Differences

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--- biac:analysis:resting_pipeline [2012/07/06 12:37] – [Step 7] gadde
+++ biac:analysis:resting_pipeline [2012/07/09 18:59] – [Step 3] 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 151: / Line 153: @@
   * the functional run is meaned across time with fslmaths, then bet is applied.  the resulting mask is then applied to the entire run of data
   * if you find that bet is doing a poor job finding the edges you can adjust the intensity threshold with **--betfval**
-    * this is equivalent of **-f** when actually running bet.  the default is 0.5, but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask )
+    * this is equivalent of **-f** when actually running bet.  the default is 0.4 (same as feat), but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask )
+  * if provided T1 anatomical is skull stripped. **--anatbetfval** is used to control intensity threshold, the default is 0.5 (same as feat)
 ==== Step 4 ====
   * normalize the data using flirt