Hello,
I would like to measure the size of a bunch of surface reconstructions (ventral-dorsal, posterior-anterior, medial-lateral), but I wouldn't like that the different orientation of the subject's head may affect the measurements (if the head is tilted, for example). Is there a simple way of doing this? ... otherwise, which of the talairach transforms should I use to recover the orientation of the brain (among talairach.xfm, .lta, etc)
thank you very much in advance!
roberto
Hi Roberto,
the tal xforms will have scaling normalization in them, which I assume you don't want?
Bruce On Tue, 13 Mar 2007, roberto toro wrote:
Hello,
I would like to measure the size of a bunch of surface reconstructions (ventral-dorsal, posterior-anterior, medial-lateral), but I wouldn't like that the different orientation of the subject's head may affect the measurements (if the head is tilted, for example). Is there a simple way of doing this? ... otherwise, which of the talairach transforms should I use to recover the orientation of the brain (among talairach.xfm, .lta, etc)
thank you very much in advance!
roberto _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 14 Mar 2007, at 00:28, Bruce Fischl wrote:
Hi Roberto,
the tal xforms will have scaling normalization in them, which I assume you don't want?
Bruce
Hi Bruce,
you are right. I would like to know only the orientation of the head and then compute the hemisphere size from the reconstructions. If I compute the eigenvalues of the rotation part of the matrix (the first 3 columns) I can recover the scaling factors, and then I should be able to get the rotation matrix by dividing the rows by their corresponding eigenvalue, isn't it?
thanks for your help, roberto
but is it the dimensions of the cortex that you are trying to generate? Say, from frontal pole to occipital pole? That I would do by specifying those points in fsaverage as labels, then mapping them to individuals using mri_label2label and computing their distance in native coords.
cheers, Bruce
On Wed, 14 Mar 2007, roberto toro wrote:
On 14 Mar 2007, at 00:28, Bruce Fischl wrote:
Hi Roberto,
the tal xforms will have scaling normalization in them, which I assume you don't want?
Bruce
Hi Bruce,
you are right. I would like to know only the orientation of the head and then compute the hemisphere size from the reconstructions. If I compute the eigenvalues of the rotation part of the matrix (the first 3 columns) I can recover the scaling factors, and then I should be able to get the rotation matrix by dividing the rows by their corresponding eigenvalue, isn't it?
thanks for your help, roberto
Hi, I obtained the maps with the statistical linear model provided by Freesurfer and now I need to localize the spots; I'd like to know if it is possible to obtain the exact coordinates of the spots and how I can do that on tksurfer. Thanks Valentina
Hi, I have two questions about the spherical morphometry:
Is the "rh.lh.sphere.reg" of each subject the sphere of the subject registered on an average spherical cortical surface provided by Freesurfer?
If the "lh.sphere" of a subject is good but his "lh.sphere.reg" doesn't look very good, what does it means?
Thanks Valentina
what does not looking very good mean? The ?h.sphere is the metrically optimal spherical representation, the ?h.sphere.reg is that sphere warped to be in register with the atlas (so it will always be more distorted than the ?h.sphere)
On Mon, 19 Mar 2007, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have two questions about the spherical morphometry:
Is the "rh.lh.sphere.reg" of each subject the sphere of the subject registered on an average spherical cortical surface provided by Freesurfer?
If the "lh.sphere" of a subject is good but his "lh.sphere.reg" doesn't look very good, what does it means?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce, Thanks for replying. Yes the sphere.reg is warped. I send you two images (the sphere and the sphere.reg of a subject), can you please let me know your opinion about them? Is this a normal result? What does exactly mean? Thanks
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, March 20, 2007 11:05 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spherical morphometry
what does not looking very good mean? The ?h.sphere is the metrically optimal spherical representation, the ?h.sphere.reg is that sphere warped to be in register with the atlas (so it will always be more distorted than the ?h.sphere)
On Mon, 19 Mar 2007, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have two questions about the spherical morphometry:
Is the "rh.lh.sphere.reg" of each subject the sphere of the subject registered on an average spherical cortical surface provided by Freesurfer?
If the "lh.sphere" of a subject is good but his "lh.sphere.reg"
doesn't
look very good, what does it means?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hmmm, this looks like a bug we've been chasing down that results in more distortion than we used to have in the spherical registration.
On Tue, 20 Mar 2007, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Dear Bruce, Thanks for replying. Yes the sphere.reg is warped. I send you two images (the sphere and the sphere.reg of a subject), can you please let me know your opinion about them? Is this a normal result? What does exactly mean? Thanks
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, March 20, 2007 11:05 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spherical morphometry
what does not looking very good mean? The ?h.sphere is the metrically optimal spherical representation, the ?h.sphere.reg is that sphere warped to be in register with the atlas (so it will always be more distorted than the ?h.sphere)
On Mon, 19 Mar 2007, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have two questions about the spherical morphometry:
Is the "rh.lh.sphere.reg" of each subject the sphere of the subject registered on an average spherical cortical surface provided by Freesurfer?
If the "lh.sphere" of a subject is good but his "lh.sphere.reg"
doesn't
look very good, what does it means?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Durastanti, Valentina (NIH/NINDS) [F] -
roberto toro