This has been my experience as well. Not much seems to predict which scans will need to be edited.
On 10/19/15 10:23 AM, Harms, Michael 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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