To my knowledge, Caret won't apply any dynamic volume-based thresholding. (Then again, I didn't know about the Cluster Minimum Size feature until you told me.)
Most people do this sort of thing by thresholding the volume using some volume-oriented tool (e.g., FSL, SPM, AFNI, fidl). Then they map the resulting thresholded volume. On Aug 26, 2011, at 11:19 AM, Muriel LOBIER wrote: > I'm not sure I've made myself very clear. > > What I'm trying to do is the following: > I have mapped my SPM data to Caret, but it shows all activated clusters. > I want to be able to display only those clusters that are larger than 50 vxls. > >From what I had understood, that would be done in the metric modification > >window (attributes/metric/clustering and smoothing ), where there is a box > >where you can select "Cluster Minimum Size" either by min nb of nodes or min > >surface area. > It is those values that I've tried modifying without any luck: I create a new > metric column with my cluster min size, change the column name in my > visualization, but all my clusters remain. > > > > > > > On Fri, Aug 26, 2011 at 18:06, Donna Dierker <[email protected]> wrote: > Hmmm. I don't know that Caret can do this. There are several cluster-based > tests that find the minimum area required to correct for multiple > comparisons, given an input cluster-forming threshold (say, t=+/-3.0): > > caret_command.txt: caret_command -metric-statistics-anova-one-way > caret_command.txt: caret_command -metric-statistics-anova-two-way > caret_command.txt: caret_command > -metric-statistics-coordinate-difference > caret_command.txt: caret_command > -metric-statistics-interhemispheric-clusters > caret_command.txt: caret_command -metric-statistics-one-sample-t-test > caret_command.txt: caret_command -metric-statistics-paired-t-test > caret_command.txt: caret_command -metric-statistics-two-sample-t-test > > These are permutation tests that find the smallest alpha*iterations cluster > at the specified threshold. And they output a paint/region file showing the > clusters that survived significance cut-off. > > But interactively in the GUI, I'm not aware of such a feature. If you've > checked the metric/smoothing dialog, then Surface: Region of Interest is the > other place I'd look. And I don't recall it. > > Since we adopted TFCE, we don't use the cluster-based tests anymore. > > > On Aug 26, 2011, at 8:40 AM, Muriel LOBIER wrote: > >> Hi all, >> >> I'm just beginning to use CARET to map activations from SPM5 to 3D brains. >> There is still one thing I can't quite succeed in doing, and that's limiting >> visible clusters to clusters above a certain size threshold. I've used the >> appropriate attributes/metric/clustering and smoothing command as I've seen >> in tutorials and previous posts to the mailing lists, but it doesn't ever >> seem to apply changes I make to the visualization (I've made sure I use the >> modified column). >> >> Is there anything obvious I could have missed ? >> >> Thanks, >> >> Muriel >> -- >> -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- >> Muriel LOBIER >> Doctorante en Sciences cognitives psychologie et neurocognition >> PhD student in Cognitive science, psychology, and neurocognition >> >> [email protected] >> [email protected] >> tel : +33 6 88 67 15 55 >> >> Laboratoire de Psychologie et Neurocognition (CNRS UMR 5105) >> Bureau 220 >> Tel : +33 4 76 82 58 93 >> >> Bâtiment Sciences de l'Homme et des Mathématiques >> BP 47, 38040 Grenoble Cedex 9 >> >> >> Web : http://webu2.upmf-grenoble.fr/LPNC/membre_muriel_lobier >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > -- > -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- - - -- > Muriel LOBIER > Doctorante en Sciences cognitives psychologie et neurocognition > PhD student in Cognitive science, psychology, and neurocognition > > [email protected] > [email protected] > tel : +33 6 88 67 15 55 > > Laboratoire de Psychologie et Neurocognition (CNRS UMR 5105) > Bureau 220 > Tel : +33 4 76 82 58 93 > > Bâtiment Sciences de l'Homme et des Mathématiques > BP 47, 38040 Grenoble Cedex 9 > > > Web : http://webu2.upmf-grenoble.fr/LPNC/membre_muriel_lobier > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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