Hi Gang, First, you need some method to generate 5000 iterations of your data, randomized by some method like the ones in Nichols & Holmes primer paper:
http://www.fil.ion.ucl.ac.uk/spm/doc/papers/NicholsHolmes.pdf The "Primer Paper", TE Nichols and APHolmes. Nonparametric Permutation Tests for Functional Neuroimaging: A Primer with Examples. Human Brain Mapping, 15:1-25, 2002. FSL's randomise does this for volumes, and caret_stats supports some simple models on the surface: ANOVA One-Way -inferential-anova-one-way ANOVA One-Way Coordinate Difference -inferential-anova-one-way-coordinate-difference Data Smoothing -data-smoothing Data Transform - Threshold Free Cluster Enhancement -data-transform-tfce Descriptive Statistics -descriptive Development - Metric Monotonic Test -development-monotonic-test Development coordinate metric combination -development-metric-coord File Information -file-information Interhemispheric -inferential-interhemispheric Signficance - Cluster-based Thresholding -significance-cluster-threshold Signficance - Threshold Free -significance-threshold-free T-Test One-Sample -inferential-t-test-one-sample T-Test Paired -inferential-t-test-paired T-Test Two-Sample -inferential-t-test-two-sample Then you need to smooth the resulting real and random t-/f-maps a bit, before feeding it to caret_stats -significance-threshold-free, which builds a distribution of max tfce values and thresholds it at 0.025, or whatever alpha you specify. It generates a report and label file -- nice. We never released caret_stats formally, though I've provided to a few people off-list. The hard part is usually getting the 5000 or so random iterations of your data, permuted/flipped in the manner described in the primer paper -- what FSL's randomise does for volumes. FSL is working on supporting both surface and volume data, but it will be a while before randomise can easily read surfaces, I think. If Freesurfer can generate these randomised statistics, then these could be input into caret_stats -significance-threshold-free pretty easily. Donna > Hi, > > I have some cortical surfaces aligned in the spherical space in FreeSurfer > format. I would like to know how can I use the TFCE method in Caret to do > statistical analysis of the attributes on the cortical surface such as the > sulcal depth, surface area or 3D vertex coordinate. Thanks a lot. > > Gang > _______________________________________________ > 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
