[Swift-commit] r2637 - SwiftApps/SIDGrid/swift/swift_scripts/afni

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-03-03 13:12:14 -0600 (Tue, 03 Mar 2009)
New Revision: 2637

Added:
   SwiftApps/SIDGrid/swift/swift_scripts/afni/SNRvol2surf.swift
Log:
3dVol2Surf for mapping surfaces from SUMA directory

Added: SwiftApps/SIDGrid/swift/swift_scripts/afni/SNRvol2surf.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/afni/SNRvol2surf.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/swift_scripts/afni/SNRvol2surf.swift	2009-03-03 19:12:14 UTC (rev 2637)
@@ -0,0 +1,37 @@
+#--- this is for the PK2 SNR surface projections
+type file{}
+
+type AFNI_obj{
+    file HEAD;
+    file BRIK;
+}
+
+
+app (file out_1d) 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(out_1d);
+}
+
+
+string declarelist[] = ["PK2"];
+string mapFunctions[] = ["ave"];
+string hemis[] = ["lh","rh"];
+string conditions[] = ["SNR"];
+
+foreach subject in declarelist{
+    foreach map in mapFunctions{
+        foreach h in hemis{
+            foreach cc in conditions{
+                string baseDir = @strcat("/disks/ci-gpfs/fmri/cnari/swift/projects/andric/peakfitTESTS/",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,"SNR/AFNIsnr"), prefix=@strcat("snr.",subject,".ALLruns+orig.")>;
+                file output1D<single_file_mapper; file=@strcat(subject,"_",h,"_",cc,"map",map,".1D")>;
+                output1D = AFNI_Vol2Surf(spec_file, smoothwm, pial, map, surfvol, grid_parent);
+            }
+        }
+    }
+}