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 BaldacchiniThe 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.