Dear Experts, I still got a super big cluster that covers the whole brain for the F test, please help...
Thanks, Lena From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: 21 August 2015 19:07 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] F test results You need to use 1 -1 0 0 1 0 -1 0 On 8/19/15 11:38 AM, Lim, Lena wrote: Dear experts, I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a F test on the cortical thickness but the output doesn't make sense as it covered the whole brain (please see attached). I used the following commands: mris_preproc --fsgd 3gps_IQ.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.3gps_IQ.thickness.10.mgh mri_glmfit --y lh.3gps_IQ.thickness.10.mgh --fsgd 3gps_IQ.fsgd doss --C 3gps_IQ_Ftest.mtx --C 3gps_IQ_AbusedmorethanHC.mtx --C 3gps_IQ_AbusedmorethanPC.mtx --C 3gps_IQ_PCmorethanHC.mtx --surf fsaverage lh --cortex --glmdir lh.3gps_IQ_thickness mri_glmfit-sim --glmdir lh.3gps_IQ_thickness --cache 2 abs --cwp 0.05 --2spaces F contrast: 1 -1 0 0 0 0 -1 0 What went wrong? Please kindly help... Many thanks, Lena -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 04 August 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] contrasts The F would be 1 -1 0 0 0 0 -1 0 Your t-contrasts are correct (you don't need to do both directions) On 08/03/2015 03:40 PM, Lim, Lena wrote: Hi experts, I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how should I define the F contrast? Would it still be: I -1 0 ? 1 0 -1 And would the t contrast for say A>PC be: 1 -1 0 0 and for A < PC be -1 1 0 0 etc Many thanks, Lena _______________________________________________ Freesurfer mailing list 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> 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> 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/08/14-14:59:29-GMT # cmdline mri_surfcluster --in lh.3gps_IQ_thickness/3gps_IQ_Ftest/sig.mgh --csd /software/system/freesurfer/freesurfer-5.3.0//average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/abs/th20/mc-z.csd --mask lh.3gps_IQ_thickness/mask.mgh --cwsig lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.cluster.mgh --vwsig lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.voxel.mgh --sum lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.cluster.summary --ocn lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.ocn.mgh --oannot lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.ocn.annot --annot aparc --csdpdf lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.pdf.dat --cwpvalthresh 0.05 --o lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /home/spjwker_PAC/Lena/CT_SA/FSL # sysname Linux # hostname nanlnx1.iop.kcl.ac.uk # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.3gps_IQ_thickness/3gps_IQ_Ftest/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /home/spjwker_PAC/Lena/CT_SA/FSL # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 23.1633 at vertex 102919 # Overall min 0 at vertex 8 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 23.163 102919 76038.98 -35.4 7.0 -9.7 0.00020 0.00000 0.00040 149021 insula
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