[Swift-commit] r3025 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-03 00:04:13 -0500 (Mon, 03 Aug 2009)
New Revision: 3025

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNIprocss.swift
Log:
my standard preprocessing workflow. includes tshift option in volreg

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNIprocss.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNIprocss.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/preprocessingDos/AFNIprocss.swift	2009-08-03 05:04:13 UTC (rev 3025)
@@ -0,0 +1,50 @@
+#---- doing volreg, despike, mean, percent sig change for PK2
+#-- now using 'tshift' for slice timing correction
+type file{}
+
+type AFNI_obj{
+    file HEAD;
+    file BRIK;
+};
+
+
+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]") "-tshift" 4 "-prefix" @strcat("volreg.",baseName) @inputTS.BRIK;
+}
+
+app (AFNI_obj despikeResult) AFNI_despike (string baseName, AFNI_obj volregdInputTS){
+    AFNI_3dDespike "-prefix" @strcat("despiked.",baseName) @volregdInputTS.BRIK;
+}
+
+app (AFNI_obj meanResult) AFNI_mean (AFNI_obj despikeResult, string baseName){
+    AFNI_3dTstat "-mean" "-prefix" @strcat("mean.",baseName) @despikeResult.BRIK;
+}
+
+app (AFNI_obj nrmlzPerChngResult) AFNI_normalizePerChng (AFNI_obj despikeResult, AFNI_obj meanResult, string baseName){
+    AFNI_3dcalc "-a" @despikeResult.BRIK "-b" @meanResult.BRIK "-expr" @strcat( "((a-b)/b)*100" ) "-fscale" "-prefix" @strcat("nrmlzdPerChng.",baseName);
+}
+
+(AFNI_obj despikeResult, AFNI_obj meanResult, AFNI_obj nrmlzPerChngResult) AFNI_PerChngTS (string baseName, AFNI_obj volregdInput){
+    (despikeResult) = AFNI_despike(baseName, volregdInput);
+    (meanResult) = AFNI_mean(despikeResult, baseName);
+    (nrmlzPerChngResult) = AFNI_normalizePerChng(despikeResult, meanResult, baseName);
+}
+
+
+string declarelist[] = ["PK2"];
+foreach subject in declarelist{
+    int runs[] = [1:8];
+    foreach run in runs{
+        string baseName = @strcat(subject,".run",run);
+        AFNI_obj inputTS<simple_mapper; prefix=@strcat("ts.",run,"+orig.")>;
+        AFNI_obj volregResult<simple_mapper;prefix=@strcat("volreg.",baseName,"+orig.")>;
+        file resultVolregMotion<single_file_mapper; file=@strcat("mot_",baseName)>;
+        AFNI_obj volregRefTS<simple_mapper; prefix=@strcat("ts.4+orig.")>;
+        string volregBaseString = @strcat("ts.4");
+        AFNI_obj despikeResult<simple_mapper; prefix=@strcat("despiked.",baseName,"+orig.")>;
+        AFNI_obj meanResult<simple_mapper; prefix=@strcat("mean.",baseName,"+orig.")>;
+        AFNI_obj nrmlzPerChngResult<simple_mapper; prefix=@strcat("nrmlzdPerChng.",baseName,"+orig.")>;
+        (volregResult, resultVolregMotion) = AFNI_volreg(baseName, inputTS, volregRefTS, volregBaseString);
+        (despikeResult, meanResult, nrmlzPerChngResult) = AFNI_PerChngTS(baseName, volregResult);
+    }
+}