Differences

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--- biac:analysis:resting_pipeline [2012/07/09 18:59] – [Step 3] admin
+++ biac:analysis:resting_pipeline [2013/02/13 20:28] – [Step 7] petty
@@ 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 ====
@@ Line 197: / Line 202: @@
 * that is the zr_values from the subject.graphml displayed in matplotlib.  the cursor shows the intersecting region at the bottom, and if you click, time courses are displayed.  we're working on a release (cp - 3/30/12)
-For a beta version of the viewer:
+For the rs-pipeline viewer:
 <code>
-/usr/local/packages/biacpython/bin/beta_viewer.py --help
+/usr/local/packages/biacpython/bin/rspipe_viewer.py --help
 Usage:
-beta_viewer.py --graphml /path/to/subject.graphml --stat zrvalue
+rspipe_viewer.py --graphml /path/to/subject.graphml --stat zrvalue
 Program to display graphml output from resting_pipeline