Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Douglas N. Greve 

And how does the parcellation look on the surface?

On 3/7/2024 9:53 AM, Hyunchul Lee wrote:


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Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
 wrote:


Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


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Hello,
I'm using Freesurfer recon-all to create reconstructions to use
with MNE-python for source estimation of SEEG data. My work
relies on having correct labeling of segmentation data. For most
cases, there has been no trouble but I am having trouble where
the cortical parcellation shows up as dots in one hemisphere.
Please see image attached. I also noticed that the lh.ribbon.mgz
is also 'dotty' (also attached). There is no issue with the right
hemisphere. This reconstruction was not manually edited, but only
recon-all was used.

I have tried using mris_volmask --label_left_ribbon, setting the
argument to various values. That didn't work that great -
reducing to 0 basically whites everything out except for the
white matter on the ipsilateral hemisphere and anything 1 or more
produces the same 'dots'. Interestingly the pial and wm surfaces
all look ok. Also, I am not sure if creating the correct
ribbon.mgz is going to fix the aparc.a2009+aseg file.

I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Hyunchul Lee 
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Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
wrote:

> Have you looked at the actual surface?
>
> On 3/7/2024 2:29 AM, Hyunchul Lee wrote:
>
> External Email - Use Caution
> Hello,
> I'm using Freesurfer recon-all to create reconstructions to use with
> MNE-python for source estimation of SEEG data. My work relies on having
> correct labeling of segmentation data. For most cases, there has been no
> trouble but I am having trouble where the cortical parcellation shows up as
> dots in one hemisphere. Please see image attached. I also noticed that the
> lh.ribbon.mgz is also 'dotty' (also attached). There is no issue with the
> right hemisphere. This reconstruction was not manually edited, but only
> recon-all was used.
>
> I have tried using mris_volmask --label_left_ribbon, setting the argument
> to various values. That didn't work that great - reducing to 0 basically
> whites everything out except for the white matter on the ipsilateral
> hemisphere and anything 1 or more produces the same 'dots'. Interestingly
> the pial and wm surfaces all look ok. Also, I am not sure if creating the
> correct ribbon.mgz is going to fix the aparc.a2009+aseg file.
>
> I would really appreciate your advice.
>
> Best regards,
>
> *Hyunchul Lee*  MBBS PhD
>
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Re: [Freesurfer] Cortical parcellation showing dots

2024-03-07 Thread Douglas N. Greve 

Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use with 
MNE-python for source estimation of SEEG data. My work relies on 
having correct labeling of segmentation data. For most cases, there 
has been no trouble but I am having trouble where the cortical 
parcellation shows up as dots in one hemisphere. Please see image 
attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also 
attached). There is no issue with the right hemisphere. This 
reconstruction was not manually edited, but only recon-all was used.


I have tried using mris_volmask --label_left_ribbon, setting the 
argument to various values. That didn't work that great - reducing to 
0 basically whites everything out except for the white matter on the 
ipsilateral hemisphere and anything 1 or more produces the same 
'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am 
not sure if creating the correct ribbon.mgz is going to fix the 
aparc.a2009+aseg file.


I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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