External Email - Use Caution
Dear Martin,
actually, when your primary problem is very high local maxima on p-map, but no
significant cluster-wise p after thresholding, I guess, that you should try the
opposite, i.e. increase cluster forming threshold.
This will increase sensitivity to clusters with smaller extent but comprising
larger p-values before thresholding.
Antonin Skoch
did you do this?
First, install a new version of mri_glmfit-sim from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim
(copy it to $FREESURFER_HOME/bin and make it executable with chmod a+rx
mri_glmfit-sim).On 12/06/2018 01:28 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Thanks Dough for your suggestions. I tried to use permutation method,
> but its giving me following error:
>
> ERROR: design matrix is not orthogonal, cannot be used with permutation.
>
> If this something you really want to do, run with --perm-force
>
>
> Can you please tell me how can I fix this issue or if I can run with
> --perm-force?
>
>
> Thanks for the help.
>
>
> On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
>
> For it to show up in the output file, the cluster-wise pvalue must
> be <
> .05 (CWT). To see all the clusters regardless of significance, run it
> with a CWT of 1. If you want to run with a more liberal cluster
> forming
> threshold (CFT), you can try using permutation. See
> http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 12/05/2018 11:44 PM, Martin Juneja wrote:
> >
> > External Email - Use Caution
> >
> >
> > Dear experts,
> >
> > Could you please help me in resolving following issue?
> >
> > Thanks.
> > ---------- Forwarded message ---------
> > From: *Martin Juneja* <mj70...@gmail.com
> <mailto:mj70...@gmail.com> <mailto:mj70...@gmail.com
> <mailto:mj70...@gmail.com>>>
> > Date: Wed, Nov 28, 2018 at 2:23 PM
> > Subject: Overall maxima is high and still no significant cluster
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> >
> >
> > Hi FS experts,
> >
> > I am estimating the group-behavioral thickness interaction using
> > contrast 2 FSGD file:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT <
> 0.01 and
> > CWT < 0.05 at FWHM of 12 mm.
> >
> > I do not find any significant clusters and my output summary
> text file
> > looks like the following. This file shows that overall maxima is
> > 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) =
> 4, so
> > I am just wondering despite the fact that maxima is > 4, why I
> do not
> > see this cluster in the summary/output *.mgh file?
> >
> > I would really appreciate any clarification and tips to modify my
> > input thresholds so that I do not miss any significant findings
> here.
> >
> > Thanks.
> > -----------------------------
> >
> > # SearchSpace_mm2 76467.1
> > # SearchSpace_vtx 149953
> > # Bonferroni 2
> > # 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 10000
> > # CSD simtype null-z
> > # CSD contrast NA
> > # CSD confint 90.000000
> > # Overall max 4.58212 at vertex 10608
> > # Overall min -2.84277 at vertex 75476
> > # NClusters 0
> > # FixMNI = 0
> > #
> > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
> > CWPLow CWPHi NVtxs WghtVtx Annot
> >
> >
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