Hi, FWIW, I've looked at a number of these measures in 500+ subjects from HCP data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they relate to each other, and whether they correlate with mean cortical thickness, white matter surface area, or number of SurfaceHoles (prior to topology correction).
I didn't find much of note. e.g., the highest correlations were: r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz) r = -0.25 between white surface area and wmanatsnr r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from norm.mgz) Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r = 0.49). G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80. G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97 In another context (but smaller number of subjects), I've looked to see if these various snr, cnr measures from FS were related to manual quality ratings, and the relationship was rather weak. All-in-all, I haven't seen much that would indicate that these measures can be used as a sort of "automated" QC measure. Manual review of the structurals and FS results is still needed. That said, the structurals from the HCP 500 release were all of reasonably good quality to begin with. So, it is possible that these snr/cnr measures might be more informative in identifying truly awful scans in a clinical population with a wider variability in MPRAGE scan quality. I'd certainly be interested in hearing from anyone if they have found that to be the case in their data. BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from orig.mgz and norm.mgz respectively. Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 10/19/15 8:09 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: probably similar, although maybe Doug can comment. You probably want to run it on the orig.mgz as the intensity normalization can artificially increase the SNR (which is kind of the point) Bruce On Mon, 19 Oct 2015, John Anderson wrote: > Hi Bruce, > Thanks a lot!! this is really great! > I ran the command as the following : > > mri_cnr subj_01/surf subj_01/mri/norm.mgz > processing MRI volume subj_01/mri/norm.mgz... > white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5 > gray/white CNR = 2.291, gray/csf CNR = 0.848 > lh CNR = 1.569 > white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0 > gray/white CNR = 2.278, gray/csf CNR = 0.798 > rh CNR = 1.538 > total CNR = 1.554 > > > I noticed that the normal range for the SNR (15-20) when using the >command > "wm-anat-snr" > > What is the normal range for cnr generated by the binary "mri_cnr"? > > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > Sent: Monday, October 19, 2015 at 8:36 AM > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: j.haen...@psychologie.uzh.ch > Subject: Re: [Freesurfer] MPRAGE SNR > Hi John > > there is also a binary called mri_cnr that will compute the > contrast-to-noise ratio (CNR), which is really the more interesting > metric. It will also spit out the WM means+- std, and the ratio of these > two can be used as an SNR measure. > > cheers > Bruce > > > On Mon, 19 Oct 2015, John Anderson wrote: > > > Dear Jürgen > > This really helps! > > I highly appreciate your input on this. > > > > Bests, > > John Anderson > > > > Senior Research Associate > > Psychological and Brain Sciences Dept. > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > > Phone: +1 (603) 646-9834 > > Fax: +1 (603) 646-1419 > > Sent: Monday, October 19, 2015 at 1:30 AM > > From: JuergenHaenggi <j.haen...@psychologie.uzh.ch> > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] MPRAGE SNR > > Dear John > > FS's QA tools provide the SNR > > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools > > > > there is also a FS function called wm-anat-snr that can be used for >that. > > > > Hope this helps > > Cheers > > Jürgen > > > >>------------------------------------------------------------------------- >>-- > > > -------------------------- > > Jürgen Hänggi, Ph.D. > > Division of Neuropsychology > > Institute of Psychology > > University of Zurich > > Binzmuehlestrasse 14, PO Box 25 > > 8050 Zurich, Switzerland > > 0041 44 635 73 97 (phone office) > > 0041 76 445 86 84 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > j.haen...@psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > http://www.juergenhaenggi.ch (private website) > > > > This e-mail (and any attachment/s) contains confidential and/or >privileged > > information. If you are not the intended recipient (or have received >this > > e-mail in error) please notify the sender immediately and destroy this > > e-mail. Any unauthorised copying, disclosure or distribution of the > > material in this e-mail is strictly forbidden. > >>------------------------------------------------------------------------- >>-- > > > -------------------------- > > > > > > > > Am 18.10.2015 um 16:48 schrieb John Anderson: > > > > Dear Experts, > > Is there any tool in Freesurfer that can help to evaluate the SNR for > > T1 MPRAGE images directly ( i.e script). If not knidly can any help me > > to figure out the best way to dao it. > > > > I highly appreciate your help! > > > > Bests, > > John Anderson > > > > Senior Research Associate > > Psychological and Brain Sciences Dept. > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > > Phone: +1 (603) 646-9834 > > Fax: +1 (603) 646-1419 > > _______________________________________________ > > 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 Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . 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