--- /global/apps/freesurfer/5.1.0/bin/trac-all.orig	2012-08-06 11:57:49.461719000 +0200
+++ /global/apps/freesurfer/5.1.0/bin/trac-all	2012-08-14 09:33:07.569208000 +0200
@@ -8,8 +8,8 @@
 # Original Author: Anastasia Yendiki
 # CVS Revision Info:
 #    $Author: ayendiki $
-#    $Date: 2011/05/24 06:49:09 $
-#    $Revision: 1.22.2.6 $
+#    $Date: 2011/09/02 19:19:22 $
+#    $Revision: 1.35 $
 #
 # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
 #
@@ -25,11 +25,10 @@
 
 umask 002
 
-set VERSION = '$Id: trac-all,v 1.22.2.6 2011/05/24 06:49:09 ayendiki Exp $'
+set VERSION = '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'
 set ProgName = `basename $0`
 set inputargs = ($argv)
 
-
 if ($?PBS_JOBID) then
   echo "ERROR: Do not submit $ProgName as a job with pbsubmit or qsub."
   echo "ERROR: Run it directly on the command line."
@@ -38,10 +37,9 @@
   exit 1
 endif
 
-
 set onpbs = 0
 set hname = `hostname -s`
-if ($hname == seychelles || $hname == launchpad ) then
+if ($hname == seychelles || $hname == launchpad || $hname == stallo-1 || $hname == stallo-2 ) then
   set onpbs = 1
 endif
 
@@ -143,7 +141,7 @@
 set ntrainlist = ()
 set avgname = ()
 set reinit = 0
-set usetrunc = 0
+set usetrunc = 1
 set do1out = 0
 set doprior = 0
 set dosegprior = 1
@@ -454,10 +452,10 @@
     set bedmask = $dtdir/dlabel/diff/lowb_brain_mask.nii.gz
 
     if ($usemaskanat) then
-      if ($doregbbr && -e $dtdir/dlabel/diff/anat_brain_mask.bbr.nii.gz) then
-        set bedmask = $dtdir/dlabel/diff/anat_brain_mask.bbr.nii.gz
-      else if (-e $dtdir/dlabel/diff/anat_brain_mask.flt.nii.gz) then
-        set bedmask = $dtdir/dlabel/diff/anat_brain_mask.flt.nii.gz
+      if ($doregbbr && -e $dtdir/dlabel/diff/aparc+aseg_mask.bbr.nii.gz) then
+        set bedmask = $dtdir/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
+      else if (-e $dtdir/dlabel/diff/aparc+aseg_mask.flt.nii.gz) then
+        set bedmask = $dtdir/dlabel/diff/aparc+aseg_mask.flt.nii.gz
       endif
     endif
 
@@ -509,7 +507,7 @@
   if ($dopreproc) then
     if (! $?MYPBSWAIT) setenv MYPBSWAIT 30
     if ($doregcvs) then
-      if ($hname == launchpad)  setenv MYPBSARCH "ppn=2"
+      if ($hname == launchpad)  setenv MYPBSARCH "ppn=4,vmem=28gb"
       if ($hname == seychelles)	setenv MYPBSARCH "bigmem:ppn=2"
     endif
     echo Queueing pre-processing
@@ -521,7 +519,7 @@
   else if ($dopaths) then
     if (! $?MYPBSWAIT) setenv MYPBSWAIT 30
     if ($doregcvs) then
-      if ($hname == launchpad)  setenv MYPBSARCH "ppn=2"
+      if ($hname == launchpad)  setenv MYPBSARCH "ppn=4,vmem=28gb"
       if ($hname == seychelles)	setenv MYPBSARCH "bigmem:ppn=2"
     endif
     echo Queueing path reconstruction
@@ -782,15 +780,6 @@
 ############--------------##################
 check_params:
   if (! $DoVersionsOnly) then
-    if ($doregcvs) then
-      echo "WARN: CVS template is not unavailable in the current version"
-      set doregcvs = 0
-    endif
-    if (! $doregmni) then
-      echo "WARN: MNI is the only available inter-subject registration template"
-      set doregmni = 1
-    endif
-
     if (-e $trainfile) then
       if ($do1out) then
         # Leave-one-out training file: