External Email - Use Caution Hi Doug,
Deleting the .csd files and re-running worked. Thank you! Meaghan On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > *Message sent from a system outside of UConn.* > > Hmm, there should have been a lot more terminal output than that. > Try this, delete the CSD files: > rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd > Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files > > On 9/14/2020 2:58 PM, Meaghan Perdue wrote: > > External Email - Use Caution > Hi Doug, > > Here is the command: > > mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 > abs --cwp 0.05 --2spaces --bg 4 > > And here is the output: > > mri_glmfit simulation done 4.78645 > > > mri_glmfit simulation done 4.806 > > > mri_glmfit simulation done 4.81553 > > > mri_glmfit simulation done 4.81997 > > > mri_surfcluster --in > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask > lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh > --sum > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary > --ocn > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh > --annot aparc --cwpvalthresh 0.05 --o > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh > --no-fixmni --csd > lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd > --csd > lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd > --csd > lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd > --csd > lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd > --csdpdf > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat > --vwsig > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh > --vwsigmax > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat > --oannot > lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot > --bonferroni 2 --surf white > ERROR: CSDmerge: CSDs have same seed > > > Thank you! > Meaghan > > On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> *Message sent from a system outside of UConn.* >> >> please send the full command line and terminal output >> >> On 9/9/2020 3:19 PM, Meaghan Perdue wrote: >> >> External Email - Use Caution >> Hello Freesurfer experts, >> >> We're receiving the following error message when trying to run >> mri_glmfit-sim: >> ERROR: CSDmerge: CSDs have same seed >> >> This only occurs when we try to run the permutation on the LH for >> thickness. We've been able to run the simulation successfully on LH surface >> area and RH thickness and area. >> >> How can we troubleshoot this problem? >> >> Thank you, >> Meaghan Perdue >> >> -- >> Meaghan Perdue >> she | her | hers >> >> PhD Student >> Developmental Psychology >> Neurobiology of Language >> University of Connecticut >> Bousfield A302 >> Visit my website <https://mvperdue16.wixsite.com/meaghanperdue> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > > -- > Meaghan Perdue > she | her | hers > > PhD Student > Developmental Psychology > Neurobiology of Language > University of Connecticut > Bousfield A302 > Visit my website <https://mvperdue16.wixsite.com/meaghanperdue> > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 -- Meaghan Perdue she | her | hers PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302 Visit my website <https://mvperdue16.wixsite.com/meaghanperdue>
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