Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote:
Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates" Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 _______________________________________________ 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 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 <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.
Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari
On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152
coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates" Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 _______________________________________________ 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 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 <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.-- 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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Hi Gari,
The transformation actually consists of a 3 x 3 matrix and a 3 x 1 translation vector. The use of a 4 x 4 matrix allows the representation of an affine transformation as a matrix multiplication (http://en.wikipedia.org/wiki/Affine_transformation#Representation).
--Thomas
On Wed, Sep 11, 2013 at 4:21 PM, Garikoitz Lerma-Usabiaga garikoitz@gmail.com wrote:
Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari
On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates" Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 _______________________________________________ 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 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.edumailto: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.-- 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 4th handles any translation. The 3x3 handles rotation and any scale.
On 9/11/13 10:21 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari
On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: > Thanks, Doug. I am really hoping to get MNI152 (because I also use > fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? > > Best, > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > On 9/10/13 5:14 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: > > > It is an estimate of Tal coords from the MNI305. See > > http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach > > If you want MNI305, run mri_surfcluster with --nofixmni > > doug > > > > On 09/10/2013 05:08 PM, Yang, Daniel wrote: > > Hi all, > > The output of mri_surfcluster --sum shows TalX TalY TalZ. I am > wondering if they are based on the Talairach system or some > sort of > MNI-Talairach system. If the latter, can you tell me something > more > about it? Like a webpage that describes its relationship > between the > MNI152 or the Talairach system? > > I find it confusing because mri_surfcluster said: "INFO: > fixing MNI > talairach coordinates" > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > > _______________________________________________ > 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> > 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> <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. > > -- 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
Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1
The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct?
In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also.
Thanks so much! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 6:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote:
Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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/
That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug
On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1
The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct?
In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also.
Thanks so much! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 6:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 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%3E>> wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates" Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 _______________________________________________ Freesurfer mailing list 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> 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 <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. -- 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 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/
Thanks, Doug!! That sounds good.
I think if FreeSurfer can include MNI152 output option in its next release, that would be awesome!
Best, Daniel
On Sep 15, 2013, at 3:54 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug
On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1
The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct?
In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also.
Thanks so much! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 6:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu%3E> wrote:
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote:
Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://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.edumailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Doug,
I'm looking at the $FREESURFER_HOME/average/mni152.register.dat and I can see some relation with the formula you provided.
It appears that y and z are swapped, and the offsets are all different. Do you know why they are so? By the way, is there a way I can ask mri_surfcluster to read mni152.register.dat?
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
Thanks a lot! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/15/13 3:53 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug
On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1
The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct?
In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also.
Thanks so much! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 6:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu%3E> wrote:
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote:
Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system?
I find it confusing because mri_surfcluster said: "INFO: fixing MNI talairach coordinates"
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://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.edumailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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