Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

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
1.00
1.00
0.15
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" 
mailto:gr...@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" 
mailto:gr...@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   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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" 
mailto:gr...@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
 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@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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Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

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" 
mailto:gr...@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" 
mailto:gr...@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   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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" 
mailto:gr...@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
 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@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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 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
gr...@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

Re: [Freesurfer] TALx coordinates

[Douglas 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" > wrote:


Hi Yang, I've computed a matrix that should do the trick. If you
are in
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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"
mailto:gr...@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

 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
gr...@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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 contains patient information, please contact the Partners
 Compliance HelpLine at
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 dispose of t

Re: [Freesurfer] TALx coordinates

[Douglas Greve]

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 
mailto:gr...@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   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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" mailto:gr...@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

> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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.
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
  

Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

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" 
mailto:gr...@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   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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" 
mailto:gr...@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
 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@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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 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
gr...@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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Re: [Freesurfer] TALx coordinates

[Thomas Yeo]

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
 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
>  wrote:
>>
>> Hi Yang, I've computed a matrix that should do the trick. If you are in
>> matlab, then
>>
>> M = [0.9975   -0.00730.0176   -0.0429
>>  0.01461.0009   -0.00241.5496
>> -0.0130   -0.00930.99711.1840
>>   0 0 01.]
>> 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" > > > 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
>> > 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@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.
>> >
>> >
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] TALx coordinates

[Garikoitz Lerma-Usabiaga]

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  wrote:

> Hi Yang, I've computed a matrix that should do the trick. If you are in
> matlab, then
>
> M = [0.9975   -0.00730.0176   -0.0429
>  0.01461.0009   -0.00241.5496
> -0.0130   -0.00930.99711.1840
>   0 0 01.]
> 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"  > > 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
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@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  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
> gr...@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
>
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TALx coordinates

[Douglas N Greve]

Hi Yang, I've computed a matrix that should do the trick. If you are in 
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
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"  > 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
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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.
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

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" 
mailto:gr...@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


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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[Freesurfer] TALx coordinates

[Yang, Daniel]

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
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TALx coordinates

[Douglas N Greve]

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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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