Dear Dr Bruce, Fischl,

Thank you very much for the detailed explanation. I would like to ask two additional questions and I highly appreciate your input.

 

-          The output of “mri_normalize” on a T1 image is something like:

 

3d normalization pass 1 of 2

white matter peak found at 110

white matter peak found at 109

gm peak at 71 (71), valley at 38 (38)

csf peak at 36, setting threshold to 59

building Voronoi diagram...

 

In this manuscript MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://pubmed.ncbi.nlm.nih.gov/9931268/ three intensity-based contrasts WM_low (90), WM_high (140 and Gray_high (100) were defined. I understand that the command “mri_normalzie” reports the peak intensity of WM, GM and CSF but the highest limit of WM in any “norm.mgz” is 140 by default. Is this correct?

 

-          The output of the command “mri_cnr” is something like this:

white = 86.5+-22.1, gray = 77.6+-29.0, csf = 66.8+-35.2

lh CNR = 0.058

 

Does this mean that the mean white matter intensity in the left hemisphere is 86.5 and the standard deviation is 22.1? In this example, can we say that the highest limit of white matter intensity in the image is 108?

 

I apologize for asking too many questions. I appreciate the opportunity to learn.

Sincerely,

James

 

 

Hi James

 

It really depends on your sequence. Some sequences, like mprage, trade off SNR for CNR, so the distance between gray and white is larger, but the noise in each is also larger. In that case white might end up brighter because of the noise. There are also inflow effects where you get non-inverted spins coming in through arteries that are very bright in mprage, that you won’t see in a flash scan. We don’t actually set the gm peak, just scale the white to 110-ish, then gray lands wherever the intrinsic contrast of the image puts it

 

Cheers

Bruce