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
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
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
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.
>
>_______________________________________________
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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
> 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.
_______________________________________________ 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.
