[Swift-commit] r2502 - SwiftApps/SIDGrid/swift/swift_scripts/freesurfer

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-02-06 13:01:51 -0600 (Fri, 06 Feb 2009)
New Revision: 2502

Added:
   SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon2_3.swift
Log:
for running autorecon 2 and 3

Added: SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon2_3.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon2_3.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon2_3.swift	2009-02-06 19:01:51 UTC (rev 2502)
@@ -0,0 +1,45 @@
+type file {}						
+type mgzfile;
+
+(file subj_dir) autorecon2 (string subj file subj_dir_r1) { 			
+    app {
+        autorecon2_BOTH @arg("user") subj @subj_dir;
+    }
+}
+
+(file subj_dirL) recon2L (string subj, file subj_dir) {
+    app {
+	recon2L @arg("user") subj @subj_dir;
+	}
+}
+
+
+(file subj_dirR) recon2R (string subj, file subj_dir) {
+    app {
+	recon2R @arg("user") subj @subj_dir;
+	}
+}
+
+(file subj_dirCOMPLETE) reconFINAL (string subj, file subj_dirL, file subj_dirR) {
+    app {
+	reconFINAL @arg("user") subj @subj_dirL @subj_dirR;
+	}
+}
+	
+
+string subj = @arg("subj");
+# initial input subject dir should already be tar'ed 
+file subject_data_r1 <single_file_mapper;file=@strcat(subj, ".tar")>;
+
+file subject_data <single_file_mapper;file=@strcat(subj, ".tar")>;
+file subject_data2L <single_file_mapper;file=@strcat(subj,"L.tar")>;
+file subject_data2R <single_file_mapper;file=@strcat(subj,"R.tar")>;
+file subject_dataCOMPLETE <single_file_mapper;file=@strcat(subj,"COMPLETE.tar")>;
+
+subject_data = autorecon2(subj, subject_data_r1);
+subject_data2L = recon2L (subj, subject_data);
+subject_data2R = recon2R (subj, subject_data);
+subject_dataCOMPLETE = reconFINAL (subj, subject_data2L, subject_data2R);
+
+
+