Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Also robust register (at least the standard version that you use) is not designed to do cross modal registration. So I am amazed it can register a CT to an MRI at all (if that is what you are doing). To get a better registration try - using a different cost functions, e.g. --cost nmi (normalized mutual information)
Also you could try using bb_register if you have surfaces on the mri.
Best, Martin
On 04/28/2014 02:32 PM, Douglas N Greve wrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
FYI, it is bbregister not bb_register :-)
On 04/28/2014 02:51 PM, Martin Reuter wrote:
Also robust register (at least the standard version that you use) is not designed to do cross modal registration. So I am amazed it can register a CT to an MRI at all (if that is what you are doing). To get a better registration try
- using a different cost functions, e.g.
--cost nmi (normalized mutual information)
Also you could try using bb_register if you have surfaces on the mri.
Best, Martin
On 04/28/2014 02:32 PM, Douglas N Greve wrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for the response. I'm not seeing lta_convert as an executable that I can run. I have freesurfer v5.3.0 installed - is there another version that I should be using?
For using tkregister2, I'm a bit confused as to what I should be doing. I had assumed (erroneously, it seems) that the .lta and .dat files contained the same information. I just tried re-running tkregister2 with the command: tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s average --lta reg_avg.lta Such that I can pass in the reg_avg.lta file created from robust register, and have it output a reg_avg.dat file. The contents of these two files, however, seem to be exactly the same.
I also running tkregister2 with the --fslregout and --freeview flags, but neither of those produced a correct transformation either.
Martin: We are indeed registering the CT to an average MRI, and for the moment we are correcting inaccuracies manually with tkregister2. I just tried bbregister with one of our problem subjects, and it still produced a matrix that had to be significantly adjusted in tkregister2. Furthermore, the matrix that it produced still did not transform the coordinates correctly in MATLAB.
-Isaac
On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
Hi All,
I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject.
By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should.
However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying:
inv(Reg_avg) * Tmov * CT_coords
with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended).
As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this?
Thanks, Isaac
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
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.
When you say the content is the same, do you mean exactly the same or just the matrix? Also, what coordinate system are you trying to go to? The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use
inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords
On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
Hi Doug, Thanks for the response. I'm not seeing lta_convert as an executable that I can run. I have freesurfer v5.3.0 installed - is there another version that I should be using?
For using tkregister2, I'm a bit confused as to what I should be doing. I had assumed (erroneously, it seems) that the .lta and .dat files contained the same information. I just tried re-running tkregister2 with the command: tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s average --lta reg_avg.lta Such that I can pass in the reg_avg.lta file created from robust register, and have it output a reg_avg.dat file. The contents of these two files, however, seem to be exactly the same.
I also running tkregister2 with the --fslregout and --freeview flags, but neither of those produced a correct transformation either.
Martin: We are indeed registering the CT to an average MRI, and for the moment we are correcting inaccuracies manually with tkregister2. I just tried bbregister with one of our problem subjects, and it still produced a matrix that had to be significantly adjusted in tkregister2. Furthermore, the matrix that it produced still did not transform the coordinates correctly in MATLAB.
-Isaac
On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > Hi All, > > I am attempting to transform sets of coordinates from subject CRS > space into the surfaceRAS space of an average subject, made with > make_average_subject. > > By our current method, we register the individual CT to the average > surface using mri_robust_register with the command: > mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta > reg_avg.lta --iscale --satit > and then check and adjust the registration with: > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average > > These steps work fine, and when I load the average brain in freeview, > then load the subject CT with with the registration file reg_avg.lta > applied, the two overlap just as they should. > > However, when I attempt to do the same thing in matlab, some (though > not all) of the subjects present a problem. > I do the coordinate transformation (as suggested on > http://freesurfer.net/fswiki/CoordinateSystems) by applying: > > inv(Reg_avg) * Tmov * CT_coords > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space > from the CT (with a vector of ones appended). > > As I said, some of the scans come out fine, with the coordinates in > the correct place on the average surface, while others are very far > removed from their correct location. How can I fix this? > > Thanks, > Isaac > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I believe. I'm a little unclear as to what exactly anat space means, but I know that I'm trying to get it from CRS in the CT to the space in which the surface is plotted in MATLAB, which I believe is tkrRAS, anatomical. I'm certain it's no longer CRS space, as the x-coordinates must contain some negative indices.
On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
When you say the content is the same, do you mean exactly the same or just the matrix? Also, what coordinate system are you trying to go to? The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use
inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords
On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
Hi Doug, Thanks for the response. I'm not seeing lta_convert as an executable that I can run. I have freesurfer v5.3.0 installed - is there another version that I should be using?
For using tkregister2, I'm a bit confused as to what I should be doing. I had assumed (erroneously, it seems) that the .lta and .dat files contained the same information. I just tried re-running tkregister2 with the command: tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s average --lta reg_avg.lta Such that I can pass in the reg_avg.lta file created from robust register, and have it output a reg_avg.dat file. The contents of these two files, however, seem to be exactly the same.
I also running tkregister2 with the --fslregout and --freeview flags, but neither of those produced a correct transformation either.
Martin: We are indeed registering the CT to an average MRI, and for the moment we are correcting inaccuracies manually with tkregister2. I just tried bbregister with one of our problem subjects, and it still produced a matrix that had to be significantly adjusted in tkregister2. Furthermore, the matrix that it produced still did not transform the coordinates correctly in MATLAB.
-Isaac
On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The matrix in the lta is probably not the right one. Try using lta_convert or tkregister2 to change it to a register.dat file (which is what is expected in your formula) doug On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > Hi All, > > I am attempting to transform sets of coordinates from subject CRS > space into the surfaceRAS space of an average subject, made with > make_average_subject. > > By our current method, we register the individual CT to the average > surface using mri_robust_register with the command: > mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta > reg_avg.lta --iscale --satit > and then check and adjust the registration with: > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average > > These steps work fine, and when I load the average brain in freeview, > then load the subject CT with with the registration filereg_avg.lta
> applied, the two overlap just as they should. > > However, when I attempt to do the same thing in matlab, some(though
> not all) of the subjects present a problem. > I do the coordinate transformation (as suggested on > http://freesurfer.net/fswiki/CoordinateSystems) by applying: > > inv(Reg_avg) * Tmov * CT_coords > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space > from the CT (with a vector of ones appended). > > As I said, some of the scans come out fine, with the coordinates in > the correct place on the average surface, while others are very far > removed from their correct location. How can I fix this? > > Thanks, > Isaac > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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/
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It sounds like you are doing the right thing with the right equation. Can you elaborate on what is going wrong?
On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote:
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I believe. I'm a little unclear as to what exactly anat space means, but I know that I'm trying to get it from CRS in the CT to the space in which the surface is plotted in MATLAB, which I believe is tkrRAS, anatomical. I'm certain it's no longer CRS space, as the x-coordinates must contain some negative indices.
On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
When you say the content is the same, do you mean exactly the same or just the matrix? Also, what coordinate system are you trying to go to? The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote: > Hi Doug, > Thanks for the response. > I'm not seeing lta_convert as an executable that I can run. I have > freesurfer v5.3.0 installed - is there another version that I should > be using? > > For using tkregister2, I'm a bit confused as to what I should be > doing. I had assumed (erroneously, it seems) that the .lta and .dat > files contained the same information. > I just tried re-running tkregister2 with the command: > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s > average --lta reg_avg.lta > Such that I can pass in the reg_avg.lta file created from robust > register, and have it output a reg_avg.dat file. The contents of these > two files, however, seem to be exactly the same. > > I also running tkregister2 with the --fslregout and --freeview flags, > but neither of those produced a correct transformation either. > > Martin: > We are indeed registering the CT to an average MRI, and for the moment > we are correcting inaccuracies manually with tkregister2. > I just tried bbregister with one of our problem subjects, and it still > produced a matrix that had to be significantly adjusted in > tkregister2. Furthermore, the matrix that it produced still did not > transform the coordinates correctly in MATLAB. > > -Isaac > > > On Mon, Apr 28, 2014 at 2:32 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: > > > The matrix in the lta is probably not the right one. Try using > lta_convert or tkregister2 to change it to a register.dat file > (which is > what is expected in your formula) > doug > > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > > Hi All, > > > > I am attempting to transform sets of coordinates from subject CRS > > space into the surfaceRAS space of an average subject, made with > > make_average_subject. > > > > By our current method, we register the individual CT to the average > > surface using mri_robust_register with the command: > > mri_robust_register --mov [subj_CT].img --dst average_orig.mgz > --lta > > reg_avg.lta --iscale --satit > > and then check and adjust the registration with: > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial > --s average > > > > These steps work fine, and when I load the average brain in > freeview, > > then load the subject CT with with the registration file reg_avg.lta > > applied, the two overlap just as they should. > > > > However, when I attempt to do the same thing in matlab, some (though > > not all) of the subjects present a problem. > > I do the coordinate transformation (as suggested on > > http://freesurfer.net/fswiki/CoordinateSystems) by applying: > > > > inv(Reg_avg) * Tmov * CT_coords > > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as > > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space > > from the CT (with a vector of ones appended). > > > > As I said, some of the scans come out fine, with the coordinates in > > the correct place on the average surface, while others are very far > > removed from their correct location. How can I fix this? > > > > Thanks, > > Isaac > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel: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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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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The purpose of what I'm trying to do is getting specific points from the CT onto the average surface. These points lie on the surface of the brain.
Originally, we were using flirt to register the CT to the MRI, then registering the MRI to the talairach brain, to get the CT into the same space as the surface. This method worked okay, but we were hoping to improve on it.
The new method, using robust register and tkregsiter2, produces coordinates that are on the surface of the brain in freeview, but not in matlab (for some subjects).
Here is the info for one problem subject:
mri_info --vox2ras-tkr [subj]_CT_combined.img INFO: using NIfTI-1 qform -0.47461 0.00000 0.00000 121.50000 0.00000 0.00000 0.62634 -69.83636 0.00000 -0.47461 0.00000 121.50000 0.00000 0.00000 0.00000 1.00000
# transform file reg_avg.lta # created by ---- on Thu Mar 27 15:55:39 2014 type = 1 nxforms = 1 mean = 256.0000 228.0000 111.0000 sigma = 10000.0000 1 4 4 9.349995851516724e-01 -2.874486744403839e-01 -2.077235281467438e-01 -3.043334960937500e+01 3.062604963779449e-01 9.497789144515991e-01 6.422379612922668e-02 1.133301696777344e+02 1.788303703069687e-01 -1.236666887998581e-01 9.760769009590149e-01 -1.039845886230469e+02 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = [subj]_CT_combined.img volume = 512 512 223 voxelsize = 4.746093750000000e-01 4.746093750000000e-01 6.263351440429688e-01 xras = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 9.703245759010315e-01 2.418061196804047e-01 zras = -0.000000000000000e+00 -2.418061196804047e-01 9.703245759010315e-01 cras = 7.629394531250000e-06 -1.615307769775391e+02 1.476517486572266e+02 dst volume info valid = 1 # volume info valid filename = /data/eeg/freesurfer/subjects/average/mri/orig.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = -2.220446049250313e-16 -1.490116119384766e-08 -1.000000000000000e+00 zras = 4.440892098500626e-16 1.000000000000000e+00 8.443226899772703e-18 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
Here are a set of eight coordinates, all of which are on the surface in CRS space on the CT: 242 267 47 241 283 36 234 298 28 221 313 23 203 321 19 183 323 24 172 312 33 164 297 42
After applying the transform, these coordinates come out as: 5.2486 -168.8798 78.8261 2.2243 -174.6209 70.8729 2.5230 -179.4546 62.9121 6.0596 -183.3221 54.4805 12.6010 -187.6878 48.8390 22.2656 -187.3245 46.1419 29.8070 -184.1168 50.5152 36.3566 -180.7347 57.0374
Those middle coordinates are all off the brain - the coordinates are far too negative.
When run through the first method, they come out to: 20.6235 -15.8172 -23.1366 19.041 -5.94338 -28.5567 20.8091 3.8041 -32.346 25.8047 13.9764 -34.4435 34.3347 20.7722 -36.4294 44.7823 23.7184 -33.5718 52.1009 18.1343 -29.1088 58.3186 10.0044 -24.8649
Which are (approximately) on the surface of the brain.
However, when I load up the average surface in freeview, and apply reg_avg.lta to the CT, the two overlay exactly.
I'm mostly trying to figure out why the coordinates that I get in MATLAB do not agree with the coordinates that I see in freeview.
Thanks again for your help, Isaac
On Tue, Apr 29, 2014 at 1:43 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It sounds like you are doing the right thing with the right equation. Can you elaborate on what is going wrong?
On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote:
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I believe. I'm a little unclear as to what exactly anat space means, but I know that I'm trying to get it from CRS in the CT to the space in which the surface is plotted in MATLAB, which I believe is tkrRAS, anatomical. I'm certain it's no longer CRS space, as the x-coordinates must contain some negative indices.
On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
When you say the content is the same, do you mean exactly the same or just the matrix? Also, what coordinate system are you trying to goto?
The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote: > Hi Doug, > Thanks for the response. > I'm not seeing lta_convert as an executable that I can run. I have > freesurfer v5.3.0 installed - is there another version that Ishould
> be using? > > For using tkregister2, I'm a bit confused as to what I should be > doing. I had assumed (erroneously, it seems) that the .lta and .dat > files contained the same information. > I just tried re-running tkregister2 with the command: > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s > average --lta reg_avg.lta > Such that I can pass in the reg_avg.lta file created from robust > register, and have it output a reg_avg.dat file. The contents of these > two files, however, seem to be exactly the same. > > I also running tkregister2 with the --fslregout and --freeview flags, > but neither of those produced a correct transformation either. > > Martin: > We are indeed registering the CT to an average MRI, and for the moment > we are correcting inaccuracies manually with tkregister2. > I just tried bbregister with one of our problem subjects, and it still > produced a matrix that had to be significantly adjusted in > tkregister2. Furthermore, the matrix that it produced still did not > transform the coordinates correctly in MATLAB. > > -Isaac > > > On Mon, Apr 28, 2014 at 2:32 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: > > > The matrix in the lta is probably not the right one. Try using > lta_convert or tkregister2 to change it to a register.dat file > (which is > what is expected in your formula) > doug > > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > > Hi All, > > > > I am attempting to transform sets of coordinates from subject CRS > > space into the surfaceRAS space of an average subject, made with > > make_average_subject. > > > > By our current method, we register the individual CT to the average > > surface using mri_robust_register with the command: > > mri_robust_register --mov [subj_CT].img --dst average_orig.mgz > --lta > > reg_avg.lta --iscale --satit > > and then check and adjust the registration with: > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial > --s average > > > > These steps work fine, and when I load the average brain in > freeview, > > then load the subject CT with with the registration file reg_avg.lta > > applied, the two overlap just as they should. > > > > However, when I attempt to do the same thing in matlab, some (though > > not all) of the subjects present a problem. > > I do the coordinate transformation (as suggested on > > http://freesurfer.net/fswiki/CoordinateSystems) by applying: > > > > inv(Reg_avg) * Tmov * CT_coords > > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as > > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space > > from the CT (with a vector of ones appended). > > > > As I said, some of the scans come out fine, with the coordinates in > > the correct place on the average surface, while others are very far > > removed from their correct location. How can I fix this? > > > > Thanks, > > Isaac > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel: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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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>
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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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Any other thoughts as to what might be going wrong with our coordinate transformations / any other transformations that we might not be taking into account?
Thanks, Isaac
On Tue, Apr 29, 2014 at 4:52 PM, ISAAC PEDISICH iped@sas.upenn.edu wrote:
The purpose of what I'm trying to do is getting specific points from the CT onto the average surface. These points lie on the surface of the brain.
Originally, we were using flirt to register the CT to the MRI, then registering the MRI to the talairach brain, to get the CT into the same space as the surface. This method worked okay, but we were hoping to improve on it.
The new method, using robust register and tkregsiter2, produces coordinates that are on the surface of the brain in freeview, but not in matlab (for some subjects).
Here is the info for one problem subject:
mri_info --vox2ras-tkr [subj]_CT_combined.img INFO: using NIfTI-1 qform -0.47461 0.00000 0.00000 121.50000 0.00000 0.00000 0.62634 -69.83636 0.00000 -0.47461 0.00000 121.50000 0.00000 0.00000 0.00000 1.00000
# transform file reg_avg.lta # created by ---- on Thu Mar 27 15:55:39 2014 type = 1 nxforms = 1 mean = 256.0000 228.0000 111.0000 sigma = 10000.0000 1 4 4 9.349995851516724e-01 -2.874486744403839e-01 -2.077235281467438e-01 -3.043334960937500e+01 3.062604963779449e-01 9.497789144515991e-01 6.422379612922668e-02 1.133301696777344e+02 1.788303703069687e-01 -1.236666887998581e-01 9.760769009590149e-01 -1.039845886230469e+02 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = [subj]_CT_combined.img volume = 512 512 223 voxelsize = 4.746093750000000e-01 4.746093750000000e-01 6.263351440429688e-01 xras = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 9.703245759010315e-01 2.418061196804047e-01 zras = -0.000000000000000e+00 -2.418061196804047e-01 9.703245759010315e-01 cras = 7.629394531250000e-06 -1.615307769775391e+02 1.476517486572266e+02 dst volume info valid = 1 # volume info valid filename = /data/eeg/freesurfer/subjects/average/mri/orig.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = -2.220446049250313e-16 -1.490116119384766e-08 -1.000000000000000e+00 zras = 4.440892098500626e-16 1.000000000000000e+00 8.443226899772703e-18 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
Here are a set of eight coordinates, all of which are on the surface in CRS space on the CT: 242 267 47 241 283 36 234 298 28 221 313 23 203 321 19 183 323 24 172 312 33 164 297 42
After applying the transform, these coordinates come out as: 5.2486 -168.8798 78.8261 2.2243 -174.6209 70.8729 2.5230 -179.4546 62.9121 6.0596 -183.3221 54.4805 12.6010 -187.6878 48.8390 22.2656 -187.3245 46.1419 29.8070 -184.1168 50.5152 36.3566 -180.7347 57.0374
Those middle coordinates are all off the brain - the coordinates are far too negative.
When run through the first method, they come out to: 20.6235 -15.8172 -23.1366 19.041 -5.94338 -28.5567 20.8091 3.8041 -32.346 25.8047 13.9764 -34.4435 34.3347 20.7722 -36.4294 44.7823 23.7184 -33.5718 52.1009 18.1343 -29.1088 58.3186 10.0044 -24.8649
Which are (approximately) on the surface of the brain.
However, when I load up the average surface in freeview, and apply reg_avg.lta to the CT, the two overlay exactly.
I'm mostly trying to figure out why the coordinates that I get in MATLAB do not agree with the coordinates that I see in freeview.
Thanks again for your help, Isaac
On Tue, Apr 29, 2014 at 1:43 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
It sounds like you are doing the right thing with the right equation. Can you elaborate on what is going wrong?
On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote:
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I believe. I'm a little unclear as to what exactly anat space means, but I know that I'm trying to get it from CRS in the CT to the space in which the surface is plotted in MATLAB, which I believe is tkrRAS, anatomical. I'm certain it's no longer CRS space, as the x-coordinates must contain some negative indices.
On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
When you say the content is the same, do you mean exactly the sameor
just the matrix? Also, what coordinate system are you trying to goto?
The equation you have below takes CRS in the CT and maps it to tkrRAS in the anatomical. If you want to map the CRS in the anat then use inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote: > Hi Doug, > Thanks for the response. > I'm not seeing lta_convert as an executable that I can run. I have > freesurfer v5.3.0 installed - is there another version that Ishould
> be using? > > For using tkregister2, I'm a bit confused as to what I should be > doing. I had assumed (erroneously, it seems) that the .lta and.dat
> files contained the same information. > I just tried re-running tkregister2 with the command: > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s > average --lta reg_avg.lta > Such that I can pass in the reg_avg.lta file created from robust > register, and have it output a reg_avg.dat file. The contents of these > two files, however, seem to be exactly the same. > > I also running tkregister2 with the --fslregout and --freeview flags, > but neither of those produced a correct transformation either. > > Martin: > We are indeed registering the CT to an average MRI, and for the moment > we are correcting inaccuracies manually with tkregister2. > I just tried bbregister with one of our problem subjects, and it still > produced a matrix that had to be significantly adjusted in > tkregister2. Furthermore, the matrix that it produced still didnot
> transform the coordinates correctly in MATLAB. > > -Isaac > > > On Mon, Apr 28, 2014 at 2:32 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: > > > The matrix in the lta is probably not the right one. Try using > lta_convert or tkregister2 to change it to a register.dat file > (which is > what is expected in your formula) > doug > > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote: > > Hi All, > > > > I am attempting to transform sets of coordinates from subject CRS > > space into the surfaceRAS space of an average subject, made with > > make_average_subject. > > > > By our current method, we register the individual CT to the average > > surface using mri_robust_register with the command: > > mri_robust_register --mov [subj_CT].img --dst average_orig.mgz > --lta > > reg_avg.lta --iscale --satit > > and then check and adjust the registration with: > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surfpial
> --s average > > > > These steps work fine, and when I load the average brain in > freeview, > > then load the subject CT with with the registration file reg_avg.lta > > applied, the two overlap just as they should. > > > > However, when I attempt to do the same thing in matlab, some (though > > not all) of the subjects present a problem. > > I do the coordinate transformation (as suggested on > > http://freesurfer.net/fswiki/CoordinateSystems) byapplying:
> > > > inv(Reg_avg) * Tmov * CT_coords > > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as > > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space > > from the CT (with a vector of ones appended). > > > > As I said, some of the scans come out fine, with the coordinates in > > the correct place on the average surface, while others are very far > > removed from their correct location. How can I fix this? > > > > Thanks, > > Isaac > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel: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 sentto
> 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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>
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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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Douglas N Greve -
ISAAC PEDISICH -
Martin Reuter