Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation?

Cheers, Souheil

-------------------------

Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.inati@nih.govmailto:souheil.inati@nih.gov

On May 7, 2013, at 2:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain.

cheers Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

no, of course not :)

On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote:

...

Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation?

Cheers, Souheil

---

Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.inati@nih.govmailto:souheil.inati@nih.gov

On May 7, 2013, at 2:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain.

cheers Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

This is available online now:

http://authors.elsevier.com/sd/article/S1053811913005053

On 5/7/13 3:10 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote:

...

thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

no, of course not :)

On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote:

...

Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation?

Cheers, Souheil

---

Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.inati@nih.govmailto:souheil.inati@nih.gov

On May 7, 2013, at 2:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain.

cheers Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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.

Gordon Xu who helped us set up the protocol reminded me of the following:

"The main benefit of the readout PF is to reduce echo spacing, hence less blurring in the slice direction. The side benefit is that it also reduces the minimum TE, hence less dropout. However, you do give up some SNR at the high spatial frequency as Souheil mentioned. There are two senarios of this, a) the SNR is adequate, you only lose some SNR due to less sampling, b) if the SNR is borderline or worse, in addition to losing SNR you also lose some spatial resolution in the readout direction as the other side of the high spatial frequency k-space is less reliable.

I remember we did pilot acquisition with and without "asymmetric echo" in two subjects. You looked at the images and you either liked the one with asymmetric echo because of less blurring or at least indifferent between the two. So I assume with the Siemens 32ch coil we are in senario a) above."

If I had to guess, we probably went with the readout partial fourier to reduce the dropout regions in the gradient echo MPRAGE and didn't see an obvious loss in resolution.

Peace,

Matt.

On 5/13/13 1:03 PM, "Inati, Souheil (NIH/NIMH) [E]" souheil.inati@nih.gov wrote:

Hi Matt,

Thanks for the link.

Reading on pages 29-31, I am struck by the complexity of the procedure. Not to say that it doesn't work, or that the single T1w image free-surfer stuff is simple :-), on the contrary, it's just that I was expecting to see something about an optimization that used both images, rather than something based on the T1w image followed by an exclusion criterion based on the T2w image. Anyway, works better than without.

Minor question on the acquisition of the anatomicals:

• Why are you using partial fourier in the read direction? You're

throwing away a lot of SNR at the high spatial frequencies, seems a shame to go to 0.7mm and then do that.

Cheers, Souheil

On May 12, 2013, at 10:54 PM, Matt Glasser matt@ma-tea.com wrote:

...

This is available online now:

http://authors.elsevier.com/sd/article/S1053811913005053

On 5/7/13 3:10 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote:

...

thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

no, of course not :)

On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote:

...

Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation?

Cheers, Souheil

---

Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.inati@nih.govmailto:souheil.inati@nih.gov

On May 7, 2013, at 2:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain.

cheers Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

---

Freesurfer mailing list

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---

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Hi Katie,

yes, give mris_make_surfaces the -T2dura <T2/FLAIR volume name) command after recon-all has completed.

cheers Bruce

On Fri, 10 May 2013, Katie Surrence wrote:

Thanks very much for your response, Bruce.  We already collect T2 in our scanner -- not sure about FLAIR.  Is there a way for them to work analogously with the mri_make_surfaces command (as outlined here)?:

FreeSurfer command to correct dura:     mris_make_surfaces    –dura filename_%d.mgz                 -${lastecho}                 -aseg aseg.auto.mgz                 -mgz                 -sdir ${SUBJECTS_DIR}                 -output _dura_1and${lastecho}                 $({target} ${hemi} where filename_%d.mgz refers to the four separated echoes of the MEMPRAGE and lastecho = 4 Generates:     lh.pial_dura_1and4, rh.pial_dura_1and4,     lh.white_dura_1and4, rh.white_dura_1and4

Thanks again for your help!

On Tue, May 7, 2013 at 2:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Katie

  I'm really not sure. These days I would recommend a highres
  (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The
  T2* can help, but it's pretty noisy in brain.

  cheers
  Bruce

  On Tue, 7 May 2013, Katie Surrence wrote:

        Dear Freesurfer gurus,

        At the course, André van der Kouwe mentioned in his
        morphometry methods talk that T2* weighted contrast
        from
        MEMPRAGE could be used to further seperate dura from
        cortex, as also discussed in this paper:
        http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. 
        We have a GE scanner in our lab.  The internet
        suggests
        that a Multi-echo FSPGR/FGRE exists.  Would this be
        the analog?  Would it work the same way?  Could you
        also
        use these images with the mris_make_surfaces
        command?

        Thanks very much for your insight -- and I enjoyed
        the course!

        /Katie Surrence

        --
        Research Coordinator
        Social Cognition Laboratory
        New York State Psychiatric Institute

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.

-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute