I would check your results to see if it is doing the right thing. I also think that the input to mri_segment is not the norm.mgz, but rather the brain.mgz, which is more aggressively normalized
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of James Brown Sent: Monday, October 24, 2022 2:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segment
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Dear Dr Bruce, Fischl,
The command was: mri_cnr $SUBJECTS_DIR/subjID/surf $SUBJECTS_DIR/subjID/mri/norm.mgz I would like to understand the highest limit of WM intensity in a normalized image. I am a little bit confused about that. For instance, the command “mri_normlaize” puts white matter intensity around 110. It seems there is a high limit threshold for white matter (i.e. mri_segment puts wm high limit at 125 but in the manuscript I referenced it seems to be 140). If the image is showing higher intensity values due to a noise is it correct procedure to increase the high limit of WM up to 125 or 140?
On Mon, Oct 24, 2022 at 1:46 PM James Brown <jb1979000@gmail.commailto:jb1979000@gmail.com> wrote:
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/1kLafUZhzq_EhLTyLNQ1MxMPAmSGjY2jbMGnlh44uboBMu_zOP6sk35jSHkP8jY8Mc1JqpvqVCVC7oDaL_sOyhs5CHJkpF2PfUpDKJhvuELYBXud52otlISM86vzcYW2WEdllqfOkQx14XBFpGxuR5RwbTnlZ85xTlcgBWb-0FqjXSXG9VoG2rsCUokxcFnHfIjpYsrtDEkZ6XF7iquX0ckfjAD942Y3jgqPhC6TRyn4eFnwq1LisR2V-AHffxnWOlA8IxYAuur7z8BnZGE5_M5iUfzxr6Wefl16qYJvZDSCSzDGUS_2eY7m4oYvbLgFnjV9r4K1fAWOTBMgllQvrdw/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 <jb1979000@gmail.commailto:jb1979000@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