That worked, didn't work out that good for the significance of my data though... :-(
Thanks, Doug & Mike! On Wed, Mar 2, 2011 at 1:19 PM, Michael Waskom <mwas...@mit.edu> wrote: > 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. > > > > >
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