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" fischl@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Cc: j.haenggi@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.haenggi@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.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/%C2%A0(website) http://www.juergenhaenggi.ch%C2%A0(private website)
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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
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