Thanks Emma for sharing the link. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Boyd, Emma [ebo...@mgh.harvard.edu] Sent: 07 July 2017 15:51 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn
Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 Emma ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Das S. <sarbani....@soton.ac.uk> Sent: Friday, July 7, 2017 4:58:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > 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 > > > _______________________________________________ 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
