Thank you for the clarification. So even though it is a vertex-wise threshold, there is no minimum amount of vertices, it goes by area?
Tara
On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Area in mm^2
On 01/06/2016 01:16 PM, Tara Miskovich wrote:
Thank you so much, this is incredibly helpful. And just to be clear is this the minimum area or vertices?
Tara
On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
First, look in the qdec output folder to determine the FWHM in the fwhm.dat file. Assuming the value is 10, you are looking at the left hemisphere, you used a positive tail, and the voxel-wise thresholdwas
1.3 (p<.05), then you would find the following file$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
This will have 8 columns, but you will be interested in columns 2 and 4 (MaxClustBin and MaxClustCDF). The MaxClustCDF is the p-value for the given cluster size MaxClustBin. Eg, on line 25: 25 473.758087 0.021000 0.169000 0.045775 11.261296 0.002800 0.325000 indicates that the clustersize must be at least 473.758 to have a cluster p-value of .045775 clear? doug On 01/05/2016 08:35 PM, Tara Miskovich wrote: > Hello Freesurfer experts, > > I need help me finding how to get the minimum number of vertices > required to pass the cluster-corrected threshold with monte carlo > simulations used in qdec for a surface based analysis? > > This is per a reviewer request, but I cannot find anything on the wiki > or in the mail archives on how to get this value. > > Can someone please help me with this issue? > > -- > Thank you, > > Tara > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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Tara A. Miskovich, M.S. Affective Neuroscience Laboratory Department of Psychology University of Wisconsin-Milwaukee 334 Garland Hall miskovi2@uwm.edu mailto:miskovi2@uwm.edu
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