Don't use --thmax. doug Fernanda Palhano wrote: > Hello, > > I'm running a cortical thickness analysis using Qdec. When I do Find > Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max > threshold 5): > ============================================================ > Generating cluster stats using min threshold of 3... > Found 9 clusters > Contrast: 'lh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > --------- --- ------ --------- ---- ---- ---- ----- ---------- > 1 8.8371 89238 5.07 -28.2 12.0 -14.5 16 insula > 2 -5.3729 64233 428.45 -35.4 50.5 -8.5 583 > parsorbitalis > 3 -5.1786 73273 192.98 -8.0 46.4 -13.0 292 > medialorbitofrontal > 4 -3.8763 121706 38.22 -19.6 61.0 1.5 53 > rostralmiddlefrontal > 5 -3.8612 93042 93.07 -23.8 40.2 -11.0 153 > lateralorbitofrontal > 6 -3.5732 14941 41.60 -7.0 41.1 -22.2 79 > medialorbitofrontal > 7 3.3511 160348 0.34 -30.3 10.7 -14.1 1 insula > 8 3.3502 111085 31.96 -33.8 -13.2 -4.6 68 insula > 9 -3.2412 99299 19.05 -34.6 47.2 18.4 26 > rostralmiddlefrontal > ============================================================ > > Why when using the command line mri_surfcluster with the same > thresholds I do not have the same results (same clusters)? > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.48 2010/04/12 17:36:58 greve Exp $ > # $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > # CreationTime 2011/05/02-19:07:52-GMT > # cmdline mri_surfcluster --in > qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh > --subject fsaverage --hemi lh --thmin 3 --thmax 5 --sign abs --annot > aparc --sum summary_3_5 --olab lh_g1_g2 > # cwd /Applications/freesurfer/subjects/dados > # sysname Darwin > # hostname Fernanda-Palhanos-Mac-Pro.local > # machine i386 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input > qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh > # Frame Number 0 > # srcsubj fsaverage > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /Applications/freesurfer/subjects/dados > # Minimum Threshold 3 > # Maximum Threshold 5 > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # Area Threshold 0 mm^2 > # Overall max 8.83713 at vertex 89238 > # Overall min -5.37286 at vertex 64233 > # NClusters 12 > # Total Cortical Surface Area 65416.6 (mm^2) > # FixMNI = 1 > # > # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs > Annot > 1 -4.995 29209 398.78 -33.5 48.6 -10.8 548 > rostralmiddlefrontal > 2 -4.995 16744 185.39 -8.3 45.3 -12.5 283 > medialorbitofrontal > 3 4.914 28205 0.34 -28.4 11.8 -11.8 1 insula > 4 4.850 22061 2.37 -26.8 9.7 -13.8 8 insula > 5 4.512 52766 0.38 -29.8 11.0 -11.4 1 insula > 6 -3.876 121706 38.22 -19.4 59.1 -1.6 53 > rostralmiddlefrontal > 7 -3.861 93042 93.07 -23.5 38.5 -11.2 153 > lateralorbitofrontal > 8 3.691 89239 0.68 -27.5 11.7 -12.5 2 insula > 9 -3.573 14941 41.60 -7.0 38.8 -20.6 79 > medialorbitofrontal > 10 3.351 160348 0.34 -29.9 9.7 -12.3 1 insula > 11 3.350 111085 31.96 -33.5 -12.9 -3.2 68 insula > 12 -3.241 99299 19.05 -34.2 46.6 14.7 26 > rostralmiddlefrontal > > In the right hemisphere I have the same problem: > > ============================================================ > Generating cluster stats using min threshold of 3... > Found 6 clusters > Contrast: 'rh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > --------- --- ------ --------- ---- ---- ---- ----- ---------- > 1 16.5175 22102 2.89 33.5 10.7 -13.0 7 insula > 2 6.0843 160464 1.08 30.8 13.1 -13.1 3 insula > 3 -5.9997 62430 1.08 36.1 3.3 -19.1 3 insula > 4 -3.3483 60593 24.75 35.9 55.5 -7.6 36 > rostralmiddlefrontal > 5 3.2156 23631 10.78 19.8 -65.1 1.5 15 lingual > 6 3.1968 120630 0.28 29.1 11.5 -15.8 1 insula > ============================================================ > > cmdline mri_surfcluster --in > qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh > --subject fsaverage --hemi rh --thmin 3 --thmax 5 --sign abs --annot > aparc --sum rh_summary_3_5 --olab rh_g1_g2 > # cwd /Applications/freesurfer/subjects/dados > # sysname Darwin > # hostname Fernanda-Palhanos-Mac-Pro.local > # machine i386 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input > qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh > # Frame Number 0 > # srcsubj fsaverage > # hemi rh > # surface white > # annot aparc > # SUBJECTS_DIR /Applications/freesurfer/subjects/dados > # Minimum Threshold 3 > # Maximum Threshold 5 > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # Area Threshold 0 mm^2 > # Overall max 16.5175 at vertex 22102 > # Overall min -5.99973 at vertex 62430 > # NClusters 6 > # Total Cortical Surface Area 65020.8 (mm^2) > # FixMNI = 1 > # > # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs > Annot > 1 3.386 130519 0.70 29.7 12.4 -12.0 2 insula > 2 -3.348 60593 24.75 35.5 53.5 -9.1 36 > rostralmiddlefrontal > 3 -3.245 28242 0.36 35.3 2.9 -15.6 1 insula > 4 3.216 23631 10.78 19.6 -63.0 4.6 15 lingual > 5 3.197 120630 0.28 28.8 10.4 -13.8 1 insula > 6 3.067 89363 0.38 34.3 7.1 -12.2 1 insula > > > Am I doing something wrong? I want to use the command line to generate > the labels for each cluster found. > > Thanks in advance, > Fernanda > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.
