Hi Chris, mri_surfcluster should output coordinates in "Talairach" space (The newer 5.1 version uses MNI305 space). Internally, we always use MNI305 space. To report "Talairach" coordinates, we then apply a transform (http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html) to give particular values. I think that QDEC is doing the same thing. doug
Chris Hyatt wrote: > Dear Freesurfers, > > I know that Qdec outputs coordinates in a "Freesurfer specific space", > rather than in Talairach space, per this old thread > > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html > > However, I found that mri_surfcluster (Freesurfer v5.0) in its summary > output also outputs coordinates in this same "Freesurfer specific > space", even though the columns indicate TalX, TalY and TalZ. I was > going to use this summary info to list the location of the statistical > maxima of each cluster in a cortical thickness p-map. > > Is this a bug in mri_surfcluster? Any suggestions on how to get the > coordinate data? > > Here is the summary info for the left hemisphere (note the positive > TalX values, when all X values should be negative): > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2011/07/23-17:08:39-GMT > # cmdline mri_surfcluster --in ./lh.CvsA.glmdir/group.diff/sig.mgh > --subject fsaverage --hemi lh --surf inflated --thmin 1.301 --sum > lh.CvsA.thickness.summary --oannot ./lh.CvsA.thickness.annot > # cwd /prod4/other/freesurfer/glm_cth/age_of_onset > # sysname Linux > # hostname everest > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input ./lh.CvsA.glmdir/group.diff/sig.mgh > # Frame Number 0 > # srcsubj fsaverage > # hemi lh > # surface inflated > # SUBJECTS_DIR /prod4/other/freesurfer/subjects > # SearchSpace_mm2 62822.2 > # SearchSpace_vtx 163842 > # Bonferroni 0 > # Minimum Threshold 1.301 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # Area Threshold 0 mm^2 > # Overall max 2.53286 at vertex 81529 > # Overall min -2.67513 at vertex 24566 > # NClusters 36 > # Total Cortical Surface Area 62822.2 (mm^2) > # FixMNI = 1 > # > # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs > 1 -2.675 24566 287.98 7.6 95.9 0.5 533 > 2 2.533 81529 83.49 -7.4 -28.4 50.2 199 > 3 2.530 6795 386.88 -15.4 -86.6 -9.4 677 > 4 -2.496 129236 79.10 -27.0 27.1 22.6 166 > 5 -2.483 138360 227.18 -5.7 84.6 2.6 343 > 6 2.481 18891 211.45 3.4 -96.6 -26.2 373 > 7 2.460 33958 277.19 37.6 5.5 15.4 354 > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
