I have used the steps you described successfully before and just repeated it now with no problems.
Have you tried using extremely large values- just as a proof of principal? All of the clusters may be larger than your current threshold value. Have you adjusted your values for the "cluster value threshold"? -Matt On Fri, Aug 26, 2011 at 12:19 PM, Muriel LOBIER <[email protected]>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 > > -- R. Matthew Hutchison, PhD. Candidate Centre for Functional and Metabolic Mapping Robarts Research Institute Cuddy Wing - 9.4T Suite 100 Perth Drive London, Ontario, Canada N6A 5K8
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
