processing_stream_-_cluster_tables
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— | processing_stream_-_cluster_tables [2010/05/26 23:12] (current) – created jochen | ||
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+ | ====== Processing stream - Cluster tables ====== | ||
+ | ===== Motivation ===== | ||
+ | Many articles concerned with neuroimaging data exhibit one or several tables that represent each contiguous area (cluster) in the statistical map for which the values surpass the applied threshold (alpha level) and, if so configured, the size (cluster level). The following information is commonly shown: | ||
+ | * the peak location (real-space mm coordinate relative to the atlas/ | ||
+ | * the size of the contiguous volume or surface for which the voxel/ | ||
+ | * the statistical value and the corresponding alpha threshold (which would be surpassed) | ||
+ | * optionally also the mean statistical value throughout the contiguous cluster | ||
+ | * possibly the most likely " | ||
+ | * and, if useful for the reader, the value of other statistical tests of the location of the peak (for comparison reasons) | ||
+ | |||
+ | ===== Requirements ===== | ||
+ | **Currently NeuroElf only supports BrainVoyager QX's [[BrainVoyager QX - VMP format|VMP]] format for the creating voxel-based cluster tables and the [[BrainVoyager QX - SMP format|SMP]] format for surface-based cluster tables.** However, maps from other formats (SPM, AFNI) can easily be converted into the VMP format! | ||
+ | |||
+ | ===== Instructions ===== | ||
+ | * the VMP must be loaded (either through the [[NeuroElf GUI]] or via the command prompt, see below) | ||
+ | * the requested thresholds must be either set in the Map sub-structure of the VMP or be given at the command prompt | ||
+ | * the following code will produce cluster tables on the Matlab prompt using the pre-specified thresholds in the file, with TDclient lookup of peaks that are prior passed through [[mni2tal]]:< | ||
+ | vmp = xff(' | ||
+ | |||
+ | % call the ClusterTable method on all maps | ||
+ | for mc = 1: | ||
+ | vmp.ClusterTable(mc, | ||
+ | end</ | ||
+ | Type of map: t-Map | ||
+ | Degrees of freedom: | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | ----------------------------------------------------------- | ||
+ | | ||
+ | 56 -17 1 | 2621 | 12.212478 | 4.706610 | ||
+ | 42 -69 | ||
+ | | ||
+ | 18 -77 -26 | | ||
+ | 53 5 | ||
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+ | -3 9 | ||
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+ | 24 | ||
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+ | 24 | ||
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+ | 12 | ||
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+ | 12 | ||
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+ | ===== Additional information ===== | ||
+ | Further instructions on the syntax can be found on the [[vmp.ClusterTable|ClusterTable method reference]] page. |
processing_stream_-_cluster_tables.txt · Last modified: 2010/05/26 23:12 by jochen