Re: [Freesurfer] Cortical volume parcellation

[Mark Wagshul]

Bruce,

I haven't used tksurfer before, but it seems like the best way to do what I 
need would be to edit the pre-existing labels in the fsaverage aparc+aseg 
image.  What I want is almost exclusively from the superior and rostral-middle 
frontal labels already there, I just need to limit their extent.  Just wanted 
to know what you thought of this approach (although, to be honest, this might 
take some time, just to learn how to use tksurfer).

Thanks,

Mark 


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu


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-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, March 18, 2018 3:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume parcellation

Hi Mark

the easiest thing to do would be to draw the label you want on the fsaverage 
surface, then use mri_label2label to map from there to each of your individual 
subjects

cheers
Bruce
On Sun, 18 Mar 2018, Mark Wagshul wrote:

> Hi.  I'm new to using Freesurfer.  We are using the parc + aseg segmentation, 
> but would like to extract functionally-relevant cortical regions, which I 
> don't see specified in the output.  Specifically, I would like to calculate 
> cortical thickness of the dorsal pre-frontal cortex, which overlap with parts 
> of the cortical parcellations that I'm currently getting.  Is there any way 
> to do this within Freesurfer, or will I have to use another atlas (e.g. We 
> could generate this on the Mni template, morph it into subject space and 
> dilate to ensure that it captures the entire cortical surface).
>
> Thanks for any advice you can provide on this.
>
> Best,
>
> Mark
> ___
> Mark Wagshul, PhD
> Albert Einstein College of Medicine
> Bronx, NY
>
> Sent from my iPhone
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Re: [Freesurfer] Cortical volume parcellation

[Mark Wagshul]

Thanks!

Mark
___
Mark Wagshul, PhD
Albert Einstein College of Medicine
Bronx, NY

Sent from my iPhone

> On Mar 18, 2018, at 3:21 PM, Bruce Fischl  wrote:
> 
> Hi Mark
> 
> the easiest thing to do would be to draw the label you want on the 
> fsaverage surface, then use mri_label2label to map from there to each of 
> your individual subjects
> 
> cheers
> Bruce
>> On Sun, 18 Mar 2018, Mark Wagshul wrote:
>> 
>> Hi.  I'm new to using Freesurfer.  We are using the parc + aseg 
>> segmentation, but would like to extract functionally-relevant cortical 
>> regions, which I don't see specified in the output.  Specifically, I would 
>> like to calculate cortical thickness of the dorsal pre-frontal cortex, which 
>> overlap with parts of the cortical parcellations that I'm currently getting. 
>>  Is there any way to do this within Freesurfer, or will I have to use 
>> another atlas (e.g. We could generate this on the Mni template, morph it 
>> into subject space and dilate to ensure that it captures the entire cortical 
>> surface).
>> 
>> Thanks for any advice you can provide on this.
>> 
>> Best,
>> 
>> Mark
>> ___
>> Mark Wagshul, PhD
>> Albert Einstein College of Medicine
>> Bronx, NY
>> 
>> Sent from my iPhone
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
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Re: [Freesurfer] Cortical volume parcellation

[Bruce Fischl]

Hi Mark

the easiest thing to do would be to draw the label you want on the 
fsaverage surface, then use mri_label2label to map from there to each of 
your individual subjects

cheers
Bruce
On Sun, 18 Mar 2018, Mark Wagshul wrote:

> Hi.  I'm new to using Freesurfer.  We are using the parc + aseg segmentation, 
> but would like to extract functionally-relevant cortical regions, which I 
> don't see specified in the output.  Specifically, I would like to calculate 
> cortical thickness of the dorsal pre-frontal cortex, which overlap with parts 
> of the cortical parcellations that I'm currently getting.  Is there any way 
> to do this within Freesurfer, or will I have to use another atlas (e.g. We 
> could generate this on the Mni template, morph it into subject space and 
> dilate to ensure that it captures the entire cortical surface).
>
> Thanks for any advice you can provide on this.
>
> Best,
>
> Mark
> ___
> Mark Wagshul, PhD
> Albert Einstein College of Medicine
> Bronx, NY
>
> Sent from my iPhone
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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The information in this e-mail is intended only for the person to whom it is
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