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 mwaskom@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 pvijver@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
On cortical thickness, I’m doing a paired analysis as describedin
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)
For the subcortical volumetric analysis I use the aseg.stats. Isthe 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.
Is there a logic or rule of thumb for choosing the vertex-wisethreshold?
Thanks for your help!
Pieter
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