METRIC/SHAPE STATISTICS COORDINATE DIFFERENCE METRIC/SHAPE STATISTICS ONE-WAY ANOVA METRIC/SHAPE STATISTICS INTERHEMISPHERIC CLUSTERS METRIC/SHAPE STATISTICS KRUSKAL-WALLIS METRIC/SHAPE STATISTICS ONE SAMPLE T-TEST METRIC/SHAPE STATISTICS PAIRED T-TEST METRIC/SHAPE STATISTICS TWO SAMPLE T-TEST and WILCOXON
You can specify the number of threads you want to use, if you have a multi-processor system.
See the attached caret_command full help for more details, as well as the Williams paper:
http://brainvis.wustl.edu/resources/WmsJNsci.pdfVan Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., and Korenberg, J. (2006) Symmetry of cortical folding abnormalities in Williams syndrome revealed by surface-based analyses. J. Neuroscience 26:5470-5483.
In most cases, group membership labels are permuted to establish the significance area cut-off; for the one sample and paired t-tests, the subjects' metric/shape columns are sign-flipped, as described in Nichols & Holmes' Primer Paper.
On 08/07/2007 10:43 AM, Anthony Steven Dick wrote:
Hi Kevin-We use permutation methods outlined in some recent papers from Nichols and Hayasaka (e.g., see Nichols & Holmes, 2001; HBM 15, 1-25) to determine minimum cluster sizes.As Donna suggested, the AFNI/SUMA SurfClust command is ideal for this. We use it in combination with R statistical package, and it gives quite good results. The only downside is it takes some time to run the permutations unless you have access to a grid computing system.Anthony Donna Dierker wrote:Hi Kevin, Not directly, as far as I know. The closest two such features are these:* When you multi-fiducial map a fMRI volume onto the PALS_B12 atlas, you can specify a threshold. Then it maps the volume to each of the 12 PALS_B12 hemispheres, and calculates the suprathreshold area of each hemisphere. Then it computes an average area and generates a threshold that limits the MFM extent to that area.* After mapping your functional volume onto the surface and saving as a metric file (node:scalar pair), then you can open the metric file as a surface shape file and use Surface: ROI to do a cluster report on the metric file. I haven't tried it using 0.0 as a threshold, but it's probably possible to do so. Caret will then find all the clusters over that threshold. Save the output of that file; trim the header info; and sort on column 5 (corrected size). (If you're using a single individual's surface, rather than an average surface, then cols 4 and 5 will be identical, and you won't need a distortion metric file; for average surfaces, you need a metric like our PALS distortion metrics that pump up the area in regions of high variability (e.g., IPS), that get smoothed out during averaging.)I'm not aware of any more direct methods; you might try the AFNI list; Ziad Saad may have something like that for SUMA.Donna On 08/07/2007 09:22 AM, Kevin Guise wrote:GreetingsI've searched through previous postings and the caret documentation but I am unable to find any information regarding a method to set a minimum cluster extent threshold while projecting functional activation onto a surface map. Is this at all implemented in caret, or can anyone suggest an equivalentmethod? Best Kevin _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
caret_command.txt
Description: application/research-info-systems
