Dear Lilla, In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon. If you give me little more details will be easy for me to understand the gap. many thanks Sarbani ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: 05 July 2017 22:32 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn
We use a similar pipeline but with different atlases and processing steps for the newborns. Lilla On Wed, 5 Jul 2017, Das S. wrote: > > Thanks for the reply. If you let me know, among the below list of steps of > current recon-all, currently which is not suitable to perform on neonates MRI > image, will really appreciate. > > Autorecon Processing Stages: > Motion Correction and Conform > NU (Non-Uniform intensity normalization) > Talairach transform computation > Intensity Normalization 1 > Skull Strip > EM Register (linear volumetric registration) > CA Intensity Normalization > CA Non-linear Volumetric Registration > Remove Neck > LTA with Skull > CA Label (Volumetric Labeling, ie Aseg) and Statistics > Intensity Normalization 2 (start here for control points) > White matter segmentation > Edit WM With ASeg > Fill (start here for wm edits) > Tessellation (begins per-hemisphere operations) > Smooth1 > Inflate1 > QSphere > Automatic Topology Fixer > Final Surfs (start here for brain edits for pial surf) > Smooth2 > Inflate2 > Spherical Mapping > Spherical Registration > Spherical Registration, Contralateral hemisphere > Map average curvature to subject > Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) > Cortical Parcellation Statistics > Cortical Ribbon Mask > Cortical Parcellation mapping to Aseg > > BW > S Das > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 04 July 2017 22:04 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > Hi S Das, > > We are trying to release the infant pipeline by the end of the summer. > > Lilla > > On Tue, 4 Jul 2017, Das S. wrote: > >> Dear Freesurfer expert, >> I want to perform recon-all pipeline on neonates data.Can I do so? >> I was going through some mail archives and there it is said that on T1 image >> of neonates data we can't perform recon-all. >> But again there is another paper where it says Freesurfer can perform >> segmentation of neonates image. >> Any input will be appreciated. >> Thanks >> S Das >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
