Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a larger head (could be defined anatomically, the most outer point of the hippocampus, for example.
When finding equivalencies for surface ROIs from one subject to another we used label2label for example. If I have an overlay in volume space, how should I "move" it to another subject?
Thanks again, Gari
On 12/03/2013, at 20:29, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
_______________________________________________ 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
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.
Hi Gary, you would use the MNI305 space as the common space. Eg, Case 2 shows you how to go from RAS of a subject to MNI305 space. You would reverse that to go from MNI305 space to another subject's RAS space thus allowing a RAS-RAS transform. If you have a surface overlay for a subject, you can use mri_surf2surf to transfer it to another subject. doug
On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a larger head (could be defined anatomically, the most outer point of the hippocampus, for example.
When finding equivalencies for surface ROIs from one subject to another we used label2label for example. If I have an overlay in volume space, how should I "move" it to another subject?
Thanks again, Gari
On 12/03/2013, at 20:29, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Thanks Doug, the problem is that I have a volume overlay.
When I register avg305T1.nii with Colin27 I have a different register matrix than when using single_subject_T1.nii.
Do you think that this procedure will work (scripted for every subject)? - *bbregister --s Colin27 --mov S_01 --init-spm --reg bb_Colin27_S_01.dat --t1* * * *and then* * * *- **mri_vol2vol --mov myROI.mgh --reg bb_Colin27_S_00.dat --fstarg --interp nearest --o S_01.myROI.bb.mgh* * *
thanks again! Gari
On Wed, Mar 13, 2013 at 10:15 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Gary, you would use the MNI305 space as the common space. Eg, Case 2 shows you how to go from RAS of a subject to MNI305 space. You would reverse that to go from MNI305 space to another subject's RAS space thus allowing a RAS-RAS transform. If you have a surface overlay for a subject, you can use mri_surf2surf to transfer it to another subject. doug
On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a larger head (could be defined anatomically, the most outer point of the hippocampus, for example.
When finding equivalencies for surface ROIs from one subject to another we used label2label for example. If I have an overlay in volume space, how should I "move" it to another subject?
Thanks again, Gari
On 12/03/2013, at 20:29, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
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
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.
Hi Doug, I tried to do what you recommended but I am encountering an inconsistency.
(Note: I obtain the same results in R (with ginv() ) and Matlab (with pinv() ) )
Could you please have a look at the code and the values please? I don't know what else to do right now... (it is possible to copy paste everything in Matlab)
***************
TalXFM = [1.040797, 0.011370, -0.069615, -0.863770;0.031794, 0.939578, 0.254677 ,-32.126083; 0.048458, -0.236663 ,1.101207, -20.946930];
Norig = [-1.00000 , -0.00000 , -0.00000 , 130.38606 ;-0.00000 , 0.00000 , 1.00000, -109.95447 ;-0.00000, -1.00000 , 0.00000 , 150.14441 ; 0.00000, 0.00000 , 0.00000 , 1.00000];
Torig = [-1.00000 , 0.00000 , 0.00000 , 128.00000; 0.00000 , 0.00000 , 1.00000, -128.00000; 0.00000 , -1.00000 , 0.00000 , 128.00000; 0.00000 , 0.00000 , 0.00000 , 1.00000];
W = TalXFM * Norig * inv(Torig);
Volume_RAS = [1, -30, 1, 1];
MNI_Talairach = W * Volume_RAS' % Coincides with Tkmedit
% MNI_Talairach = (0.9133; -37.3562; 7.5331)
Volume_RAS = pinv(W)*MNI_Talairach % DOES NOT COINCIDE
% Volume_RAS = (0.4324; -2.9014; 8.7350; 3.8992) >> shouldn't be [1, -30, 1, 1]; ?
********************
Is the transformation two-way? Should it be?
Many thanks again for your help,
Gari
On Wed, Mar 13, 2013 at 10:15 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Gary, you would use the MNI305 space as the common space. Eg, Case 2 shows you how to go from RAS of a subject to MNI305 space. You would reverse that to go from MNI305 space to another subject's RAS space thus allowing a RAS-RAS transform. If you have a surface overlay for a subject, you can use mri_surf2surf to transfer it to another subject. doug
On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a larger head (could be defined anatomically, the most outer point of the hippocampus, for example.
When finding equivalencies for surface ROIs from one subject to another we used label2label for example. If I have an overlay in volume space, how should I "move" it to another subject?
Thanks again, Gari
On 12/03/2013, at 20:29, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that?
Thank you very much, Gari
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
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.
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