R: Re: R: Re: FS-FAST using MRS voxel or .label as seed - Freesurfer

21 Feb 2016

      I have checked MRS_MASK.mg and all its voxels have a value=1.
All voxels contains in the mask are well overlapped on f.nii.
The registration is accurate: the MRS mask is located on the vmPFC and its is 
equally distributed on left and right hemisphere. The orig.nii.gz and f.nii.gz 
is well overlapped, as well the MRS mask.
mri_convert $SUBJECTS_DIR/subj2/FS_space_MRS_voxel_maskFS_space_MRS_voxel_mask.
nii.gz $SUBJECTS_DIR/subj2/mri/MRS_MASK.mgz
mri_convert $SUBJECTS_DIR/subj2/FS_space_MRS_voxel_mask.nii.gz MRS_MASK.mgz
fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config -
overwrite
fcseed-sess -s subj2 -cfg MRS_MASK.config -overwrite -debug
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
foreach grp ( $grpdefs )
foreach grp ( )
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 1 == 0 ) then
if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif
goto check_params_return ;
goto check_params_return
set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( subj2 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./subj2
if ( -d $stst ) then
if ( -d ./subj2 ) then
if ( ! -r $stst ) then
if ( ! -r ./subj2 ) then
pushd $stst > /dev/null ;
pushd ./subj2
set tmp = ( $tmp `$PWDCMD` ) ;
set tmp = ( `$PWDCMD` )
pwd
popd > /dev/null ;
popd
endif
endif
end
end
set nfound = ( $#tmp ) ;
set nfound = ( 1 )
if ( $nfound == 0 ) then
if ( 1 == 0 ) then
if ( $nfound > 1 ) then
if ( 1 > 1 ) then
set SessPath = ( $SessPath $tmp ) ;
set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj2 )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /Applications/freesurfer/subjects/fMRI/subj2 )
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj2 )
endif
endif
end
end
echo $SessPath
echo /Applications/freesurfer/subjects/fMRI/subj2
exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#fcconfig == 0 ) then
if ( 1 == 0 ) then
set fcname = `cat $fcconfig | awk '{if($1 == "fcname") print $2}'`
set fcname = `cat $fcconfig | awk '{if($1 == "fcname") print $2}'`
cat MRS_MASK.config
awk {if($1 == "fcname") print $2}
set fsd = `cat $fcconfig | awk '{if($1 == "fsd") print $2}'`
set fsd = `cat $fcconfig | awk '{if($1 == "fsd") print $2}'`
cat MRS_MASK.config
awk {if($1 == "fsd") print $2}
set segstem = `cat $fcconfig | awk '{if($1 == "segstem") print $2}'`
set segstem = `cat $fcconfig | awk '{if($1 == "segstem") print $2}'`
cat MRS_MASK.config
awk {if($1 == "segstem") print $2}
set RegDOF = `cat $fcconfig | awk '{if($1 == "RegDOF") print $2}'`
set RegDOF = `cat $fcconfig | awk '{if($1 == "RegDOF") print $2}'`
cat MRS_MASK.config
awk {if($1 == "RegDOF") print $2}
set FillThresh = `cat $fcconfig | awk '{if($1 == "FillThresh") print $2}'`
set FillThresh = `cat $fcconfig | awk '{if($1 == "FillThresh") print $2}'`
cat MRS_MASK.config
awk {if($1 == "FillThresh") print $2}
set DoMean = `cat $fcconfig | awk '{if($1 == "DoMean") print $2}'`
set DoMean = `cat $fcconfig | awk '{if($1 == "DoMean") print $2}'`
cat MRS_MASK.config
awk {if($1 == "DoMean") print $2}
set DoSVD = `cat $fcconfig | awk '{if($1 == "DoSVD") print $2}'`
set DoSVD = `cat $fcconfig | awk '{if($1 == "DoSVD") print $2}'`
cat MRS_MASK.config
awk {if($1 == "DoSVD") print $2}
set DoSqr = `cat $fcconfig | awk '{if($1 == "DoSqr") print $2}'`
set DoSqr = `cat $fcconfig | awk '{if($1 == "DoSqr") print $2}'`
cat MRS_MASK.config
awk {if($1 == "DoSqr") print $2}
if ( $#MakeMask == 0 ) set MakeMask = `cat $fcconfig | awk '{if($1 == 
"MakeMask") print $2}'`
if ( 0 == 0 ) set MakeMask = `cat $fcconfig | awk '{if($1 == "MakeMask") print 
$2}'`
set MakeMask = `cat $fcconfig | awk '{if($1 == "MakeMask") print $2}'`
cat MRS_MASK.config
awk {if($1 == "MakeMask") print $2}
set WMErode = `cat $fcconfig | awk '{if($1 == "WMErode") print $2}'`
set WMErode = `cat $fcconfig | awk '{if($1 == "WMErode") print $2}'`
cat MRS_MASK.config
awk {if($1 == "WMErode") print $2}
set SVDSynth = `cat $fcconfig | awk '{if($1 == "SVDSynth") print $2}'`
set SVDSynth = `cat $fcconfig | awk '{if($1 == "SVDSynth") print $2}'`
cat MRS_MASK.config
awk {if($1 == "SVDSynth") print $2}
set DoWM = `cat $fcconfig | awk '{if($1 == "DoWM") print $2}'`
set DoWM = `cat $fcconfig | awk '{if($1 == "DoWM") print $2}'`
cat MRS_MASK.config
awk {if($1 == "DoWM") print $2}
set rlf = `cat $fcconfig | awk '{if($1 == "RunListFile") print $2}'`
set rlf = `cat $fcconfig | awk '{if($1 == "RunListFile") print $2}'`
cat MRS_MASK.config
awk {if($1 == "RunListFile") print $2}
set roicfg = `cat $fcconfig | awk '{if($1 == "roicfg") print $2}'`
set roicfg = `cat $fcconfig | awk '{if($1 == "roicfg") print $2}'`
cat MRS_MASK.config
awk {if($1 == "roicfg") print $2}
set tmp = `cat $fcconfig | awk '{if($1 == "segidlist") print $0}'`
set tmp = `cat $fcconfig | awk '{if($1 == "segidlist") print $0}'`
cat MRS_MASK.config
awk {if($1 == "segidlist") print $0}
if ( $#tmp ) set segidlist = ( $tmp[2-$#tmp] ) ;
if ( 2 ) set segidlist = ( 1 )
set segidlist = ( 1 )
set UseB0DC = 0 ;
set UseB0DC = 0
set tmp = `cat $fcconfig | awk '{if($1 == "UseB0DC") print $0}'`
set tmp = `cat $fcconfig | awk '{if($1 == "UseB0DC") print $0}'`
cat MRS_MASK.config
awk {if($1 == "UseB0DC") print $0}
if ( $#tmp ) set UseB0DC = $tmp[2] ;
if ( 2 ) set UseB0DC = 0
set UseB0DC = 0
if ( $MakeMask ) set maskfile = $fcname.mask
if ( 0 ) set maskfile = MRS_MASK.mask
if ( $#roicfg ) then
if ( 0 ) then
if ( $#regfilename == 0 ) then
if ( 0 == 0 ) then
if ( ! $UseB0DC ) set regfilename = register.dof$RegDOF.dat
if ( ! 0 ) set regfilename = register.dof6.dat
set regfilename = register.dof6.dat
if ( $UseB0DC ) set regfilename = register.dof$RegDOF.b0dc.dat
if ( 0 ) set regfilename = register.dof6.b0dc.dat
endif
endif
goto check_params_return ;
goto check_params_return
set ProjectDir = `pwd` ;
set ProjectDir = `pwd`
pwd
if ( ! $nolog ) then
if ( ! 0 ) then
mkdir -p log
mkdir -p log
set LF = $ProjectDir/log/fcseed-sess.$fcname.log
set LF = /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log
if ( $#SessList == 1 ) then
if ( 1 == 1 ) then
set sessid = `basename $SessList` ;
set sessid = `basename $SessList`
basename /Applications/freesurfer/subjects/fMRI/subj2
set LF = $LF.$sessid
set LF = /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
endif
endif
rm -f $LF
rm -f /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
else
else
echo Logfile is $LF
echo Logfile is /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.
MRS_MASK.log.subj2
Logfile is /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
date | tee -a $LF
date
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
Sun Feb 21 12:21:37 CET 2016
uname -a | tee -a $LF
uname -a
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
echo setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova
echo "cd `pwd`" | tee -a $LF
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
echo cd `pwd`
pwd
cd /Applications/freesurfer/subjects/fMRI
echo $0 | tee -a $LF
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
echo /Applications/freesurfer/fsfast/bin/fcseed-sess
/Applications/freesurfer/fsfast/bin/fcseed-sess
echo $cmdargs | tee -a $LF
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
echo -s subj2 -cfg MRS_MASK.config -overwrite -debug
-s subj2 -cfg MRS_MASK.config -overwrite -debug
cat $FREESURFER_HOME/build-stamp.txt | tee -a $LF
cat /Applications/freesurfer/build-stamp.txt
tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log.
subj2
freesurfer-Darwin-lion-stable-pub-v5.3.0
cat $fcconfig >> $LF
cat MRS_MASK.config
foreach sess ( $SessList )
foreach sess ( /Applications/freesurfer/subjects/fMRI/subj2 )
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /Applications/freesurfer/subjects/fMRI/subj2
set subject = `cat $sess/subjectname`
set subject = `cat $sess/subjectname`
cat /Applications/freesurfer/subjects/fMRI/subj2/subjectname
set RunList = ( `getrunlist $sess/$fsd $rlf` ) ;
set RunList = ( `getrunlist $sess/$fsd $rlf` )
getrunlist /Applications/freesurfer/subjects/fMRI/subj2/rest
foreach Run ( $RunList )
foreach Run ( 002 )
set rundir = $sess/$fsd/$Run
set rundir = /Applications/freesurfer/subjects/fMRI/subj2/rest/002
set LLF = $rundir/$fcname.log
set LLF = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
rm -f $LLF
rm -f /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
date | tee -a $LLF
date
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
Sun Feb 21 12:22:08 CET 2016
uname -a | tee -a $LLF
uname -a
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova
echo "cd `pwd`" | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo cd `pwd`
pwd
cd /Applications/freesurfer/subjects/fMRI
echo $0 | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo /Applications/freesurfer/fsfast/bin/fcseed-sess
/Applications/freesurfer/fsfast/bin/fcseed-sess
echo $cmdargs | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo -s subj2 -cfg MRS_MASK.config -overwrite -debug
-s subj2 -cfg MRS_MASK.config -overwrite -debug
cat $FREESURFER_HOME/build-stamp.txt | tee -a $LLF
cat /Applications/freesurfer/build-stamp.txt
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
freesurfer-Darwin-lion-stable-pub-v5.3.0
echo "" | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo
set outfile = $rundir/$fcname
set outfile = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK
set UpdateNeeded = 0 ;
set UpdateNeeded = 0
if ( ! -e $outfile ) set UpdateNeeded = 1 ;
if ( ! -e /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK ) set 
UpdateNeeded = 1
set UpdateNeeded = 1
if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $fcconfig`
if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $fcconfig`
if ( $#segidlist || $DoWM ) then
if ( 1 || 0 ) then
set f = `stem2fname $rundir/$funcstem`
set f = `stem2fname $rundir/$funcstem`
stem2fname /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr
if ( $status ) then
if ( 0 ) then
set reg = $rundir/$regfilename
set reg = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.
dat
if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $f`
if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $f`
if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $reg`
if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $reg`
else
else
if ( $UpdateOnly && ! $UpdateNeeded ) then
if ( 0 && ! 1 ) then
rm -f $outfile
rm -f /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK
set tmpdir = $rundir/tmp.fcseed-sess.$$
set tmpdir = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187
rm -rf $tmpdir
rm -rf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187
mkdir -p $tmpdir
mkdir -p /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187
if ( $#segidlist || $DoWM ) then
if ( 1 || 0 ) then
set template = `stem2fname $rundir/template`
set template = `stem2fname $rundir/template`
stem2fname /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template
if ( $DoWM ) then
if ( 0 ) then
set seganat = $SUBJECTS_DIR/$subject/mri/$segstem.mgz
set seganat = 
/Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz
endif
endif
set seg = $tmpdir/seg.$FSF_OUTPUT_FORMAT
set seg = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/seg.nii.gz
set pvf = $tmpdir/pvf.$FSF_OUTPUT_FORMAT ;
set pvf = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/pvf.nii.gz
set cmd = ( mri_label2vol --seg $seganat --reg $reg --temp $template --
fillthresh $FillThresh --o $seg --pvf $pvf ) ;
set cmd = ( mri_label2vol --seg 
/Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz --
fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --pvf 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf.
nii.gz )
echo $cmd | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo mri_label2vol --seg 
/Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz --
fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --pvf 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf.
nii.gz
mri_label2vol --seg 
/Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz --
fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --pvf 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf.
nii.gz
$cmd | tee -a $LLF
mri_label2vol --seg 
/Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz --
fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --pvf 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf.
nii.gz
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
PVF /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/pvf.nii.gz
Number of labels: 0
Annot File:      (null)
Template Volume: 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz
Outut Volume: /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/seg.nii.gz
Registration File: 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat
Fill Threshold: 0.5
Label Vox Vol:  1
ProjType:       (null)
ProjTypeId:     0
ProjStart:      0
ProjStop:       0
ProjDelta:      0.1
Subject:  (null)
Hemi:     (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: --------
-0.278   0.000   0.000   32.000;
-0.000  -0.000  -0.278   32.000;
-0.000   0.200   0.000   10.500;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 64.5752
nHits Thresh: 32.2876
Loading registration from 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat
RegMat: --------
-0.998   0.003   0.070   1.814;
 0.070  -0.089   0.994  -26.255;
-0.009  -0.996  -0.088  -3.555;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: --------
 0.278  -0.001  -0.020   31.495;
 0.003   0.277   0.025   32.989;
 0.014  -0.018   0.199   5.249;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
ASeg2Vol: Sorting 
ASeg2Vol: Mapping
ASeg2Vol: Reverse Map
nmisses = 0 (0 filled)
ASeg2Vol: done
PVF /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/pvf.nii.gz
Computing PVF 64.5752
if ( $status ) exit 1 ;
if ( 0 ) exit 1
if ( $#maskfile ) then
if ( 0 ) then
set mask = $tmpdir/mask.$FSF_OUTPUT_FORMAT
set mask = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz
endif
endif
set cmd = ( mri_binarize --i $seg --o $mask )
set cmd = ( mri_binarize --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg.
nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz )
foreach id ( $segidlist )
foreach id ( 1 )
set cmd = ( $cmd --match $id )
set cmd = ( mri_binarize --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg.
nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz --match 1 )
end
end
echo $cmd | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo mri_binarize --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg.
nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz --match 1
mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --o 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz --match 1
$cmd | tee -a $LLF
mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.
fcseed-sess.32187/seg.nii.gz --o 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz --match 1
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /Applications/freesurfer/subjects/fMRI
cmdline mri_binarize --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg.
nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz --match 1 
sysname  Darwin
hostname iMac-di-Stefano.local
machine  x86_64
user     Stefano
input      /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/seg.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz
Binarizing based on matching values
nMatch 1
 0     1
binval        1
binvalnot     0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
else
else
if ( $DoMean ) then
if ( 1 ) then
set cmd = ( mri_segstats --i $f --seg $mask --id 1 --sum $tmpdir/junk.sum --
avgwfvol $tmpdir/avgwf.mgh )
set cmd = ( mri_segstats --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/junk.sum --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/avgwf.mgh )
echo $cmd | tee -a $LLF
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
echo mri_segstats --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/junk.sum --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/avgwf.mgh
mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.
nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/junk.sum --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/avgwf.mgh
$cmd | tee -a $LLF
mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.
nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/mask.nii.gz --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/junk.sum --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/avgwf.mgh
tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --i 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/junk.sum --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/avgwf.mgh 
sysname  Darwin
hostname iMac-di-Stefano.local
machine  x86_64
user     Stefano
UseRobust  0
Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.
32187/mask.nii.gz
Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz
Voxel Volume is 64.5752 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                          0       0.000
MRIalloc(0, 1, 1): bad parm
Reporting on   0 segmentations
Computing spatial average of each frame
Writing to /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-
sess.32187/avgwf.mgh
Segmentation fault 
if ( $status ) exit 1 ;
if ( 139 ) exit 1
exit 1
...
----Messaggio originale----
Da: Douglas N Greve greve@nmr.mgh.harvard.edu
Data: 19-feb-2016 18.04
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] R: Re: FS-FAST using MRS voxel or .label as seed
Make sure that the MRS_MASK.mgz itself has some voxels with value=1, and 
make sure that there are enough of them to fit into at least one 
functional voxel.
Make sure that the registration is accurate.
When you run run fcseed-sess, add -debug, capture the output, and send 
it to me.
On 02/18/2016 06:43 PM, stdp82@virgilio.it wrote:
...
The problem persist.
Stefano
...
----Messaggio originale----
Da: Douglas N Greve greve@nmr.mgh.harvard.edu
Data: 19-feb-2016 0.25
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed
I think it may be our fcseed-config command line
fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd
rest -mean -cfg MRS_MASK.config –overwrite
It should be -seg MRS_MASK.mgz
They way you have it, fcseed will use the segmentation for Subj for all
subjects, which is why it works for one and not for others
On 02/18/2016 06:10 PM, stdp82@virgilio.it wrote:
...
Hi list,
I'm having problem to use FS-FAST fMRI connectivity using as seed a
mask of a MRS voxel or .label obtained by drawing it from surface. In
order to resolve my concern, I'm reporting step by step the command
lines which I have used. The mask, f.nii.gz, orig.nii.gz and
aparc+aseg.nii.gz showed a good overlap.
These are the features of each one:
fslinfo orig.nii.gz
data_type UINT8
dim1 256
dim2 256
dim3 256
dim4 1
datatype 2
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 0.010747
cal_max   0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo aparc+aseg.nii.gz
data_type INT32
dim1 256
dim2 256
dim3 256
dim4 1
datatype 8
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 0.010747
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo MRS_MASK.nii.gz
data_type FLOAT32
dim1 256
dim2 256
dim3 256
dim4 1
datatype 16
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 0.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
I’m using MNI2mm for subcortical analysis.
mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz
$SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz
fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd
rest -mean -cfg MRS_MASK.config –overwrite
fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite
mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh
-fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg
wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run
-overwrite
mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh
-fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg
wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run
-overwrite
mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask
-taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5
-nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite
selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh
selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh
selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305
isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast
MRS_MASK -o my-group
isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast
MRS_MASK -o my-group
isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast
MRS_MASK -o my-group
When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite,
it seem to be functioning for the first subj, but the next subj2 show
this error
Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.
gz
...
...
...
...
Voxel Volume is 64.5752 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
0 1 0       0.000
MRIalloc(0, 1, 1): bad parm
Reporting on 0 segmentations
Computing spatial average of each frame
Writing to
//Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess.
28328/avgwf.mgh
...
...
Segmentation fault

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
is
...
...
...
addressed. If you believe this e-mail was sent to you in error and the e-
mail
...
...
...
contains patient information, please contact the Partners Compliance
HelpLine
...
...
at
...
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
...
but does not contain patient information, please contact the sender and
properly
...
dispose of the e-mail.

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer