Hi all,
I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following:
First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that
if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v
Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is
1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate.
Could you please help me with this procedure?
Thank you in advance, Yolanda
Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug
Yolanda Vives wrote:
Hi all,
I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following:
First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that
if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v
Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is
1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate.
Could you please help me with this procedure?
Thank you in advance, Yolanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear all, For one of my subjects I had to correct the Talairach step manually. My manual correction, however, may not be perfect. Is it possible to re-run autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the automatic registration?
Thank you! Aga
aga,
no, its not possible to guide (initialize) the registration with your manual one. but if
recon-all -s subjid -tal-check
passes, then your tal check is likely good enough.
n.
On Tue, 2011-05-03 at 16:56 +0200, Agnieszka Burzynska wrote:
Dear all, For one of my subjects I had to correct the Talairach step manually. My manual correction, however, may not be perfect. Is it possible to re-run autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the automatic registration?
Thank you! Aga
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct.
Regards, Yolanda
2011/5/3 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug
Yolanda Vives wrote:
Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate.
Could you please help me with this procedure? Thank you in advance, Yolanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Which coordinates are you using? Can you send me the label? doug
Yolanda Vives wrote:
Hi Doug,
The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct.
Regards, Yolanda
2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug Yolanda Vives wrote: Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate. Could you please help me with this procedure? Thank you in advance, Yolanda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
I am using the coordinates obtained with the matlab function "read_label()". I send you one of my labels.
Thanks a lot, Yolanda
2011/5/3 Douglas N Greve greve@nmr.mgh.harvard.edu
Which coordinates are you using? Can you send me the label? doug
Yolanda Vives wrote:
Hi Doug,
The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct.
Regards, Yolanda
2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu>
Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug
Yolanda Vives wrote:
Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate. Could you please help me with this procedure? Thank you in advance, Yolanda
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
There's something strange going on. Did your label come from the right hemisphere? The first coordinate of all the points is negative, indicating that it is on the left side. Which MNI atlas are you using?
doug
7705 -36.725 5.727 20.658 0.000000
Yolanda Vives wrote:
I am using the coordinates obtained with the matlab function "read_label()". I send you one of my labels.
Thanks a lot, Yolanda
2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Which coordinates are you using? Can you send me the label? doug Yolanda Vives wrote: Hi Doug, The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct. Regards, Yolanda 2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug Yolanda Vives wrote: Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate. Could you please help me with this procedure? Thank you in advance, Yolanda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es <http://www.pic.es/> Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Yes, I have made a load_label from the right hemisphere and it corresponds to the position were I draw it. I send you another label just in case the other label was corrupted.
Related to the MNI atlas, I have transformed the MNI coordinates into Talairach coordinates using a mni2tal funcion from http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and then I have used a program from www.talairach.org to obtain the name of the parcel.
thank you again for your help, yolanda
2011/5/4 Douglas N Greve greve@nmr.mgh.harvard.edu
There's something strange going on. Did your label come from the right hemisphere? The first coordinate of all the points is negative, indicating that it is on the left side. Which MNI atlas are you using?
doug
7705 -36.725 5.727 20.658 0.000000
Yolanda Vives wrote:
I am using the coordinates obtained with the matlab function "read_label()". I send you one of my labels. Thanks a lot, Yolanda
2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu>
Which coordinates are you using? Can you send me the label? doug
Yolanda Vives wrote:
Hi Doug, The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct. Regards, Yolanda 2011/5/3 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug Yolanda Vives wrote: Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afterwards, I have used the matlab function read_label to obtain the RAS coordinates of this label. To transform these coordinates into mni coordinates, I have read that if v = [R A S 1]' and X matrix is the matrix from talairach.xfm, then vMNI = X*v Taking this into account, I have used the X matrix from the talairach.xfm of "fsaverage" (where the results of qdec are mapped). This matrix is 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 so vMNI is the same as v. When I introduce v (or vMNI) coordinates into a MNI atlas, I don't obtain the cingulate. Could you please help me with this procedure? Thank you in advance, Yolanda
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es <http://www.pic.es/> Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Agnieszka Burzynska -
Douglas N Greve -
Nick Schmansky -
Yolanda Vives