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.h...
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
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.h...
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
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Chris Hyatt -
Douglas N Greve