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 <gr...@nmr.mgh.harvard.edu>wrote: > > --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 >> <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@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 >>> <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>> freesurfer<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<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> >>> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >>> >>> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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