The QDEC output does not quite report what you want to report. I would run mri_glmfit-sim using --glmdir /path/to/qdec/folder and the same parameters as you used for the monte carlo simulation. this will produce several files including a summary/table file with the MNI305 coordinates of most significant voxel in the cluster. If you want the centroid, add --centroid to the cmd line.
doug On 04/03/2014 07:17 AM, Francesco Puccettone wrote: > Dear FreeSurfer list, > > When reporting coordinates of significant clusters found with Qdec, > should one report > 1) the Talairach coordinates displayed immediately after running the > MonteCarlo correction (which I imagine are the center of gravity (CoG) > coordinates?!) > or > 2) the max vertex Talairachcoordinates displayed after using the "Find > clusters and go to max" button? > > The two sets of coordinates are close for a given cluster, but never > quite the same, and I don;t know which one to report. > > Thank you! > --Francesco > > > On 31 March 2014 20:20, Francesco Puccettone > <francesco.puccett...@gmail.com > <mailto:francesco.puccett...@gmail.com>> wrote: > > I see, makes sense! I had a second question, which I repeat below. > > When reporting significant clusters, should one refer to the > cluster by > 1) its annotation label, e.g. "sig differences were found in the > precentral gyrus", > 2) its max vertex as displayed after using the "Find clusters and > go to max" button, e.g. "significant differences were found in a > cluster whose maximum vertex was at (10,20,30)" , or > 3) by its center of gravity coordinates as displayed (I think!) > immediately after running the MonteCarlo correction, e.g. > "significant differences were found in a cluster whose CoG was at > (11,21,31)"? > > > On 31 March 2014 17:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > This is just the way that the interface was programmed. It was > fairly > easy to add a button to run the correction, more difficult to > pull that > information back into the interface in a reasonable way. I > agree that it > makes using the interface less intuitive: once you get a button to > press, you come to expect that everything else will be done > for you. > Unfortunately, we don't have the resources to be able to do > that. You'll > have to look at the text file generated by QDEC > doug > > > On 03/31/2014 09:05 AM, Francesco Puccettone wrote: > > Hello, > > > > I see that after having qdec apply MonteCarlo correction to > a certain > > contrast, the CWP cluster-wise probability is displayed. > Those values, > > however, are not displayed when the "Find clusters and go to > max" > > button is used, either before or after correction. WHy is > that, when > > it seems that the CWP statistic makes sense for all 3 "stages" > > (max-vertex pre-correction, mean-cluster post-correction, > max-vertex > > post-correction)? > > > > Thank you! > > > > --Francesco > > > > > > _______________________________________________ > > 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 -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
