I don't think there is anything really wrong. There are computation
limits on the maximum significance. When the given voxel goes beyond
that, I set it to this ridiculously high level. This high level just
means that it is really significant.
On 02/02/2017 12:18 PM, Rodriguez-Thompson, Anais wrote:
> 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
>
>
> _______________________________________________
> 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
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Fax: 617-726-7422
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