FW: anat2exf.register.dat missing Hi All,
I sent the email below last week regarding the missing file anat2exf.register.dat.
I ran the command again and I manually changed the registration when tkregister popped up. I saved the registration and exited, the process continued and the output and error is below...
Your help would be greatly appreciated as we cannot get past this registration command.
Best wishes
Carolyn
**************************************************
Kate/Flatmap1> reg-feat2anat --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --feat
shift
switch ( $flag )
switch ( --feat )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set FeatDir = $argv[1] ; shift ;
set FeatDir = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --subject
shift
switch ( $flag )
switch ( --subject )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set subject = $argv[1] ; shift ;
set subject = AMoore
shift
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 ( $#FeatDir == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $FeatDir ) then
if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat ) then
if ( ! $manual ) then
if ( ! 0 ) then
if ( $#subject == 0 ) then
if ( 1 == 0 ) then
else
else
if ( $?SUBJECTS_DIR == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /disc2/Kate/Flatmap1 ) then
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore ) then
if ( $manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm != "func2std" ) then
if ( func2anat != func2anat && func2anat != std2anat && func2anat != func2std ) then
goto check_params_return ;
goto check_params_return
if ( $?DEV == 0 ) set DEV = "" ;
if ( 0 == 0 ) set DEV =
set DEV =
set TKR = tkregister2
set TKR = tkregister2
if ( $usedev ) set TKR = $DEV/$TKR/$TKR
if ( 0 ) set TKR = /tkregister2/tkregister2
set MM = mri_matrix_multiply
set MM = mri_matrix_multiply
if ( $usedev ) set MM = $DEV/$MM/$MM
if ( 0 ) set MM = /mri_matrix_multiply/mri_matrix_multiply
echo FeatDir is $FeatDir
echo FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
mkdir -p $FeatDir/reg/freesurfer/tmp
mkdir -p /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp
set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat
set exf2std_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat
if ( ! -e $exf2std_fslmat ) then
if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat ) then
set exfbase = $FeatDir/example_func
set exfbase = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func
if ( -e $exfbase.nii.gz ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz ) then
if ( -e $exfbase.nii ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii ) then
setenv FSLOUTPUTTYPE NIFTI
setenv FSLOUTPUTTYPE NIFTI
set fslext = nii ;
set fslext = nii
endif
endif
if ( -e $exfbase.img ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.img ) then
if ( $#fslext == 0 ) then
if ( 1 == 0 ) then
set tempvol = $FeatDir/example_func.$fslext
set tempvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
echo "template volume is $tempvol"
echo template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
set anat2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat
set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat
set anat2std_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat
set std2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat
set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_init_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat
set exf2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat
set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat
set std2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2exf.register.dat
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then
if ( $manual && $manxfm == func2anat ) then
if ( 0 && func2anat == func2anat ) then
if ( $manual && $manxfm == std2anat ) then
if ( 0 && func2anat == std2anat ) then
if ( $manual && $manxfm == func2std ) then
if ( 0 && func2anat == func2std ) then
set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log
set LF = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log ) mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak
mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak
echo log file is $LF
echo log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
date | tee -a $LF
date
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Mon Jun 25 10:56:41 BST 2007
pwd | tee -a $LF
pwd
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
/disc2/Kate/Flatmap1
echo $0 | tee -a $LF
echo /home/progs/freesurfer/bin//reg-feat2anat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
/home/progs/freesurfer/bin//reg-feat2anat
echo $cmdargs | tee -a $LF
echo --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
--debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
uname -a | tee -a $LF
uname -a
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then
set refvol = $FeatDir/reg/freesurfer/tmp/anat.$fslext
set refvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
set cmd = ( mri_convert $refvolcor $refvol )
set cmd = ( mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii )
echo $cmd | tee -a $LF
echo mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
$cmd | & tee -a $LF
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii...
if ( $status ) then
if ( 0 ) then
if ( $fslext == img ) then
if ( nii == img ) then
mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null
mri_info --o /tmp/reg-feat2anat.rasgood.9417 --ras_good /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ;
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$`
cat /tmp/reg-feat2anat.rasgood.9417
endif
endif
echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF
echo example_func ras_good_flag
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
example_func ras_good_flag
if ( $exf_ras_good ) then
if ( ) then
echo "-------------------------------------------------------" | tee -a $LF
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
echo -------------------------------------------------------
-------------------------------------------------------
echo "Initializing exf2anat from crude std2anat" | tee -a $LF
echo Initializing exf2anat from crude std2anat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Initializing exf2anat from crude std2anat
set cmd = ( $TKR --targ $refvolcor --mov $FSLDIR/etc/standard/avg152T1_brain.img --reg $anat2std_regdat --fslregout $std2anat_fslmat --regheader )
set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader )
if ( ! $debug ) set cmd = ( $cmd --noedit )
if ( ! 1 ) set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit )
echo $cmd | tee -a $LF
echo tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
$cmd | tee -a $LF
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
-----------------------------------------------------------------
INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
LoadVol 1
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
INFO: changing target type to float
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /home/progs/fsl/etc/standard/avg152T1_brain.img
INFO: changing move type to float
Tmov: --------------------
-2.000 0.000 0.000 91.000;
0.000 0.000 2.000 -91.000;
0.000 -2.000 0.000 109.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
---- Input registration matrix (computed) --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 30.861;
0.000 -1.000 0.000 -52.627;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 30.861;
0.000 -1.000 0.000 -52.627;
0.000 0.000 0.000 1.000;
subject = subject-unknown
Zoom Factor = 2
FOV = 256
Opening window subject-unknown
Setting scale
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
tkregister2: interface: /home/progs/freesurfer/lib/tcl/tkregister2.tcl
% ------------------------------------------------------------
Screen: 248 380 (0,0,0), inorm = 1, mov_frame = 0
Anat: (124 65 127) ( 4.0 -1.0 63.0) 0.0000 0.0
Func: ( 44 80 74) ( 4.0 57.5 -51.6) 0.0000 0.0
--------------------------------------------------------------
RegMat ---------------------------
1.000 0.000 0.000 0.000;
0.000 0.000 0.934 -9.280;
0.000 -1.000 0.000 -52.627;
0.000 0.000 0.000 1.000;
register: file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat written
% exit
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -8, ref det = -1
if ( $status ) exit 1 ;
if ( 0 ) exit 1
cp $std2anat_fslmat $std2anat_fslmat.init
cp /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat.init
set cmd = ( $MM -fsl -bin -iim $exf2std_fslmat -iim $std2anat_fslmat -om $exf2anat_init_fslmat )
set cmd = ( mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat )
echo $cmd | tee -a $LF
echo mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
$cmd | tee -a $LF
mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
if ( $status ) exit 1 ;
if ( 0 ) exit 1
endif
endif
set cmd = ( betfunc $FeatDir/example_func $FeatDir/reg/freesurfer/tmp/exfbet )
set cmd = ( betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet )
echo $cmd | tee -a $LF
echo betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet
$cmd | tee -a $LF
betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set tempvol0 = $tempvol
set tempvol0 = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
set tempvol = $FeatDir/reg/freesurfer/tmp/exfbet.$fslext ;
set tempvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii
set outvol = $FeatDir/reg/freesurfer/tmp/exf-in-anat
set outvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat
set cmd = ( flirt -ref $refvol -in $tempvol )
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii )
set cmd = ( $cmd -init $exf2anat_init_fslmat )
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat )
set cmd = ( $cmd -out $outvol -interp trilinear )
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear )
set cmd = ( $cmd -omat $exf2anat_fslmat -cost $cost -dof $dof )
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 )
set cmd = ( $cmd -searchrx -$maxangle $maxangle ) ;
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 )
set cmd = ( $cmd -searchry -$maxangle $maxangle ) ;
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 )
set cmd = ( $cmd -searchrz -$maxangle $maxangle ) ;
set cmd = ( flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 )
date | tee -a $LF
date
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Mon Jun 25 10:57:53 BST 2007
echo $cmd | tee -a $LF
echo flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
$cmd | & tee -a $LF
flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
if ( $status ) then
if ( 0 ) then
if ( fslext == img ) then
if ( fslext == img ) then
set cmd = ( $TKR --s $subject --mov $tempvol0 )
set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii )
set cmd = ( $cmd --reg $anat2exf_regdat )
set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat )
set cmd = ( $cmd --fslreg $exf2anat_fslmat )
set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat )
set tkregcheckcmd = ( $cmd --surf orig ) ;
set tkregcheckcmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig )
if ( ! $debug ) set cmd = ( $cmd --noedit )
if ( ! 1 ) set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --noedit )
if ( ! -e $SUBJECTS_DIR/$subject/mri/orig/COR-001 ) set cmd = ( $cmd --mgz )
if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/orig/COR-001 ) set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --mgz )
set cmd = ( tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --mgz )
echo "-------------------------------------------------------" | tee -a $LF
echo -------------------------------------------------------
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
-------------------------------------------------------
echo $cmd | tee -a $LF
echo tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --mgz
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --mgz
$cmd | & tee -a $LF
tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --mgz
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
niiRead(): unsupported timing pattern in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
---- FSL registration matrix --------
0.970 0.243 0.022 14.403;
-0.017 -0.021 1.000 64.061;
0.243 -0.970 -0.016 174.832;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat
LoadVol 1
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
ERROR: could not read /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii as 24
if ( $status ) then
if ( 1 ) then
echo "ERROR: tkregister2" | tee -a $LF
echo ERROR: tkregister2
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
ERROR: tkregister2
exit 1 ;
exit 1
***********************************************************************************************************************
-----Original Message-----
From: Furlong, Carolyn
Sent: Mon 18/06/2007 14:07
To: Freesurfer@nmr.mgh.harvard.edu
Subject: anat2exf.register.dat missing
Hi
We have run the command
reg-feat2anat --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
which generates several files with matricies in them but the file anat2exf.register.dat is missing.
The output is below...
tkregister2 popped up, the original surface green outline is not visible and there is a shift (3cm) with respect to the anatomical, I was wondering if the command ran successfully? Any comments and suggestions would be appreciated.
Best wishes
Carolyn
>reg-feat2anat --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --feat
shift
switch ( $flag )
switch ( --feat )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set FeatDir = $argv[1] ; shift ;
set FeatDir = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --subject
shift
switch ( $flag )
switch ( --subject )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set subject = $argv[1] ; shift ;
set subject = AMoore
shift
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 ( $#FeatDir == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $FeatDir ) then
if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat ) then
if ( ! $manual ) then
if ( ! 0 ) then
if ( $#subject == 0 ) then
if ( 1 == 0 ) then
else
else
if ( $?SUBJECTS_DIR == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /disc2/Kate/Flatmap1 ) then
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore ) then
if ( $manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm != "func2std" ) then
if ( func2anat != func2anat && func2anat != std2anat && func2anat != func2std ) then
goto check_params_return ;
goto check_params_return
if ( $?DEV == 0 ) set DEV = "" ;
if ( 0 == 0 ) set DEV =
set DEV =
set TKR = tkregister2
set TKR = tkregister2
if ( $usedev ) set TKR = $DEV/$TKR/$TKR
if ( 0 ) set TKR = /tkregister2/tkregister2
set MM = mri_matrix_multiply
set MM = mri_matrix_multiply
if ( $usedev ) set MM = $DEV/$MM/$MM
if ( 0 ) set MM = /mri_matrix_multiply/mri_matrix_multiply
echo FeatDir is $FeatDir
echo FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat
mkdir -p $FeatDir/reg/freesurfer/tmp
mkdir -p /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp
set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat
set exf2std_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat
if ( ! -e $exf2std_fslmat ) then
if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat ) then
set exfbase = $FeatDir/example_func
set exfbase = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func
if ( -e $exfbase.nii.gz ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz ) then
if ( -e $exfbase.nii ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii ) then
setenv FSLOUTPUTTYPE NIFTI
setenv FSLOUTPUTTYPE NIFTI
set fslext = nii ;
set fslext = nii
endif
endif
if ( -e $exfbase.img ) then
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.img ) then
if ( $#fslext == 0 ) then
if ( 1 == 0 ) then
set tempvol = $FeatDir/example_func.$fslext
set tempvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
echo "template volume is $tempvol"
echo template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
set anat2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat
set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat
set anat2std_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat
set std2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat
set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_init_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat
set exf2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat
set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat
set std2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2exf.register.dat
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then
if ( $manual && $manxfm == func2anat ) then
if ( 0 && func2anat == func2anat ) then
if ( $manual && $manxfm == std2anat ) then
if ( 0 && func2anat == std2anat ) then
if ( $manual && $manxfm == func2std ) then
if ( 0 && func2anat == func2std ) then
set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log
set LF = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log ) mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak
mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak
echo log file is $LF
echo log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
date | tee -a $LF
date
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Mon Jun 18 13:55:40 BST 2007
pwd | tee -a $LF
pwd
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
/disc2/Kate/Flatmap1
echo $0 | tee -a $LF
echo /home/progs/freesurfer/bin//reg-feat2anat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
/home/progs/freesurfer/bin//reg-feat2anat
echo $cmdargs | tee -a $LF
echo --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
--debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
uname -a | tee -a $LF
uname -a
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then
set refvol = $FeatDir/reg/freesurfer/tmp/anat.$fslext
set refvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
set cmd = ( mri_convert $refvolcor $refvol )
set cmd = ( mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii )
echo $cmd | tee -a $LF
echo mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
$cmd | & tee -a $LF
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii
reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii...
if ( $status ) then
if ( 0 ) then
if ( $fslext == img ) then
if ( nii == img ) then
mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null
mri_info --o /tmp/reg-feat2anat.rasgood.11254 --ras_good /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ;
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$`
cat /tmp/reg-feat2anat.rasgood.11254
endif
endif
echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF
echo example_func ras_good_flag
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
example_func ras_good_flag
if ( $exf_ras_good ) then
if ( ) then
echo "-------------------------------------------------------" | tee -a $LF
echo -------------------------------------------------------
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
-------------------------------------------------------
echo "Initializing exf2anat from crude std2anat" | tee -a $LF
echo Initializing exf2anat from crude std2anat
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
Initializing exf2anat from crude std2anat
set cmd = ( $TKR --targ $refvolcor --mov $FSLDIR/etc/standard/avg152T1_brain.img --reg $anat2std_regdat --fslregout $std2anat_fslmat --regheader )
set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader )
if ( ! $debug ) set cmd = ( $cmd --noedit )
if ( ! 1 ) set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit )
echo $cmd | tee -a $LF
echo tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
$cmd | tee -a $LF
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader
tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log
-----------------------------------------------------------------
INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
LoadVol 1
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
INFO: changing target type to float
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable /home/progs/fsl/etc/standard/avg152T1_brain.img
INFO: changing move type to float
Tmov: --------------------
-2.000 0.000 0.000 91.000;
0.000 0.000 2.000 -91.000;
0.000 -2.000 0.000 109.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
---- Input registration matrix (computed) --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 30.861;
0.000 -1.000 0.000 -52.627;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 30.861;
0.000 -1.000 0.000 -52.627;
0.000 0.000 0.000 1.000;
subject = subject-unknown
Zoom Factor = 2
FOV = 256
Opening window subject-unknown
Setting scale
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
tkregister2: interface: /home/progs/freesurfer/lib/tcl/tkregister2.tcl
%
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting