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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
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 CautionHello 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 listFreesurfer@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
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 mailto: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 Visit my website <https://mvperdue16.wixsite.com/meaghanperdue> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 dgreve@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 CautionHi 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 CautionHello 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 listFreesurfer@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 listFreesurfer@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
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Meaghan Perdue