[Swift-commit] r3038 - SwiftApps/SIDGrid/swift/swift_scripts/afni

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-03 00:30:36 -0500 (Mon, 03 Aug 2009)
New Revision: 3038

Added:
   SwiftApps/SIDGrid/swift/swift_scripts/afni/Vol2SurfSmooth.swift
Log:
for doing 3dVol2Surf and SurfSmooth in one swift workflow

Added: SwiftApps/SIDGrid/swift/swift_scripts/afni/Vol2SurfSmooth.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/afni/Vol2SurfSmooth.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/swift_scripts/afni/Vol2SurfSmooth.swift	2009-08-03 05:30:36 UTC (rev 3038)
@@ -0,0 +1,49 @@
+#--- this is for the PK2 surface projections and smoothing on the surface
+## cleanTScat_PK2allruns is a TS that has had slice time correction, covariates for motion, wm, and ventricles. 
+## did each run separate and concatenated at end.
+type file{}
+type AFNI_obj{
+    file HEAD;
+    file BRIK;
+}
+
+
+app (file vol2surfOutfile) AFNI_Vol2Surf (file spec_file, file smoothwm, file pial, string map, AFNI_obj surfvol, AFNI_obj grid_parent){
+    AFNI_3dVol2Surf "-spec" @spec_file "-surf_A" @smoothwm "-surf_B" @pial
+    "-map_func" map "-f_steps" 15 "-f_index" "voxels" "-oob_index" "-1" "-oob_value" 0 "-no_headers" "-outcols_NSD_format"
+    "-sv" @surfvol.BRIK "-grid_parent" @grid_parent.BRIK "-out_1D" @filename(vol2surfOutfile);
+}
+
+app (file surfsmoothOutfile) SurfSmooth (file spec_file, file smoothwm, file vol2surfOutfile){
+    SurfSmooth "-spec" @spec_file "-surf_A" @smoothwm "-met" "HEAT_07" "-input" @vol2surfOutfile
+    "-fwhm" 4 "-Niter" "-1" "-add_index" "-output" @filename(surfsmoothOutfile);
+}
+
+(file vol2surfOutfile, file surfsmoothOutfile) ProjectSmoothProc (file spec_file, file smoothwm, file pial, string map, AFNI_obj surfvol, AFNI_obj grid_parent){
+    (vol2surfOutfile)= AFNI_Vol2Surf(spec_file, smoothwm, pial, map, surfvol, grid_parent);
+    (surfsmoothOutfile) = SurfSmooth(spec_file, smoothwm, vol2surfOutfile);
+}
+
+
+string declarelist[] = ["PK2"];
+string mapFunctions[] = ["ave"];
+string hemis[] = ["lh","rh"];
+string conditions[] = ["cleanTScat_PK2allruns"];
+
+foreach subject in declarelist{
+    foreach map in mapFunctions{
+        foreach h in hemis{
+            foreach cc in conditions{
+                string baseDir = @strcat("/gpfs/pads/fmri/cnari/swift/projects/andric/peakfit_pilots/",subject,"/");
+                file spec_file<single_file_mapper; file=@strcat(baseDir,subject,"surfaces/SUMA/",subject,"_",h,".spec")>;
+                file smoothwm<single_file_mapper; file=@strcat(baseDir,subject,"surfaces/SUMA/",h,".smoothwm.asc")>;
+                file pial<single_file_mapper; file=@strcat(baseDir,subject,"surfaces/SUMA/",h,".pial.asc")>;
+                AFNI_obj surfvol<simple_mapper; location=@strcat(baseDir,subject,"surfaces/SUMA"), prefix=@strcat(subject,"_SurfVol_Alnd_Exp+orig.")>;
+                AFNI_obj grid_parent<simple_mapper; location=@strcat(baseDir,"preprocessingDos"), prefix=@strcat(cc,"+orig.")>;
+                file vol2surfOutfile<single_file_mapper; file=@strcat(baseDir,"preprocessingDos/",cc,"_",h,"_map",map,".1D")>;
+                file surfsmoothOutfile<single_file_mapper; file=@strcat(baseDir,"preprocessingDos/",cc,"_",h,"Smooth_map",map,".1D.dset")>;
+                (vol2surfOutfile, surfsmoothOutfile) = ProjectSmoothProc(spec_file, smoothwm, pial, map, surfvol, grid_parent);
+            }
+        }
+    }
+}