[Swift-commit] r2607 - SwiftApps/SIDGrid/scripts

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-02-25 15:28:28 -0600 (Wed, 25 Feb 2009)
New Revision: 2607

Added:
   SwiftApps/SIDGrid/scripts/recon1.sh
Log:
fs wrapper1

Added: SwiftApps/SIDGrid/scripts/recon1.sh
===================================================================
--- SwiftApps/SIDGrid/scripts/recon1.sh	                        (rev 0)
+++ SwiftApps/SIDGrid/scripts/recon1.sh	2009-02-25 21:28:28 UTC (rev 2607)
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# $1 == user
+# $2 == subject
+# $3 == input image
+
+####export FREESURFER_HOME=/soft/community/SIDGrid/freesurfer
+
+echo "freesurfer home is:::::"
+echo $FREESURFER_HOME
+
+export SUBJECTS_DIR=$PWD
+source $FREESURFER_HOME/SetUpFreeSurfer.sh
+
+mkdir -p $2/mri/transforms
+mkdir $2/label
+mkdir $2/stats
+mkdir $2/surf
+mkdir $2/scripts
+mkdir $2/mri/orig
+
+echo "finished making directory tree, about to do converts"
+echo "mri_convert $3 $1/$2/mri/rawavg.mgz..........."
+echo "mri_convert $1/$2/mri/rawavg.mgz $1/$2/mri/orig.mgz
+--conform........"
+
+mri_convert $3 $2/mri/rawavg.mgz
+mri_convert $2/mri/rawavg.mgz $2/mri/orig.mgz --conform
+
+recon-all -s $2 -nuintensitycor
+recon-all -s $2 -talairach
+recon-all -s $2 -normalization
+recon-all -s $2 -skullstrip
+
+## 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 $2.tar $2 
+


Property changes on: SwiftApps/SIDGrid/scripts/recon1.sh
___________________________________________________________________
Name: svn:executable
   + *