Re: [Freesurfer] midline to cut the brain stem into Left and Right

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Thanks Doug,

Is there a function in freesurfer that allows to cut a ROI by the coordinates?

On Wed, Sep 2, 2020 at 4:15 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

yes, seems good

On 9/2/2020 2:40 AM, 刘梦醒 wrote:

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Sorry I mean the talairach transform matrix in /mri/transform/talairach.xfm.

In this way, no matter how the brain is aligned when the data is collected, by translating it to a talairach coordinate system, the brain will be aligned to ac-pc at y-axis, the longitudinal fissure is aligned to z-axis, so x-axis is fixed. Then x=0 is the center of left and right hemisphere.

I checked the results it seems ok, but just want to make sure the logic is correct.

Many thanks!

On Tue, 1 Sep 2020 at 21:05, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

What is TLRC? Otherwise, it sounds reasonable. I'd definitely look

at the image to make sure:)

On 9/1/2020 12:11 PM, 刘梦醒 wrote:

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Thanks!

I have a work-around solution but want to hear your comment

on it.

I use the TLRC transform matrix in mri/transform to

translate the coordinates in native to TLRC, so that the

origin set to anterior commisure. Then I cut the brain stem to

left and right, by x>0 and x<0, then I use the inverse

matrix to translate the left and right brain stem back.

How do you feel about this?

Many thanks!

Mengxing

On Tue, Sep 1, 2020 at 4:42 PM

Douglas Greve dgreve@mgh.harvard.edu wrote:

...

Not that I know of, sorry

On 9/1/20 10:20 AM, 刘梦醒 wrote:

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Hi Freesurfer group,

For some reason, I have to use the left and right

brain stem separately.

I wonder if there is one way to have a midline, to

cut the brain stem into Left and Right?

Many thanks,

Mengxing

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