will this future pipeline include processing neonatal data? If so, will it use both T1/T2 acquisitions? Thanks. JIm ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Friday, March 21, 2014 10:12 AM To: Francesco Baldacchini Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reconstruction problem with pediatric images

Hi Francesco,

Given that the recon pipeline is built on an adult atlas it is not expected to work for such young subjects. In the past, with high quality images, we managed to get reasonable recons for ages down to 4 (or sometimes 3). For the younger population though it will not work. We are in the process of creatig a pipeline for them, but it is not yet ready for distribution.

Lilla

On Thu, 20 Mar 2014, Francesco Baldacchini wrote:

Hi Lilla,

They range from neonates to 6 years old,

Francesco

2014-03-19 19:21 GMT+01:00 Lilla Zollei lzollei@nmr.mgh.harvard.edu:

  Hi Francesco,

  How old are your subjects?

  Lilla

  On Wed, 19 Mar 2014, Francesco Baldacchini wrote:

        I have some quality problems with my scans. I'm trying to run recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently get some problem in the reconstruction of the cortical surface as well as of the segmentation. I
        was wondering whether
        there is a tool making use of i.e. the T2 not only to improve the surface (by the way I cannot see the –T2 option in the help of recon –all to do so)  but particularly to improve the contrast of the T1. In a nutshell, there is a way to increase quality and contrast by using T1 together
        with T2 weighted images
        during recon-all? Another question is how important it is to use the mprage option in recon-all?  Thanks,

        Francesco Baldacchini

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Ciao Lilla,

Thank you so much for the quick answer. Sorry to bother you again but I've got some other questions to ask. First of all how have you managed to obtain reasonable recons with patients of 3-4 years old? There is a pipeline or particular settings to follow and if yes which ones? Then I would like to know if you can briefly summarise the technical reasons on why Recon all is not working with young patient's brain (in general for neonates and for babies from 3yr on); I assume there should be different reasons but it is more due to the low contrast between gray and white matter or to the atlas used? The last question is about the pipeline you are working on but not ready yet. It is somewhat linked to this article I've found http://www.ncbi.nlm.nih.gov/pubmed/19936261? I understand there are problems to do so, but there is a possibility to try it now before the final release? I would be really glad to use it and make few tests with it on my patients. Thank you for the attention and for your time,

Francesco Baldacchini

2014-03-21 16:12 GMT+01:00 Lilla Zollei lzollei@nmr.mgh.harvard.edu:

Hi Francesco,

Given that the recon pipeline is built on an adult atlas it is not expected to work for such young subjects. In the past, with high quality images, we managed to get reasonable recons for ages down to 4 (or sometimes 3). For the younger population though it will not work. We are in the process of creatig a pipeline for them, but it is not yet ready for distribution.

Lilla

On Thu, 20 Mar 2014, Francesco Baldacchini wrote:

Hi Lilla,

...

They range from neonates to 6 years old,

Francesco

2014-03-19 19:21 GMT+01:00 Lilla Zollei lzollei@nmr.mgh.harvard.edu:

  Hi Francesco,

  How old are your subjects?

  Lilla

  On Wed, 19 Mar 2014, Francesco Baldacchini wrote:

        I have some quality problems with my scans. I'm trying to run

recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently get some problem in the reconstruction of the cortical surface as well as of the segmentation. I was wondering whether there is a tool making use of i.e. the T2 not only to improve the surface (by the way I cannot see the -T2 option in the help of recon -all to do so) but particularly to improve the contrast of the T1. In a nutshell, there is a way to increase quality and contrast by using T1 together with T2 weighted images during recon-all? Another question is how important it is to use the mprage option in recon-all? Thanks,

        Francesco Baldacchini

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.