Hi Pieter, I think I may have run into this problem before by using mri_glmfit on a surface dataset and forgetting to to include --surf <subject> <hemi>. The model fitting runs fine, but you end up with confusing problems at the corrections stage because the residual smoothness estimation doesn't work properly. Do you happen to know whether you included --surf in your mri_glmfit call?
Cheers, Mike On Sun, Feb 27, 2011 at 6:37 PM, Pieter van de Vijver <pvij...@gmail.com> wrote: > 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 > > > 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
