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--- biac:analysis:resting_pipeline [2012/07/06 12:34] – [Python/FSL Resting State Pipeline] gadde
+++ biac:analysis:resting_pipeline [2012/07/09 18:57] – [Python/FSL Resting State Pipeline] admin
@@ Line 34: / Line 34: @@
                         run
   -p func, --prefix=func
                         prefix for all resulting images, defaults to name of
                         input
+  --t1=/path/to/BXH     bxh ( or nifti ) file for the anatomical T1
   -s 0,1,2,3, --steps=0,1,2,3
                         comma seperated string of steps. 'all' will run
@@ Line 59: / Line 60: @@
                         AC point of reference image if not using standard MNI
                         brain
-  --betfval=0.5         f value to use while skull stripping. default is 0.5
+  --betfval=0.4         f value to use while skull stripping. default is 0.4
+  --anatbetfval=0.5     f value to use while skill stripping ANAT. default is 0.5
   --lpfreq=0.08         frequency cutoff for lowpass filtering in HZ.  default
                         is .08hz
@@ Line 172: / Line 174: @@
 ==== Step 7 ====
   * if defaults are used, then the aal_MNI_V4 label file is used to extract the average timeseries for each of the 116 regions
+  * if --dvarsthreshold or --motionthreshold are specified, then the ROI-averaged timeseries are further filtered ("scrubbed") by removing timepoints that exceed the given thresholds
   * cross correlation coefficients are found for the entire matrix of 116x116 regions
   * this step produces 4 files: