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" <gr...@nmr.mgh.harvard.edu<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" <gr...@nmr.mgh.harvard.edu<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 -0.0073 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" <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@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 gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto: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<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> 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<mailto: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<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 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.
