Re: [Freesurfer] Checking segmentations with aseg.mgz

[Reema Jayakar]

Hi Dr. Fischl,

Thank you for clarifying that about norm.mgz for checking segmentations.
Good to know that brain and brainmask wash out low contrast borders.

Cheers,
Reema


-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu

On Mon, Jul 18, 2016 at 4:42 PM, Reema Jayakar 
wrote:

> Hello FS Listserv members,
>
> With regard to checking amygdala segmentation, is it appropriate to
> overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying
> aseg.mgz on norm.mgz? I am aware of the general rule of thumb that
> editing the subcortical segmentations generally is not recommended.
>
> Also, where can I find documentation on the Freeview options "Resample to
> standard RAS space" and
>
> "Apply registration file". I am trying to understand whether or not it is 
> necessary for me to use any of these options for what I am doing with the 
> subcortical segmentations.
>
>
> Thanks in advance for your help!
>
> Reema
>
>
>
> --
> *Reema Jayakar, M.A.*
> Doctoral Candidate - Clinical Neuropsychology
> Health Resources and Services Administration (HRSA) Fellow
> Department of Psychology
> Georgia State University
> Email: rjayak...@student.gsu.edu
>
>
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Re: [Freesurfer] Checking segmentations with aseg.mgz

[Bruce Fischl]

Hi Reema

you should visualize it over the norm.mgz. The brainmask and brain will 
wash out many low contrast borders (e.g. thalamus, pallidum)


cheers
Bruce
On Mon, 18 Jul 
2016, Reema Jayakar wrote:



Hello FS Listserv members,
With regard to checking amygdala segmentation, is it appropriate to overlay
the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz
on norm.mgz? I am aware of the general rule of thumb that editing the
subcortical segmentations generally is not recommended. 

Also, where can I find documentation on the Freeview options "Resample to
standard RAS space" and

"Apply registration file". I am trying to understand whether or not it is ne
cessary for me to use any of these options for what I am doing with the subc
ortical segmentations.

Thanks in advance for your help!

Reema


--
Reema Jayakar, M.A.Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu


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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
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Checking segmentations with aseg.mgz

[Reema Jayakar]

Hello FS Listserv members,

With regard to checking amygdala segmentation, is it appropriate to overlay
the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz
on norm.mgz? I am aware of the general rule of thumb that editing the
subcortical segmentations generally is not recommended.

Also, where can I find documentation on the Freeview options "Resample to
standard RAS space" and

"Apply registration file". I am trying to understand whether or not it
is necessary for me to use any of these options for what I am doing
with the subcortical segmentations.


Thanks in advance for your help!

Reema



-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu
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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.