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 <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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--
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer