[Swift-commit] r2636 - SwiftApps/SIDGrid/swift/swift_scripts/afni

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-03-03 13:05:23 -0600 (Tue, 03 Mar 2009)
New Revision: 2636

Added:
   SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIdeconvolve.swift
Log:
3dDeconvolve for event related design

Added: SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIdeconvolve.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIdeconvolve.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/swift_scripts/afni/AFNIdeconvolve.swift	2009-03-03 19:05:23 UTC (rev 2636)
@@ -0,0 +1,62 @@
+#---- pinche deconvolution
+type file{}
+
+type AFNI_obj{
+    file HEAD;
+    file BRIK;
+}
+
+type stims{
+    string labels[];
+    string fnames[];
+}
+
+app (AFNI_obj deconvBucketResult, AFNI_obj irfResult, file deconvXsave) AFNI_pincheDeconvolution (AFNI_obj normalized, stims stimuli, file censor, file concat, file motionfile, file designmatrix, string outPrefix){
+    AFNI_3dDeconvolve "-input" @filename(normalized.BRIK) "-polort" 3 "-tshift" "-num_stimts" 10
+    "-stim_file" 1 stimuli.fnames[0] "-stim_label" 1 stimuli.labels[0]
+    "-stim_file" 2 stimuli.fnames[1] "-stim_label" 2 stimuli.labels[1]
+    "-stim_file" 3 stimuli.fnames[2] "-stim_label" 3 stimuli.labels[2]
+    "-stim_file" 4 stimuli.fnames[3] "-stim_label" 4 stimuli.labels[3]
+    "-stim_file" 5 stimuli.fnames[4] "-stim_base" 5 "-stim_label" 5 stimuli.labels[4]
+    "-stim_file" 6 stimuli.fnames[5] "-stim_base" 6 "-stim_label" 6 stimuli.labels[5]
+    "-stim_file" 7 stimuli.fnames[6] "-stim_base" 7 "-stim_label" 7 stimuli.labels[6]
+    "-stim_file" 8 stimuli.fnames[7] "-stim_base" 8 "-stim_label" 8 stimuli.labels[7]
+    "-stim_file" 9 stimuli.fnames[8] "-stim_base" 9 "-stim_label" 9 stimuli.labels[8]
+    "-stim_file" 10 stimuli.fnames[9] "-stim_base" 10 "-stim_label" 10 stimuli.labels[9]
+    "-stim_maxlag" 1 11
+    "-stim_maxlag" 2 11
+    "-stim_maxlag" 3 11
+    "-stim_maxlag" 4 11
+    "-censor" @filename(censor)
+    "-iresp" 1 @strcat(outPrefix,".IRF")
+    "-full_first" "-tout" "-nodmbase" "-xsave" "-nfirst" "0" "-concat" @filename(concat) "-bucket"
+    outPrefix;
+}
+
+
+string declarelist[] = ["PK2"];
+foreach subject in declarelist{
+    ## map inputs
+    file designmatrix<single_file_mapper; file="for3dDecon.PK2_4condSHORTcat_all.1D">;
+    file motionfile<single_file_mapper; file=@strcat("motion_",subject,".1D")>;
+    file concat<single_file_mapper; file=@strcat("concat_runs",subject,".1D")>;
+    file censor<single_file_mapper; file=@strcat("motion_",subject,"_censor.1D")>;
+    AFNI_obj normalized<simple_mapper; prefix=@strcat("TScat_nrmlzdPerChng.",subject,"+orig.")>;
+
+    ## map outputs
+    string outPrefix = @strcat("DeconvResults_",subject);
+    file xsave<single_file_mapper; file=@strcat(outPrefix,".xsave")>;
+    AFNI_obj bucket<simple_mapper; prefix=@strcat(outPrefix,"+orig.")>;
+    AFNI_obj irf<simple_mapper; prefix=@strcat(outPrefix,".IRF+orig.")>;
+
+    #---- stimuli info
+    stims stimuli;
+    stimuli.labels = ["still_pa","move_pa","still_noise","move_noise","roll","pitch","yaw","dx","dy","dz"];
+    stimuli.fnames = [@strcat(@filename(designmatrix),"[0]"), at strcat(@filename(designmatrix),"[1]"),
+            @strcat(@filename(designmatrix),"[2]"), at strcat(@filename(designmatrix),"[3]"),
+            @strcat(@filename(motionfile),"[1]"), at strcat(@filename(motionfile),"[2]"),
+            @strcat(@filename(motionfile),"[3]"), at strcat(@filename(motionfile),"[4]"),
+            @strcat(@filename(motionfile),"[5]"), at strcat(@filename(motionfile),"[6]")];
+
+    (bucket, irf, xsave) = AFNI_pincheDeconvolution(normalized, stimuli, censor, concat, motionfile, designmatrix, outPrefix);
+}