Thank you so much for the reply Lilla. Lilla and Freesurfer community, I have few more questions.
Before the Freesurfer compliant default pediatric atlas is not released, my option would be to use age specific pediatric atlases from other sources such as: 1. Sanchez et al. pediatric atlases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399736/ 2. UNC Infant 0-1-2 atlases https://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases Do Freesurfer even recommend using these non-default atlases? I would assume it should not be problem as long as it is in proper .gca format. Please correct me if I am wrong. Assuming these non-default atlases can be converted into Freesurfer compliant gca atlases that can be used in recon-all preprocessing workflow, is there any documentation/publication on this? I found a discussion between Mark Plantz of Northwestern and Bruce Fischl in Freesurfer mailing list ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-August/032333.html) where Mark was trying to use UNC Infant 0-1-2 brain atlases in recon-all workflow. I could not figure it out if Mark had any success. Regards, Gajen On Fri, Sep 30, 2016 at 9:59 AM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu> wrote: > > Hi Gajendra, > > The recon stream exists in a beta version and will not make it to 6.0. I > am hoping to release the stream and the atlas though before the end of the > year. > > Lilla > > > On Thu, 29 Sep 2016, GAJENDRA KATUWAL (RIT Student) wrote: > > Hello FreeSurfer experts, >> >> I am considering using Freesurfer recon-all for segmentation of T1 brain >> MRIs of young subjects (1-4 years). I am planning to use a Freesurfer >> compliant pediatric template to maximize the >> segmentation accuracy. >> >> In the publication titled A FreeSurfer-compliant consistent manual >> segmentation of infant brains spanning the 0–2 year age range ( >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by Katyucia >> de Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, >> Marie Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla >> Zöllei, it has been mentioned that "Furthermore, we are >> also planning on making an atlas generated from our training data sets >> available to the scientific community (as part of the FreeSurfer package), >> which can serve as a template in structural and >> functional studies and as a teaching tool for trainees." >> >> Has the pediatric template been released yet? Is there anyway >> the pediatric template can be accessed if it has been released? Is it >> available in the dev version or upcoming Freesurfer 6? >> >> Regards, >> Gajendra Jung Katuwal >> PhD Candidate in Imaging Science >> >> >> > > 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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