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