Great! Thank you for all the help. On Wed, Jan 6, 2016 at 12:38 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Yes. In theory you can compute the number of vertices by dividing by the > average vertex area > > On 01/06/2016 01:34 PM, Tara Miskovich wrote: > > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 > > threshold was > > > 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> > > > <mailto: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 > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://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> > > > <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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto: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. > > > > > > > > > > > > > > > -- > > > Thank you, > > > > > > Tara A. Miskovich, M.S. > > > Affective Neuroscience Laboratory > > > Department of Psychology > > > University of Wisconsin-Milwaukee > > > 334 Garland Hall > > > misko...@uwm.edu <mailto:misko...@uwm.edu> > > <mailto:misko...@uwm.edu <mailto:misko...@uwm.edu>> > > > > > > > > > _______________________________________________ > > > 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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Thank you, > > > > Tara A. Miskovich, M.S. > > Affective Neuroscience Laboratory > > Department of Psychology > > University of Wisconsin-Milwaukee > > 334 Garland Hall > > misko...@uwm.edu <mailto:misko...@uwm.edu> > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Thank you, Tara A. Miskovich, M.S. Affective Neuroscience Laboratory Department of Psychology University of Wisconsin-Milwaukee 334 Garland Hall misko...@uwm.edu
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