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 <dgreve@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

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