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 %