External Email - Use Caution Dear Dr Bruce, Fischl, Indeed, the input to mri_segment is "brain.mgz", when I run mri_cnr on brain.mgz I see white = 102.3+-6.1, gray = 74.8+-16.7, csf = 51.5+-17.1
WM intensity is around 110 . I didn't know that intensity normalization takes two steps! Thank you for pointing this out. 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 On Mon, Oct 24, 2022 at 2:01 PM James Brown <jb1979...@gmail.com> wrote: > 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 <jb1979...@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 >> https://secure-web.cisco.com/1EhsES1ZezvIMDMxuS_URulqoaO_a1ha4QdRkq190T-vG90Ak4cg_CraqmjR8CUOtYb254N4k6pFa3b6Qi5g-MNzrqgnkFgGfoYbtwlO3XZmL_bi5ozDGEZmc_TyJbEG0wCGHLWBJPHxKZYlq26C29235IYTfatsx9a5WrZ_qtUO9G9OKnbzMqB0WVrBzE-E8kLexr19DdvYkXM1yoSuksq8Ufh2okemFrcBrQo-5gu4_A0zps-zNf4XVU0eX1irMeY_P9Ym0CIVRAIjRBCbokooOaR1abOR01Atpz12p-u3A93wtsK1OHbY-nPx4qQ27OO-iEIMCGDLagFJdmelJ5w/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> 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 >>> >>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.