[Freesurfer] Alignment of segmented brainstem in Freesurfer

[Sadia Sheikh]

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Dear FreeSurfer experts

I did brainstem segmentation using BrainstemSubstructure method. Then after
segmentation, I aligned all my segmented brainstem to Talairach coordinates
using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.
Alignment seems to be fine. But the boundary of the aligned brainstem looks
distorted with different other colors. Why does the boundary look like
this? and how can I improve this?
I have attached the image of brainstem after alignment.

Thanks in advance.

Regards
Sadia
Research Student



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Re: [Freesurfer] Alignment of segmented brainstem in Freesurfer

[Bruce Fischl]

What command did you use to apply the transform? If mri_convert add -rt nearest 
to your command line.
The issue is that you are using trilinear interpolation our a label map instead 
of nearest neighbor

> On Apr 20, 2019, at 5:22 AM, Sadia Sheikh  wrote:
> 
> External Email - Use Caution
> 
> Dear FreeSurfer experts
> 
> I did brainstem segmentation using BrainstemSubstructure method. Then after 
> segmentation, I aligned all my segmented brainstem to Talairach coordinates 
> using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.
> Alignment seems to be fine. But the boundary of the aligned brainstem looks 
> distorted with different other colors. Why does the boundary look like this? 
> and how can I improve this?
> I have attached the image of brainstem after alignment.
> 
> Thanks in advance.
> 
> Regards 
> Sadia
> Research Student
> 
> 
>   I’m protected online with Avast Free Antivirus. Get it here — it’s free 
> forever.
> 
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Re: [Freesurfer] Alignment of segmented brainstem in Freesurfer

[Sadia Sheikh]

External Email - Use Caution

Thankyou, Sir.
It really helped me a lot.

On Sat, Apr 20, 2019 at 11:46 PM Bruce Fischl 
wrote:

> What command did you use to apply the transform? If mri_convert add -rt
> nearest to your command line.
> The issue is that you are using trilinear interpolation our a label map
> instead of nearest neighbor
>
> On Apr 20, 2019, at 5:22 AM, Sadia Sheikh 
> wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts
>
> I did brainstem segmentation using BrainstemSubstructure method. Then
> after segmentation, I aligned all my segmented brainstem to Talairach
> coordinates using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.
> Alignment seems to be fine. But the boundary of the aligned brainstem
> looks distorted with different other colors. Why does the boundary look
> like this? and how can I improve this?
> I have attached the image of brainstem after alignment.
>
> Thanks in advance.
>
> Regards
> Sadia
> Research Student
>
>
>
> 
>  I’m
> protected online with Avast Free Antivirus. Get it here — it’s free
> forever.
> 
> <#m_7470614486553680194_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> 
>
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