What was your mri_cnr command line? I’m not really sure I understand all your
questions. It might be helpful if you told us what you are trying to achieve,
as the different algorithms you reference below do somewhat different things
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of James Brown
Sent: Monday, October 24, 2022 1:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segment
External Email - Use Caution
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/<https://secure-web.cisco.com/1sJwe_Z3H8ctyteSDndmgRa0Ulf0sp7KGqwyHsKQ37WNo3_OibqswecVVwiHErJG4z2hZP_5sY7eb0pCKPGBLGPBsc5B6NzrJ_A016Fxef5ipkg23QZv4iWmOXZmeAHXwH_P12s-r_odrdLUskh6P0hkFx_9u6QrxFUd82xfnFV4SWecxrWJ94i6ZTen56P_sMyKYrC4qkaGX-OAG9ulSy8Wbq-pIVXJtBBVnWBdp0Zfkafhk4BlJLfQWbPr42oH6_LtwL-oxJlLyAAW7ZtifyjqTQyIm9DtajAcUv9ctZakiGaS8U_esSA4R59k5xs-2vhmaoQ00AGMQBe6H4COauA/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F9931268%2F>
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
On Sat, Oct 22, 2022 at 10:18 PM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
I would like to inquire about the flags "-whi" and "-ghi" in the command
"mri_segement".
According to FS wiki, the command "mri_normalize" sets white matter voxels
around ~110 and gray matter around ~70.
- The default white matter high limit in the command mri_segemnt is 125, what
is the highest value to consider white matter voxels in an image? Is it 125?
- What are the situations where we need to set the gray and white matter voxels
at a high limit of 100 and 125 respectively in the command mri_segment? Does
the brightness of the image or motion play a role in the decision of choosing
high limits values?
Thank you,
James
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