[Swift-commit] r2626 - SwiftApps/SIDGrid/scripts

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-02-28 13:21:41 -0600 (Sat, 28 Feb 2009)
New Revision: 2626

Added:
   SwiftApps/SIDGrid/scripts/autorecon2_BOTH.sh
Log:
wrapper for fs workflow

Added: SwiftApps/SIDGrid/scripts/autorecon2_BOTH.sh
===================================================================
--- SwiftApps/SIDGrid/scripts/autorecon2_BOTH.sh	                        (rev 0)
+++ SwiftApps/SIDGrid/scripts/autorecon2_BOTH.sh	2009-02-28 19:21:41 UTC (rev 2626)
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# $1 == user
+# $2 == subject
+# $3 == <subject>.tar
+
+echo "untarring subject dir.................."
+echo $3
+
+tar -xf $3
+
+
+echo "freesurfer home is:::::"
+echo $FREESURFER_HOME
+
+export SUBJECTS_DIR=$PWD
+source $FREESURFER_HOME/SetUpFreeSurfer.sh
+
+## end recon1 proper, begin recon2 both hemis
+
+recon-all -s $2 -gcareg
+recon-all -s $2 -canorm
+recon-all -s $2 -careg
+recon-all -s $2 -rmneck
+recon-all -s $2 -skull-lta
+recon-all -s $2 -calabel
+recon-all -s $2 -segstats
+recon-all -s $2 -normalization2
+recon-all -s $2 -segmentation
+recon-all -s $2 -fill
+recon-all -s $2 -tessellate
+
+tar cf $3 $2 
+cp $3 results/
+


Property changes on: SwiftApps/SIDGrid/scripts/autorecon2_BOTH.sh
___________________________________________________________________
Name: svn:executable
   + *