Dear freesurfers,
I have a set of dot locations (300~400) in a template brain, indicated by indices of a 3-D array of the template MRI data, which can be easily transformed to RAS coordinates. I wish to project these dot locations to individual MRIs, ideally also as indicated by indices in the 3-D array of the individual MRI data. Is it possible to do it in freesurfer? I guess the surface-based procedure shall work well for this. It might be a very junior question, if it was documented somewhere before, please let me know the link. Thank you very much for help.
best Peng
Do you mean you want to display them in the MRI volume or on the surface (or both)? When you say that they are in "RAS coordinates", what do you mean? How are the coords defined? doug
On 03/08/2014 07:26 AM, peng wrote:
Dear freesurfers,
I have a set of dot locations (300~400) in a template brain, indicated by indices of a 3-D array of the template MRI data, which can be easily transformed to RAS coordinates. I wish to project these dot locations to individual MRIs, ideally also as indicated by indices in the 3-D array of the individual MRI data. Is it possible to do it in freesurfer? I guess the surface-based procedure shall work well for this. It might be a very junior question, if it was documented somewhere before, please let me know the link. Thank you very much for help.
best Peng
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug for your reply. In fact I need both. I do this mainly for computation (in volume); and display (in surface) is also cool.
The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume of the template (icbm152). This can be implemented as an Nx3 matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in the volume. RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3 dimensions are taking right, anterior, superior as positive, e.g An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior and nz0 mm superior of AC. The above two systems can be easily transformed by a transformation matrix.
I wish to know the correspondent locations of An in individual subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish to find the center of V1 in the subject as B1. So far, all the locations are represented in volume. However, I guess to normalise the individual brain to the template, freesurfer will extract the volumes to surfaces. I imagine the procedure will be like An (volume representation of dots in template) -> ASn (surface representation of dots in template) -> BSn(surface representation of dots in individual) -> Bn(volume representation of dots in individual). If this assumption is correct, I would like to use Bn for my computation and ASn for display later.
I hope I have made myself clearer.
best Peng
On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Do you mean you want to display them in the MRI volume or on the surface (or both)? When you say that they are in "RAS coordinates", what do you mean? How are the coords defined? doug
On 03/08/2014 07:26 AM, peng wrote:
Dear freesurfers,
I have a set of dot locations (300~400) in a template brain, indicated by indices of a 3-D array of the template MRI data, which can be easily transformed to RAS coordinates. I wish to project these dot locations to individual MRIs, ideally also as indicated by indices in the 3-D array of the individual MRI data. Is it possible to do it in freesurfer? I guess the surface-based procedure shall work well for this. It might be a very junior question, if it was documented somewhere before, please let me know the link. Thank you very much for help.
best Peng
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-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 Peng, there's a lot going on there, and it is not specific enough for me to make recommendations. Take a look at the docs we have on our coordinate systems
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile...
you might get the answer you need from there or at least use our terminology to point me in the right direction
doug
On 03/10/2014 12:20 PM, peng wrote:
Thanks Doug for your reply. In fact I need both. I do this mainly for computation (in volume); and display (in surface) is also cool.
The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume of the template (icbm152). This can be implemented as an Nx3 matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in the volume. RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3 dimensions are taking right, anterior, superior as positive, e.g An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior and nz0 mm superior of AC. The above two systems can be easily transformed by a transformation matrix.
I wish to know the correspondent locations of An in individual subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish to find the center of V1 in the subject as B1. So far, all the locations are represented in volume. However, I guess to normalise the individual brain to the template, freesurfer will extract the volumes to surfaces. I imagine the procedure will be like An (volume representation of dots in template) -> ASn (surface representation of dots in template) -> BSn(surface representation of dots in individual) -> Bn(volume representation of dots in individual). If this assumption is correct, I would like to use Bn for my computation and ASn for display later.
I hope I have made myself clearer.
best Peng
On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Do you mean you want to display them in the MRI volume or on the surface (or both)? When you say that they are in "RAS coordinates", what do you mean? How are the coords defined? doug On 03/08/2014 07:26 AM, peng wrote: > Dear freesurfers, > > I have a set of dot locations (300~400) in a template brain, > indicated by indices of a 3-D array of the template MRI data, which > can be easily transformed to RAS coordinates. I wish to project these > dot locations to individual MRIs, ideally also as indicated by indices > in the 3-D array of the individual MRI data. Is it possible to do it > in freesurfer? I guess the surface-based procedure shall work well for > this. It might be a very junior question, if it was documented > somewhere before, please let me know the link. Thank you very much for > help. > > best > Peng > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, With the terminology in the document you provided, I can summarize what I want to do exactly as part of the flow chart in page 7. I listed it as between==. As described in the document, I can get Ta, Tb by <mri_info –vox2ras-tkr vol>; and R from a file <register.dat>; am I right? Practically, I may put my template as a subject a0, and individuals as subjects a1, a2 ..., an. What is the file name of [Vol A TkReg "RAS"] under the subject folder? ============== [Volume A CRS] -> (Ta) -> [Vol A TkReg "RAS"] <- (R) <- [ Vol B TkReg "RAS"] <- (Tb) <- [Volume B CRS] ============== Thanks a lot.
On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Peng, there's a lot going on there, and it is not specific enough for me to make recommendations. Take a look at the docs we have on our coordinate systems
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile...
you might get the answer you need from there or at least use our terminology to point me in the right direction
doug
On 03/10/2014 12:20 PM, peng wrote:
Thanks Doug for your reply. In fact I need both. I do this mainly for computation (in volume); and display (in surface) is also cool.
The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume of the template (icbm152). This can be implemented as an Nx3 matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in the volume. RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3 dimensions are taking right, anterior, superior as positive, e.g An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior and nz0 mm superior of AC. The above two systems can be easily transformed by a transformation matrix.
I wish to know the correspondent locations of An in individual subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish to find the center of V1 in the subject as B1. So far, all the locations are represented in volume. However, I guess to normalise the individual brain to the template, freesurfer will extract the volumes to surfaces. I imagine the procedure will be like An (volume representation of dots in template) -> ASn (surface representation of dots in template) -> BSn(surface representation of dots in individual) -> Bn(volume representation of dots in individual). If this assumption is correct, I would like to use Bn for my computation and ASn for display later.
I hope I have made myself clearer.
best Peng
On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Do you mean you want to display them in the MRI volume or on the surface (or both)? When you say that they are in "RAS coordinates", what do you mean? How are the coords defined? doug On 03/08/2014 07:26 AM, peng wrote: > Dear freesurfers, > > I have a set of dot locations (300~400) in a template brain, > indicated by indices of a 3-D array of the template MRI data, which > can be easily transformed to RAS coordinates. I wish to project these > dot locations to individual MRIs, ideally also as indicated by indices > in the 3-D array of the individual MRI data. Is it possible to doit
> in freesurfer? I guess the surface-based procedure shall work well for > this. It might be a very junior question, if it was documented > somewhere before, please let me know the link. Thank you very much for > help. > > best > Peng > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 03/11/2014 05:10 PM, peng wrote:
Hi Doug, With the terminology in the document you provided, I can summarize what I want to do exactly as part of the flow chart in page 7. I listed it as between==. As described in the document, I can get Ta, Tb by <mri_info –vox2ras-tkr vol>; and R from a file <register.dat>; am I right? Practically, I may put my template as a subject a0, and individuals as subjects a1, a2 ..., an. What is the file name of [Vol A TkReg "RAS"] under the subject folder?
That is not meant to be a volume, just the name of the space/coordinate system (distinguishes it from other spaces). doug
============== [Volume A CRS] -> (Ta) -> [Vol A TkReg "RAS"] <- (R) <- [ Vol B TkReg "RAS"] <- (Tb) <- [Volume B CRS] ============== Thanks a lot.
On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Peng, there's a lot going on there, and it is not specific enough for me to make recommendations. Take a look at the docs we have on our coordinate systems http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf you might get the answer you need from there or at least use our terminology to point me in the right direction doug On 03/10/2014 12:20 PM, peng wrote: > Thanks Doug for your reply. In fact I need both. I do this mainly for > computation (in volume); and display (in surface) is also cool. > > The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in > volume of the template (icbm152). This can be implemented as an Nx3 > matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in > the volume. > RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3 > dimensions are taking right, anterior, superior as positive, e.g > An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior > and nz0 mm superior of AC. > The above two systems can be easily transformed by a transformation > matrix. > > I wish to know the correspondent locations of An in individual > subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish > to find the center of V1 in the subject as B1. > So far, all the locations are represented in volume. However, I guess > to normalise the individual brain to the template, freesurfer will > extract the volumes to surfaces. I imagine the procedure will be like > An (volume representation of dots in template) -> ASn (surface > representation of dots in template) -> BSn(surface representation of > dots in individual) -> Bn(volume representation of dots in > individual). If this assumption is correct, I would like to use Bn for > my computation and ASn for display later. > > I hope I have made myself clearer. > > best > Peng > > > On Mon, Mar 10, 2014 at 4:21 PM, 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>>> wrote: > > > Do you mean you want to display them in the MRI volume or on the > surface > (or both)? When you say that they are in "RAS coordinates", what > do you > mean? How are the coords defined? > doug > > > > On 03/08/2014 07:26 AM, peng wrote: > > Dear freesurfers, > > > > I have a set of dot locations (300~400) in a template brain, > > indicated by indices of a 3-D array of the template MRI data, which > > can be easily transformed to RAS coordinates. I wish to project > these > > dot locations to individual MRIs, ideally also as indicated by > indices > > in the 3-D array of the individual MRI data. Is it possible to do it > > in freesurfer? I guess the surface-based procedure shall work > well for > > this. It might be a very junior question, if it was documented > > somewhere before, please let me know the link. Thank you very > much for > > help. > > > > best > > Peng > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 > > > 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. > > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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