Try out Freesurfer's QAtools. It still isn't "automatic", but you can get a bunch of screenshots and view them all on an html page.

On 09/18/2014 11:42 AM, Harms, Michael wrote:

Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the data.

cheers, -MH

-- Michael Harms, Ph.D.

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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

From: <Wegbreit>, Ezra <ezra_wegbreit@brown.edu mailto:ezra_wegbreit@brown.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 18, 2014 9:56 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] quick quality assessment for MPRAGE images

Dear Freesurfer Users,

I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?

Thanks! Ezra *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbreit@brown.edu mailto:ezra_wegbreit@brown.edu (preferred) ewegbreit@lifespan.org mailto:ewegbreit@lifespan.org *___________________________________________________________*

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Thanks, Michael and Chris for your comments. I had suspected that I would need to engage in "ocular inspection" of all ~200 scans before running each of them through the ~12 hrs of processing needed by recon-all.

Does anyone know if there are examples of scans along the continuum between "perfect" and "completely useless mess" by which to judge T1s? Some of my scans are very obviously unusable, but others have more subtle issues that appear to come from very slight movements (see attachments). It would also be nice to quantify the image quality somehow so that I could test it between groups (or covary in resulting analyses).

Thanks to all for any answers! Ezra

___________________________________________________________ Ezra Wegbreit, PhD NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbreit@brown.edu (preferred) ewegbreit@lifespan.org ___________________________________________________________

On Thu, Sep 18, 2014 at 3:13 PM, Harms, Michael mharms@wustl.edu wrote:

Yes, that can be helpful. As a caution though, the overall quality may appear fine, but things like topology correction errors can still occur and will be quite local. Thus, they would easily be missed if the density of your screenshots isn't high enough. Personally, I find it only marginally more time consuming to navigate through the entire set of slices in 'tkmedit', and the quality of your QA will be better.

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: mharms@wustl.edu

From: Chris Watson Christopher.Watson@childrens.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 2:00 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick quality assessment for MPRAGE images

Try out Freesurfer's QAtools. It still isn't "automatic", but you can get a bunch of screenshots and view them all on an html page.

On 09/18/2014 11:42 AM, Harms, Michael wrote:

Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the data.

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: mharms@wustl.edu

From: <Wegbreit>, Ezra ezra_wegbreit@brown.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 9:56 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] quick quality assessment for MPRAGE images

Dear Freesurfer Users,

I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all?

Thanks! Ezra ___________________________________________________________ Ezra Wegbreit, PhD NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbreit@brown.edu (preferred) ewegbreit@lifespan.org ___________________________________________________________

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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.

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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 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 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

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.