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/ (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.
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)
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.
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)
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.
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: mharms@wustl.edu
On 10/19/15 8:09 AM, "Bruce Fischl" fischl@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" 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/ (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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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-bounces@nmr.mgh.harvard.edu on behalf of mharms@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: mharms@wustl.edu
On 10/19/15 8:09 AM, "Bruce Fischl" fischl@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" 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/ (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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: mharms@wustl.edu
On 10/19/15 8:09 AM, "Bruce Fischl" fischl@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" 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/ (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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think you would just be wasting your power Bruce On Mon, 19 Oct 2015, John Anderson wrote:
Hi All, Thank you very much for your comments! Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it make sence ? 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 11:48 AM From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MPRAGE SNR 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: mharms@wustl.edu
On 10/19/15 8:09 AM, "Bruce Fischl" fischl@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" 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/ (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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Harms, Michael -
John Anderson -
JuergenHaenggi -
Matt Glasser