Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary
The fa.avg.dat will have a table of data. Each row will be a subject, each column a cluster (matching that found in permcsd.sig.cluster.summary) doug Antonella Kis wrote: > > > Hi Doug, > > Thank you very much for your help. I attached the log file. I can get > the clusters summary if I run the mri_volcluster but it will give the > correct clusters if I am not mentioning the --reg option? > Also, when I am visualizing my clusters using tkmedit: > > tkmedit cvs_avg35 norm.mgz \ > -ov > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh > > \ > -seg > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh > > \ > > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut > > \ > -fthresh 0.2 -fmax 1 > > I can read the functional value for each cluster. What exactly this > value represents? Is my FA value or -log10(p)? > > How can I get my FA values within each cluster in a table? > > > > Thank you so much. > Antonella > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com> > *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Wednesday, February 8, 2012 11:37 AM > *Subject:* Re: Reposting: Clusters by Multiple comparison > > Hi Antonella, the right way to do it is to figure out what is going > wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you > send the log file? Should be permcsd.mri_glmfit-sim.log. If you need > to run it for debugging purposes, you can run it with 10 iterations > (change permcsd to permcsdtmp so you don't overwrite what is there). > This should produce all the files, so if something is not there, it > should be easy to track down why. > doug > > Antonella Kis wrote: > > > > > > Dear Doug, > > > > When I run the: > > mri_glmfit-sim \ > > --glmdir GroupAnalysis_pos.glmdir \ > > --sim perm 10000 3 permcsd \ > > --sim-sign pos \ > > --cwpvalthresh .05 > > > > I am not getting my clusters file permcsd.sig.cluster.mgh with the > clusters summary so as you recommended I am running the > > > > mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask > Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn > Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 > --seg cvs_avg35 norm.mgz --csdpdf > Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd > Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig > Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh > > > > > > My question is: it is OK if I am not mentioning any registration or > what should I input under --reg while I running the mri_volcluster if > my for DTI preprocessing I used the dt_recon which computes for each > subject an fa.nii and register.dat using the Talairach registration > and later I registered all my subjects on the CVS space? > > > > Thank you. > > AK > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto: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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
