hi Glen, no cluster will show up if the p-value for all clusters is
above .05. You can change this with --cwpvalthresh to something like
.99. That should give you all the clusters. Also, you don't have to run
the full simulation again; you can use the --no-sim option and it will
use the simulation that you already did.
doug
On 6/3/13 9:45 PM, Glen Lee wrote:
Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
You will need more like 10000 iterations instead of 100.
doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result
(which was
> already done using mri_glmfit), but I was not able to get any result
> out of it.
>
> Even with a quite liberal threshold (2), no vertices came out
(below
> is what I typed in for the random permutation).
>
> mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign
> abs --overwrite
>
> What is strange is that I was clearly see a number of clusters
when I
> overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster
> shows up in perm.abs.2.sig.cluster.mgh.
> I should be able to see the identical map between those right?
>
> FYI, I also pasted the content in perm.abs.2.sig.cluster.summary
below.
> As can be seen, nothing is listed in the stats table.
>
> Any of your help would be greatly appreciated.
> -Glen
>
>
>
>
>
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
> # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> # CreationTime 2013/06/03-20:19:31-GMT
> # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
> GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
> GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
> GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
> GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
> GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
> GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
> GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
> GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
> # cwd /glen/2D/results/LH
> # sysname Linux
> # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu>
<http://sumo.uphs.upenn.edu>
> # machine x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input GLM/osgm/sig.mgh
> # Frame Number 0
> # srcsubj fsaverage_sym
> # hemi lh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
> # SearchSpace_mm2 59961.4
> # SearchSpace_vtx 82070
> # Bonferroni 0
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Sign abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold 0 mm^2
> # CSD thresh 2.000000
> # CSD nreps 100
> # CSD simtype perm
> # CSD contrast osgm
> # CSD confint 90.000000
> # Overall max 3.495 at vertex 61659
> # Overall min -4.18843 at vertex 73402
> # NClusters 0
> # Total Cortical Surface Area 59961.4 (mm^2)
> # FixMNI = 0
> #
> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
> CWPLow CWPHi NVtxs Annot
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
