Hi Adam, your simulation is based on a whole-brain search space and so it is not appropriate to use a label constraint when running mri_surfcluster. If you want to constrain the correction of multiple comparisons to a label, you have to do it when you do the simulation. The best approach is actually to constrain when running mri_glmfit, then use mri_glmfit-sim rather than running mri_glmfit with the simulation options.
doug Adam Nitenson wrote: > Hi Freesurfers > > I'm a bit confused as to some recent Monte Carlo findings I've been > looking at. After generating 10,000 estimations with mri_glmfit. I used > mri_surfcluster to generate nii, ocn.nii, and .sum files to analyze the > clusters. However I found that, when looking at the dACC, the cluster > within an ROI (label) specific analysis, which almost filled the entire > label, was not significant, yet the dACC region cluster in the label-free, > whole brain analysis was significant. > > I figured that, since the whole brain (no label) monte carlo analysis > compares the clusters to the entire brain and the label analysis confines > the cluster to just the label, that the latter would result in a more > signifcant cluster (since it fills up almost all of the space under > consideration). However, I have found the opposite, and don't understand > why this is. > > Any ideas would be greatly appreciated. I've written my commands below > (Stable 4). > > Thanks, > > Adam > > > mri_glmfit --y > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/error_vs_correct/lh.ces.005.nii > --fsgd > /autofs/space/ventzl_036/users/RespMon12C/fsgd_and_contrast_files/Adam_25MatchedControls_genotyped.fsgd > --C > /autofs/space/ventzl_036/users/RespMon12C/fsgd_and_contrast_files/CHomozyg_Minus_TCarrier.mtx > --surf fsaverage lh --sim mc-full 1000 1.3 > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1 > --fwhm 16.351771 > > mri_surfcluster --in > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/LH_error_vs_correct_6sec/CHomozyg_Minus_TCarrier/sig.mgh > --csd > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1-CHomozyg_Minus_TCarrier.csd > ....(rest of monte carlo files).... --srcsubj fsaverage --thmax infinity > --annot aparc --clabel > /autofs/space/ventzl_036/users/RespMon12C/subjects/fsaverage/label/lh.dACC.All56Grouplabel > --sum > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.sum > --o > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.nii > --ocn > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.ocn.nii > > > mri_surfcluster --in > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/LH_error_vs_correct_6sec/CHomozyg_Minus_TCarrier/sig.mgh > --csd > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1-CHomozyg_Minus_TCarrier.csd > ........ --srcsubj fsaverage --thmax infinity --annot aparc --sum > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.sum > --o > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.nii > --ocn > /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.ocn.nii > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > _______________________________________________ > 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.
