External Email - Use Caution
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
Not that I know of, sorry
On 9/1/20 10:20 AM, 刘梦醒 wrote:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use CautionHi 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
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 mailto:dgreve@mgh.harvard.edu> wrote:
Not that I know of, sorry On 9/1/20 10:20 AM, 刘梦醒 wrote:External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - UseCaution
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:
ExternalEmail - Use Caution
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
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, seems good
On 9/2/2020 2:40 AM, 刘梦醒 wrote:
External Email - Use Caution
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 mailto: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:External Email - Use Caution 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 <mailto:dgreve@mgh.harvard.edu>> wrote: Not that I know of, sorry On 9/1/20 10:20 AM, 刘梦醒 wrote:External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use CautionSorry 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:
External Email - UseCaution
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:
ExternalEmail - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No, sorry
On 9/2/2020 11:28 AM, 刘梦醒 wrote:
External Email - Use Caution
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 mailto:dgreve@mgh.harvard.edu> wrote:
yes, seems good On 9/2/2020 2:40 AM, 刘梦醒 wrote:External Email - Use Caution 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 <mailto: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:External Email - Use Caution 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 <mailto:dgreve@mgh.harvard.edu>> wrote: Not that I know of, sorry On 9/1/20 10:20 AM, 刘梦醒 wrote:External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That is reasonable
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ??? Sent: Tuesday, September 1, 2020 12:11 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] midline to cut the brain stem into Left and Right
External Email - Use Caution 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.edumailto:dgreve@mgh.harvard.edu> wrote: Not that I know of, sorry On 9/1/20 10:20 AM, 刘梦醒 wrote:
External Email - Use Caution 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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N. Greve
-
Fischl, Bruce -
刘梦醒