Doug -- Sorry for asking your help again as I can't seem to resolve this on my own.
I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below).
mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim /csd/mc-z.negative.j001-osgm.csd --overwrite
Also see the output below. -------- Original mri_glmfit command line: cmdline mri_glmfit --y Bb_Bp_sm8_i6_n13_L.mgh --osgm --glmdir GLM --surf fsaverage_sym lh
DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 5.124509 ERROR: cannot find any csd files
On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug
On 06/04/2013 09:11 AM, Glen Lee wrote:
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this csd folder?
Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite
-Glen
On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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