There is also the issue that grey and white matter are not truly a homogeneous single intensity anatomically.
Peace, Matt. On 10/19/15, 9:23 AM, "Harms, Michael" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of mha...@wustl.edu> wrote: > >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 . If the e-mail was sent to you >> > in error >> > but does not contain patient information, please contact the sender >> > and properly >> > dispose of the e-mail. >> > >> > _______________________________________________ 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 . If the e-mail was sent to you >>in >> > error but does not contain patient information, please contact the >>sender >> > and properly dispose of the e-mail. >> > >> >_______________________________________________ >> 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 . If the e-mail was sent to you >>in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > >________________________________ >The materials in this message are private and may contain Protected >Healthcare Information or other information of a sensitive nature. 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