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--- biac:analysis:resting_pipeline [2014/02/10 20:13] – [Download Source] cmp12
+++ biac:analysis:resting_pipeline [2019/05/31 13:27] – cmp12
@@ Line 47: / Line 47: @@
                         (1,3,5,2,4,6), up=ascending, down=descending,
                         even=interleaved (2,4,6,1,3,5) ).  Default is to read
-                        this from input image, if available.
+                        this from input BXH, if available.
   --tr=MSEC             TR of functional data in MSEC
   --ref=FILE            pointer to FLIRT reference image if not using standard
@@ Line 181: / Line 181: @@
   * run fsl's slice time correction ( slicetimer )
   * if starting with a BXH header, you'll likely have the sliceorder field which will be used to create a custom sliceorder file to be used by fsl
+  * the default is to run bxh_slicetiming to extract a timing file from the BXH header
   * if this isn't present, then you'll need to define **--sliceorder** so that we can generate the file for you
     * "odd" is interleaved with odd, then even slice ordering: 1,3,5,2,4,6,etc
@@ Line 186: / Line 187: @@
     * "up" is ascending data, from the bottom up: 1,2,3,4,5,6
     * "down" is descending data, from the top down: 6,5,4,3,2,1
+  * this gets much more complicated with multi-band data, so using the default extraction is recommended
 ==== Step 2 ====
@@ Line 429: / Line 431: @@
   - source files assume you have a working install of FSL and all imported python modules
   - need a working install of the [[http://www.nitrc.org/projects/bxh_xcede_tools/|BIRN BXH/Xcede tools]]
+  - will need to edit any paths that may be different at your install location ( FSL FAST segmentations of the MNI brain and base sets of ROIs )
+  - **Chou et al. AJNAR(2012), May; 33(5): 833–838 **
+  - fcdm algorithm adapted from **Dardo Tomasi, PNAS(2010), vol. 107, no. 21. 9885–9890**