brainstorm); i found it was helping sometimes too