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--- biac:analysis:resting_pipeline [2013/09/16 18:26] – admin
+++ biac:analysis:resting_pipeline [2013/09/16 18:34] – [Step 7] admin
@@ Line 264: / Line 264: @@
 </code>
+==== Step 8 ====
+  * Functional connectivity density mapping
+  * Takes functional data from last step and calculates how connected they are to the voxels around them
+  * uses ( --fcdmthresh and --refgm ) as the pearson r-value and gray matter mask
+  * if defaults are used, then a dilated gray matter mask is used from FAST segmentation of MNI brain and a pearson r value of 0.6
+  * Iteratively goes to all neighboring voxels and counts the number that have correlated signal until they are under the r threshold
+  * adapted from Dardo Tomasi, PNAS(2010), vol. 107, no. 21. 9885–9890
+  * resulting file with be "fcdm.nii.gz"; higher voxel values indicate more correlation from neighbors
+{{:biac:analysis:fcdm.png?direct&400|}}
 ===== Things to consider =====
   * this was designed to be modular, so that you only need to run the steps you need