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--- jvs:fscan:manual:chapter2:physio [2011/10/07 17:27]
voyvodic
+++ jvs:fscan:manual:chapter2:physio [2011/11/16 21:12]
voyvodic
@@ Line 25: / Line 25: @@
     * 7 - pupilaspect
     * 010 - identify peak values
-    * 020 -
+    * 020 - identify trough values
-    * 040 -
+    * 040 - identify zero crossings (050-rising, 060-falling)
     * 0100 - generate resampled phase values
     * 0200 - generate resampled rate values
     * 0400 - generate resampled amplitude values
-    * 01000 -
+    * 01000 - calculate the amplitude range
-    * 02000 -
-    * 04000 -
     * 010000 - flip X/Y axes
@@ Line 43: / Line 41: @@
   * tr - scan TR time (sec per volume of images)
   * nz - number of slices per TR
-  * interleave - slice timeing flag: 0=sequential, 1=odd then even, 2=even then odd (1st slice# = 1)
+  * interleave - slice timing flag: 0=sequential, 1=odd then even, 2=even then odd (1st slice# = 1) (default from data hdr)
   * print - control output display options (default printing is to file 'physio_name.txt')
     * 1 - print one-line summary
@@ Line 49: / Line 47: @@
     * 4 - print resampled phase, rate, amplitude values
     * 8 - print to standard output rather than default data file
+    * 16 - print RETROICOR parameters
+    * 32 - print RHVRCOR parameters
+    * 64 - omit the column header line
+  * lowrange - minimum percent signal range needed in waveform for physio analysis (default: 2 %)
 **Examples:**\\

Brain Imaging & Analysis Center