[Swift-commit] r3026 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-03 00:06:03 -0500 (Mon, 03 Aug 2009)
New Revision: 3026

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNImaskave.swift
Log:
for getting white matter and ventricle masks (via FS parcellation)

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNImaskave.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNImaskave.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNImaskave.swift	2009-08-03 05:06:03 UTC (rev 3026)
@@ -0,0 +1,22 @@
+# getting a white matter and ventricle mask for each PK2 run
+type file{}
+
+type AFNI_obj{
+    file HEAD;
+    file BRIK;
+};
+
+app (file maskaveResult) AFNI_maskave (AFNI_obj mask, AFNI_obj inputTS){
+    AFNI_3dmaskave "-mask" @mask.BRIK @inputTS.BRIK stdout=@maskaveResult;
+}
+
+string names[] = ["white","vent"];
+int runs[] = [1:8];
+foreach nn in names{
+    foreach rr in runs{
+        AFNI_obj mask<simple_mapper; prefix=@strcat(nn,".roi.frac.qrtmask+orig.")>;
+        AFNI_obj inputTS<simple_mapper; prefix=@strcat("nrmlzdPerChng.PK2.run",rr,"+orig.")>;
+        file maskaveResult<single_file_mapper; file=@strcat(nn,"mask.nrmlzdPerChng.PK2.run",rr,".1D")>;
+        maskaveResult = AFNI_maskave(mask, inputTS);
+    }
+}