Hi freesurfer experts,
I am running a group functional connectivity analysis following the steps from the FsFast Functional Connectivity Walkthrough. When I visualize the OSGM maps, the pattern of connectivity looks normal but there are regions of ridiculously high significance values (sig= 10,000,000,000). This problem is happening bilaterally for each seed. Attached are slides showing the OSGM map for one of my seeds (left dlPFC) at a normal threshold, and then at a threshold minimum of 100 to show the regions that have this crazy significance value.
After generating my .dat files using fcseed-sess and creating nuisance regressors I run the following commands:
$ mkanalysis-sess -analysis FC_{mask}_FS5.3_SIRP.lh -surface fsaverage lh -fwhm 5 -notask -taskreg {mask}.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -nuisreg global.waveform.dat 1 -mcextreg -polyfit 5 -fsd bold -rlf funlist_fc_SIRP -TR 2 -per-run -force
$ selxavg3-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate -analysis FC_{mask}_FS5.3_SIRP.lh
$ isxconcat-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate -analysis FC_{mask}_FS5.3_SIRP.lh -all-contrasts -hemis -o $SUBJECTS_DIR/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/{mask}
$ mri_glmfit --fsgd /cluster/roffman/users/fsgd/GDD/145_GDD_FC_SerumFolate_OSGM.fsgd --osgm --fwhm 6 --no-prune --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/ces.nii.gz --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/LH_OSGM --surface fsaverage lh
Am I doing something wrong in my commands that is creating these results? Is there anything I can do to troubleshoot this issue?
Thank you,
Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215