Re: [Freesurfer] recon-all on newborn
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 on behalf of Das S. 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 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
Re: [Freesurfer] recon-all on newborn
Thanks for your reply.Much appreciated. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 07 July 2017 15:06 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn because neonate geometry and lack of myelin cause the brains to look so different from what many of our algorithms expect. cheers Bruce On Fri, 7 Jul 2017, Das S. wrote: > 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 > 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.
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 on behalf of Das S. 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 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
Re: [Freesurfer] recon-all on newborn
because neonate geometry and lack of myelin cause the brains to look so different from what many of our algorithms expect. cheers Bruce On Fri, 7 Jul 2017, Das S. wrote: > 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 > 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 >>>
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 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 &
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
Re: [Freesurfer] recon-all on newborn
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
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
Re: [Freesurfer] recon-all on newborn
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
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] recon-all on newborn
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 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.
