[Swift-commit] r3037 - SwiftApps/SIDGrid/swift/swift_scripts/afni

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-03 00:28:56 -0500 (Mon, 03 Aug 2009)
New Revision: 3037

Modified:
   SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIprocss.swift
Log:
Preprocessing procedures; now includes the 'tshift' (slice timing correction) in the volreg

Modified: SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIprocss.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIprocss.swift	2009-08-03 05:17:41 UTC (rev 3036)
+++ SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIprocss.swift	2009-08-03 05:28:56 UTC (rev 3037)
@@ -1,4 +1,5 @@
 #---- doing volreg, despike, mean, percent sig change for PK2
+#-- now using 'tshift' for slice timing correction
 type file{}
 
 type AFNI_obj{
@@ -8,7 +9,7 @@
 
 
 app (AFNI_obj volregResult, file resultVolregMotion) AFNI_volreg (string baseName, AFNI_obj inputTS, AFNI_obj referenceTS, string volregBaseString){
-    AFNI_3dvolreg "-twopass" "-twodup" "-dfile" @strcat("mot_",baseName) "-base" @strcat(volregBaseString,"+orig[225]") "-prefix" @strcat("volreg.",baseName) @inputTS.BRIK;
+    AFNI_3dvolreg "-twopass" "-twodup" "-dfile" @strcat("mot_",baseName) "-base" @strcat(volregBaseString,"+orig[225]") "-tshift" 4 "-prefix" @strcat("volreg.",baseName) @inputTS.BRIK;
 }
 
 app (AFNI_obj despikeResult) AFNI_despike (string baseName, AFNI_obj volregdInputTS){