Thanks MH,
Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.
Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help a lot!
 
any suggestions?
 
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 12:24 PM
From: "Harms, Michael" <mha...@wustl.edu>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR
 
At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.
 
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  63110 Email: mha...@wustl.edu
 
 
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" <gr...@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: 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)
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>>> http://www.juergenhaenggi.ch (private website)
>>>
>>> This e-mail (and any attachment/s) contains confidential and/or
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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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