Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That converts from MNI305 to MNI152

Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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 gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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

[Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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

Re: [Freesurfer] TALx coordinates

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]';