ately.
-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 thi
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_lab
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 s
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 w
Great - that makes sense!
Thanks again for your help in resolving this.
Eli
From: Eli Johnson
Sent: Friday, 27 January 2017 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I was reading the fourth
ted
> column represent?
>
>
> Many thanks
>
> Eli
>
>
> *From:* Eli Johnson
> *Sent:* Friday, 27 January 2017 10:24 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical
sorry for wasting so much
time!). In that case, what does the fourth/highlighted column represent?
Many thanks
Eli
From: Eli Johnson
Sent: Friday, 27 January 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked regi
ject:* Re: [Freesurfer] Cortical volume from masked region
>
> Ok sure, I will do it tomorrow as I don't have access to the stats
> file right now
>
> Many thanks!
>
>
> *From:* Eli Johnson
> *Sent
Thursday, 26 January 2017 7:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
From: Eli Johnson
Sent: Thursday, 26
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
From: Eli Johnson
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
Y
; *
>>>
>>> *Many thanks!*
>>>
>>> *Eli
>>> *
>>>
>>> *
>>> *
>>>
>>> *
>>> *
>>>
>>> *
>>> *
>>>
>>> *Douglas N Greve*greve at nmr.mgh.harvard.edu
>
might be?*
>>
>> *
>> *
>>
>> *Many thanks!*
>>
>> *Eli
>> *
>>
>> *
>> *
>>
>> *
>> *
>>
>> *
>> *
>>
>> *Douglas N Greve*greve at nmr.mgh.harvard.edu
>> <mailto:freesurf
>> *
>>
>> *Douglas N Greve*greve at nmr.mgh.harvard.edu
>> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E>
>>
t;
> *
> *
>
> *
> *
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> *Douglas N Greve*greve at nmr.mgh.harvard.edu
> <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E&
total cortical gm
> volume from the aseg.stats file). Any thoughts on why this might be?*
>
> *
> *
>
> *Many thanks!*
>
> *Eli
> *
>
> *
> *
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> *
> *
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> *
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> *Douglas N Greve*greve at nmr.mgh.harvard.edu
> <mailto:freesurf
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* Previous message: [Freesurfer] Cortical volume from masked region
<https://mail.nmr.mgh.harvard.edu/pipermail//frees
I would probably map the mask to the surface,eg,
mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
The run
mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
lh.vol.stats
On 01/17/2017 11:24 A
Hi all,
I am trying to extract the volume from a FreeSurfer segmented scan within a
pre-registered mask region, but only within the cortex, and wanted to check my
command.
The mask is a binary mask (value of 1 across the mask) and is in the same space
as the orig.mgz file. It covers part of
The equation is not quite right. The volume is first computed at each
vertex (vertex volume = vertex area * vertex thickness), then it is
summed across vertex. This does not lead to the same result as summing
the area, computing mean of the thickness, then multiplying them together.
doug
On 10
I have a quick question about FreeSurfer: is cortical volume the product of
cortical thickness and cortical surface are? Conceptually I assume that to be
the case, and I found several papers to support that. However, when I tried it
with my own data, that seems to disagree with ~12% error.
So I
Hi Knut
these are hard questions to answer. Volume is thickness x surface area,
so the question is how reliable is surface area and what does a change in
it mean? Where does the "jacobian_whitematter" measure come from?
cheers
Bruce
On Thu, 30 Aug 2012, Knut J Bjuland wrote:
> Hi,
>
> I have
Hi,I have looked into cortical surface volume and cortical
jacobian_whitematter. Can I use these measure a in similar way as cortical
thickness? Do jacobian_whitematter represent the whitematter thickness in the
cortex? How reliable are cortical volumes compared to cortical thickness?Best
regar
Hello,
After the success of running the freesurfer on the 7T human data a while
ago, I am trying now to extract the cortical volume. However, if I use
asegstats2table command to get the segmented volume then I get the
following values
Rt_cerebral_cortex = 236732
Lt_cerebral cortex = 242649
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