Hi Rysia, Your commands looks fine to me, and 5000 iterations is good enough to see significant cluster.
You might want to try lowering your threshold to 1.3 (0.05 p value). thanks pratap > Hello, > > > > I have just run a number of permutation and mc-z on data that was > previously analysed using qdec. Unfortunately none of my clusters reach > significance (in some cases there are no clusters found at all) and I am > unsure as to what I am doing wrong. I am running freesurfer v4.1.0 on > CentOS. My commands were as follows: > > > > mri_glmfit y y.mgh fsgd ./qdec.fsgd dods --surf fsaverage lh > > --fwhm 15 glmdir ./glmdir --C > ./contrasts/lh-Diff-patient-CONTROL-Intercept-thickness.mat --sim perm > 5000 2 ./glmdir/csd1 > > > > followed by: > > > > mri_surfcluster --in ./lh-Diff-patient-CONTROL-Intercept-thickness/sig.mgh > csd ./glmdir/csd1-lh-Diff-patient-CONTROL-Intercept-thickness.csd --sum > lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.sum cwsig > lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.mgh > > > > I append a log file of mri_glmfit and the output of mri_surfcluster below > there are clusters listed but none of them reach significance. It is > confusing because I was under the impression that permutation thresholding > was less conservative than fdr correction. > > > > I have also run these using sim mc-z 5000 2 - maybe I am not performing > enough iterations? > > > > Also: is RFT correction implemented in the latest version of freesurfer? > > > > Any help appreciated, > > > > Rysia > > > > mri_glmfit logfile: > > > > $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ > > cwd /cns_zfs/sphasas > > cmdline mri_glmfit --y > /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh --fsgd > /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd dods > --glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 --surf > fsaverage rh --label /cns_zfs/sphasas/fsaverage/label/rh.cortex.label --C > /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Avg-Intercept-thickness.mat > --C > /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Diff-OCD-CONTROL-Intercept-thickness.mat > > sysname Linux > > hostname haemoglobin.cns.image.iop > > machine x86_64 > > user kkvi1114 > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd > > labelmask /cns_zfs/sphasas/fsaverage/label/rh.cortex.label > > maskinv 0 > > glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 > > DoFFx 0 > > ResidualFWHM 18.998058 > > SearchSpace 75188.635931 > > anattype surface > > > > > > Output of mri_surfcluster: > > > > cwd /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 > > # sysname Linux > > # hostname haemoglobin.cns.image.iop > > # machine x86_64 > > # FixVertexAreaFlag = 1 > > # > > # Input ./lh-Diff-OCD-CONTROL-Intercept-thickness/sig.mgh > > # Frame Number 0 > > # srcsubj fsaverage > > # hemi lh > > # surface white > > # SUBJECTS_DIR /software/system/freesurfer/freesurfer-4.1.0/subjects > > # Minimum Threshold 2 > > # Maximum Threshold infinity > > # Threshold Sign abs > > # AdjustThreshWhenOneTail 1 > > # Area Threshold 0 mm^2 > > # CSD thresh 2.000000 > > # CSD nreps 5000 > > # CSD simtype perm > > # CSD contrast lh-Diff-OCD-CONTROL-Intercept-thickness > > # CSD confint 90.000000 > > # Overall max 2.18803 at vertex 126138 > > # Overall min -2.94444 at vertex 75849 > > # NClusters 6 > > # Total Cortical Surface Area 65416.6 (mm^2)þ > > # FixMNI = 1 > > ClusterNo Max VtxMax Size(mm2) TalX TalY > TalZ CWP CWPLow CWPHi NVtxs > > 1 -2.944 75846 61.98 > -17.6 -37.0 -4.2 0.84860 0.84200 > 0.85500 142 > > 2 -2.672 22094 96.92 > -29.6 0.5 -24.2 0.80680 0.79960 > 0.81400 182 > > 3 2.188 126138 41.24 > -22.1 -56.8 40.5 0.87160 0.86560 > 0.87760 74 > > 4 2.095 81711 45.09 > -32.4 -38.2 39.4 0.86860 0.86240 > 0.87480 105 > > 5 2.061 147756 12.32 > -6.2 -61.7 38.4 0.90520 0.89980 > 0.91040 20 > > 6 2.001 133188 0.60 > -32.0 -44.7 59.0 0.91660 0.91160 > 0.92160 1 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
