[Swift-commit] r2608 - SwiftApps/SIDGrid/scripts

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-02-25 15:29:05 -0600 (Wed, 25 Feb 2009)
New Revision: 2608

Added:
   SwiftApps/SIDGrid/scripts/recon2L.sh
Log:
fs wrapper for left hemi workflow

Added: SwiftApps/SIDGrid/scripts/recon2L.sh
===================================================================
--- SwiftApps/SIDGrid/scripts/recon2L.sh	                        (rev 0)
+++ SwiftApps/SIDGrid/scripts/recon2L.sh	2009-02-25 21:29:05 UTC (rev 2608)
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# $1 == user
+# $2 == subject
+# $3 == <subject>.tar
+
+echo "untarring.................."
+
+tar -xf $3
+
+####export FREESURFER_HOME=/soft/community/SIDGrid/freesurfer
+
+echo "freesurfer home is :::::"
+echo $FREESURFER_HOME
+
+export SUBJECTS_DIR=$PWD
+source $FREESURFER_HOME/SetUpFreeSurfer.sh
+
+recon-all -s $2 -smooth1 -hemi lh
+recon-all -s $2 -inflate1 -hemi lh
+recon-all -s $2 -qsphere -hemi lh
+recon-all -s $2 -fix -hemi lh
+recon-all -s $2 -finalsurfs -hemi lh
+recon-all -s $2 -smooth2 -hemi lh
+recon-all -s $2 -inflate2 -hemi lh
+recon-all -s $2 -cortribbon -hemi lh
+recon-all -s $2 -sphere -hemi lh
+echo "running: mris_register -dist 5 -curv $SUBJECTS_DIR/$2/surf/lh.sphere ${FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif $SUBJECTS_DIR/$2/surf/lh.sphere.reg"
+mris_register -dist 5 -curv $SUBJECTS_DIR/$2/surf/lh.sphere ${FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif $SUBJECTS_DIR/$2/surf/lh.sphere.reg
+echo "running: mris_register -dist 5 -curv -reverse $SUBJECTS_DIR/$2/surf/lh.sphere ${FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif $SUBJECTS_DIR/$2/surf/rh.lh.sphere.reg"
+mris_register -dist 5 -curv -reverse $SUBJECTS_DIR/$2/surf/lh.sphere ${FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif $SUBJECTS_DIR/$2/surf/rh.lh.sphere.reg
+#recon-all -s $2 -surfreg -hemi lh
+#recon-all -s $2 -contrasurfreg -hemi lh
+recon-all -s $2 -avgcurv -hemi lh
+recon-all -s $2 -cortparc -hemi lh
+recon-all -s $2 -parcstats -hemi lh
+recon-all -s $2 -cortparc2 -hemi lh
+recon-all -s $2 -parcstats2 -hemi lh
+
+tar cf $2L.tar $2
+ 
+


Property changes on: SwiftApps/SIDGrid/scripts/recon2L.sh
___________________________________________________________________
Name: svn:executable
   + *