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
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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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.
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
Thanks for your reply.Much appreciated. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260
Emma
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Das S. Sarbani.Das@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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
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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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Thanks Emma for sharing the link. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Boyd, Emma [EBOYD2@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Das S. Sarbani.Das@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzollei@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.
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Boyd, Emma -
Bruce Fischl -
Das S. -
Lilla Zollei