[Swift-commit] r2956 - SwiftApps/SIDGrid/swift/swift_scripts/freesurfer

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-06-15 09:42:12 -0500 (Mon, 15 Jun 2009)
New Revision: 2956

Removed:
   SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon1.swift
Log:
no longer valid

Deleted: SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon1.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon1.swift	2009-06-13 23:19:42 UTC (rev 2955)
+++ SwiftApps/SIDGrid/swift/swift_scripts/freesurfer/autorecon1.swift	2009-06-15 14:42:12 UTC (rev 2956)
@@ -1,51 +0,0 @@
-type file {}						
-type mgzfile;
-
-(file job_00) new_subject (string subj, mgzfile inimage) { 			
-    app {
-        create_subject @arg("user") subj @inimage stdout=@filename(job_00);
-    }
-}
-
-(file job_01) autorecon1_4 (string subj, file job_00) {
-    app {
-	reconall @arg("user") @strcat("-s ", subj, " -nuintensitycor") stdout=@filename(job_01);
-    }
-}
-
-(file job_02) autorecon1_5 (string subj, file job_01) {
-    app {
-	reconall @arg("user") @strcat("-s ", subj, " -talairach") stdout=@filename(job_02);
-    }
-}
-
-(file job_03) autorecon1_6 (string subj, file job_02) {
-    app {
-	reconall @arg("user") @strcat("-s ", subj, " -normalization") stdout=@filename(job_03);
-    }
-}
-
-(file job_04) autorecon1_7 (string subj, file job_03) {
-    app {
-	reconall @arg("user") @strcat("-s ", subj, " -skullstrip") stdout=@filename(job_04);
-    }
-}
-
-### tars the subject dir on remote site for tranfer back to host
-
-(file subject_data) get_subject (string subj, file job_04) {
-    app {
-	get_subject @arg("subject_path") subj @subject_data;
-	}
-}
-
-mgzfile inimage <single_file_mapper;file=@arg("inimage")>;
-string subj = @arg("subj");
-
-file sigstring00 = new_subject(subj, inimage);		
-file sigstring01 = autorecon1_4(subj, sigstring00);
-file sigstring02 = autorecon1_5(subj, sigstring01);
-file sigstring03 = autorecon1_6(subj, sigstring02);
-file sigstring04 = autorecon1_7(subj, sigstring03);
-file subject_data <single_file_mapper;file=@arg("subj_tree")>;
-subject_data = get_subject(subj, sigstring04);