[Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
Hello FreeSurfers, 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 ___ 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.
[Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
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 ___ 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.
Re: [Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
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 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. > ___ 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.
Re: [Freesurfer] FreeSurfer Atlas
According to this website https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v 3.0 uses Aseg atlas for the segmentation of subcortical structures. It does not explicitly mention anything about Freesurfer v5.3 though. On Thu, Oct 13, 2016 at 8:02 AM, AKUDJEDU, THEOPHILUS < t.akudje...@nuigalway.ie> wrote: > > Hi All, > > > Which default atlas does FreeSurfer 5.3 use for the segmentation of > subcortical structures? > > > Thanks > > > Theo > > > ___ > 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. > > ___ 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.
