Differences

This shows you the differences between two versions of the page.

--- biac:analysis:resting_pipeline [2012/07/09 18:57] – [Python/FSL Resting State Pipeline] admin
+++ biac:analysis:resting_pipeline [2012/07/09 19:02] – [Step 4] admin
@@ Line 153: / 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
@@ Line 161: / Line 161: @@
   * if your subject has already been normalized during standard pre-processing of other runs, please provide the flirt matrix from pre-stats with **--flirtmat** ( most likely example_func2standard.mat)
     * this will apply the previously determined flirt matrix to your functional data instead of trying to calculate a new matrix based on the functionals.  the matrix from pre-stats was likely calculated using a high-resolution anatomical, also this will assure that your resting state runs are in the same space as the other runs from your subject.
+  * if you've provided at T1 anatomical image then this sequence is followed:
+    * func-2-t1
+    * t1-2-standard
+    * flirt matrices are concatenated to create func-2-standard
+  * if no T1 is provided, then the functional is used for the flirt normalization
 ==== Step 5 ====