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Merge CIVET changes #8

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3 changes: 3 additions & 0 deletions ChangeLog
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@
* Fixed some compiler warnings.
* src/Splines/TBSpline.cc: Fixed memory overwrite.

2014-10-29 Claude Lepage <claude@bic.mni.mcgill.ca>
* Set verbose=0 for calls to Spawn that return parsed values

2011-01-13 Claude Lepage <claude@bic.mni.mcgill.ca>
* Fixed typo with headers in fieldIO.cc

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4 changes: 4 additions & 0 deletions NEWS
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@@ -1,3 +1,7 @@
New in Release 1.12.1
---------------------
* Set verbose=0 for calls to Spawn that return parsed values

New in Release 1.12.0
---------------------
* Moved Splines from EBTKS to N3 (must now use EBTKS 1.6.4
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4 changes: 2 additions & 2 deletions configure.in
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Expand Up @@ -2,10 +2,10 @@ dnl Process this file with autoconf to produce a configure script.

AC_INIT
dnl AC_CONFIG_AUX_DIR(ac_config_aux)
AM_INIT_AUTOMAKE(N3, 1.12.0)
AM_INIT_AUTOMAKE(N3, 1.12.1)
AM_CONFIG_HEADER([include/config.h])

AC_REVISION($Revision: 1.15 $)
AC_REVISION($Revision: 1.16 $)

AC_PROG_INSTALL
AC_PROG_LN_S
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16 changes: 8 additions & 8 deletions src/NUcorrect/nu_estimate_np_and_em.in
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Expand Up @@ -13,9 +13,9 @@
# express or implied warranty.
#----------------------------------------------------------------------------
#$RCSfile: nu_estimate_np_and_em.in,v $
#$Revision: 1.7 $
#$Revision: 1.8 $
#$Author: claude $
#$Date: 2009-07-29 15:07:44 $
#$Date: 2014-10-29 21:15:13 $
#$State: Exp $
#---------------------------------------------------------------------------
# ------------------------------ MNI Header ----------------------------------
Expand All @@ -30,7 +30,7 @@
#@CALLS :
#@CREATED : January 15, 1996 J.G.Sled
#@MODIFIED :
# $Id: nu_estimate_np_and_em.in,v 1.7 2009-07-29 15:07:44 claude Exp $
# $Id: nu_estimate_np_and_em.in,v 1.8 2014-10-29 21:15:13 claude Exp $
#-----------------------------------------------------------------------------
use warnings "all";
use MNI::Startup qw(nocputimes);
Expand Down Expand Up @@ -305,7 +305,7 @@ sub CreateMask
if($auto_mask_flag) { # determine if brain is in talairach space
Spawn(['mincinfo', '-attvalue', 'xspace:spacetype',
qw(-attvalue yspace:spacetype -attvalue zspace:spacetype),
$input_volume], err_action => 'ignore', stdout => \$output);
$input_volume], err_action => 'ignore', verbose => 0, stdout => \$output);
@spacetype = split('\n', $output);
(@spacetype == 3) && ($spacetype[0] =~ /talairach/i)
&& ($spacetype[1] =~ /talairach/i) &&
Expand All @@ -321,7 +321,7 @@ sub CreateMask
if (defined($Mask)) {
push(@VolumeStatsCmd, ('-mask', $Mask));
}
Spawn(\@VolumeStatsCmd, stdout => \$background_threshold);
Spawn(\@VolumeStatsCmd, verbose => 0, stdout => \$background_threshold);
chop($background_threshold);
}
}
Expand Down Expand Up @@ -376,7 +376,7 @@ sub CreateMask
# Check that mask volume is not empty
my $max;
Spawn(['volume_stats', '-quiet', '-max', $mask_volume],
stdout => \$max);
verbose => 0, stdout => \$max);
die("Error: Composite mask volume is empty. Check for one of the"
." following:\n 1) the user supplied mask is empty (all zeros)\n"
." 2) the values within the region of interest are entirely"
Expand Down Expand Up @@ -599,7 +599,7 @@ sub normalize_field_volume
(-r $_[1]) || die("&normalize_field_volume. Can't read file: $_[1]\n");

Spawn(['volume_stats', '-quiet', '-mean', '-mask', $mask, $volume],
stdout => \$mean);
verbose => 0, stdout => \$mean);
if(chomp($mean) != 0) {
Spawn("mincmath -div -const $mean $volume $norm_field_volume");
Spawn("mv $norm_field_volume $volume");
Expand Down Expand Up @@ -704,7 +704,7 @@ sub field_CV

(-r $_[0]) || die("field_CV. Can't read file: $_[0]\n");
Spawn(['volume_stats', '-quiet', '-stddev', '-mean',
'-mask', $_[1], $_[0]], stdout => \$result);
'-mask', $_[1], $_[0]], verbose => 0, stdout => \$result);
($mean, $stddev) = split("\n",$result);
($stddev =~ /NAN/i) && die("function: field_CV()\n"
."Field standard deviation not defined\n");
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8 changes: 4 additions & 4 deletions src/NUcorrect/nu_evaluate.in
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Expand Up @@ -13,9 +13,9 @@
# express or implied warranty.
#----------------------------------------------------------------------------
#$RCSfile: nu_evaluate.in,v $
#$Revision: 1.4 $
#$Revision: 1.5 $
#$Author: claude $
#$Date: 2010-12-09 19:35:01 $
#$Date: 2014-10-29 21:15:13 $
#$State: Exp $
#---------------------------------------------------------------------------
# ------------------------------ MNI Header ----------------------------------
Expand All @@ -30,7 +30,7 @@
#@CALLS :
#@CREATED : August 7, 1996 J.G.Sled
#@MODIFIED :
# $Id: nu_evaluate.in,v 1.4 2010-12-09 19:35:01 claude Exp $
# $Id: nu_evaluate.in,v 1.5 2014-10-29 21:15:13 claude Exp $
#-----------------------------------------------------------------------------

use MNI::Startup qw(nocputimes);
Expand All @@ -49,7 +49,7 @@ use Getopt::Tabular;
if( !( defined $user_mask_volume ) || !( -e $user_mask_volume ) ) {
my $threshold = 0;
&Spawn(['mincstats', '-quiet', '-biModalT', $input_volume],
err_action => 'ignore', stdout => \$threshold );
err_action => 'ignore', verbose => 0, stdout => \$threshold );
$user_mask_volume = "${TmpDir}/nuc_auto_mask.mnc";
&Spawn(['minccalc', '-quiet', '-byte', '-expression',
"if(A[0]>=$threshold){out=1}else{out=0}",
Expand Down