Hi Pieter, something has gone wrong, but I'm not sure what. The smoothing level in the CSD is nan (not-a-number). Can you tar up the glmdir and drop it to me at the file drop address at the end of this email?
doug Pieter van de Vijver wrote: > > /Sorry if I'm posting double, I had some trouble with my last post and > don't know if it is published or not/ > > Dear Freesurfer experts, > > I’m doing a longitudinal study on cortical thickness and subcortical > volumes and got some questions. I used the longitudinal stream for the > preprocessing > > > > 1. On cortical thickness, I’m doing a paired analysis as > described in https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, > and then a cluster-wise correction as described in > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, > with 5000 simulations instead of 5, and a vertex-wise threshold of 3 . > But I don’t get the ocn.annot map, instead I get a ocn.mgh and ocn.lut. > The CSD file also looks weird (constantly about 150 clusters with max > size one or 2) and the resulting cluster.summary also gives a huge > list of very small but significant clusters. Am I doing something > wrong? How should I go about this? I’m using FS 4.5. Files are > included (jpg for sig.mgh and cluster.mgh for negative simulation, > and csd (zipped), summary and simulation log) > > 2. For the subcortical volumetric analysis I use the aseg.stats. > Is the ICV a reliable measure to correct for overall brain size? I > heard ICV measurements are not very reliable on T1’s (I get a mean of > 2,4% decrease over 16 months...). Are other methods preferable to this > one. > > 3. Is there a logic or rule of thumb for choosing the > vertex-wise threshold? > > > > Thanks for your help! > > > > Pieter > > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: 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 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.
