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
>
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> Jürgen Hänggi, Ph.D.
> Division of Neuropsychology
> Institute of Psychology
> University of Zurich
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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
>
> 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
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