[brain1@localhost ~]$ reg-feat2anat --debug --featdir '/home/brain1/fMRI/Homunculus/P121/Experiment.feat' --subject P121 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 = --featdir shift switch ( $flag ) switch ( --featdir ) if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set FeatDir = $argv[1] ; shift ; set FeatDir = /home/brain1/fMRI/Homunculus/P121/Experiment.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 = P121 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 ( $DoBBR ) then if ( 1 ) then which bbregister > /dev/null which bbregister if ( $status ) then if ( 0 ) then endif endif if ( $#FeatDir == 0 ) then if ( 1 == 0 ) then if ( ! -e $FeatDir ) then if ( ! -e /home/brain1/fMRI/Homunculus/P121/Experiment.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 /usr/local/freesurfer/subjects ) then if ( ! -e $SUBJECTS_DIR/$subject ) then if ( ! -e /usr/local/freesurfer/subjects/P121 ) 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 if ( ! $manual ) set TKR = $TKR"_cmdl" if ( ! 0 ) set TKR = tkregister2_cmdl set TKR = tkregister2_cmdl 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 /home/brain1/fMRI/Homunculus/P121/Experiment.feat FeatDir is /home/brain1/fMRI/Homunculus/P121/Experiment.feat mkdir -p $FeatDir/reg/freesurfer/tmp mkdir -p /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat set exf2std_fslmat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/example_func2standard.mat if ( ! -e $exf2std_fslmat ) then if ( ! -e /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/example_func2standard.mat ) then set exfbase = $FeatDir/example_func set exfbase = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func if ( -e $exfbase.nii.gz ) then if ( -e /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz ) then setenv FSLOUTPUTTYPE NIFTI_GZ setenv FSLOUTPUTTYPE NIFTI_GZ set fslext = nii.gz ; set fslext = nii.gz endif endif if ( -e $exfbase.nii ) then if ( -e /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii ) then if ( -e $exfbase.img ) then if ( -e /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.img ) then if ( $#fslext == 0 ) then if ( 1 == 0 ) then set tempvol = $FeatDir/example_func.$fslext set tempvol = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz echo "template volume is $tempvol" echo template volume is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz template volume is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat set anat2exf_regdat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat set anat2std_regdat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat set std2anat_fslmat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_init_fslmat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat set exf2anat_fslmat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat set std2exf_regdat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2exf.register.dat set exf2std_regdat = $FeatDir/reg/freesurfer/exf2std.register.dat set exf2std_regdat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat set segregdat = $FeatDir/reg/freesurfer/reg.bbr.dat set segregdat = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg.bbr.dat set stdbrain = $FeatDir/reg/standard.$fslext set stdbrain = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz if ( ! -e $refvolcor ) then if ( ! -e /usr/local/freesurfer/subjects/P121/mri/brainmask.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 = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log if ( -e $LF ) mv $LF $LF.bak if ( -e /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log ) mv /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log.bak mv /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log.bak echo log file is $LF echo log file is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log log file is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log date | tee -a $LF date tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log Sun Jun 8 11:36:04 EDT 2014 pwd | tee -a $LF pwd tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log /home/brain1 echo $0 | tee -a $LF echo /usr/local/freesurfer/bin/reg-feat2anat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log /usr/local/freesurfer/bin/reg-feat2anat echo $cmdargs | tee -a $LF echo --debug --featdir /home/brain1/fMRI/Homunculus/P121/Experiment.feat --subject P121 tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log --debug --featdir /home/brain1/fMRI/Homunculus/P121/Experiment.feat --subject P121 uname -a | tee -a $LF uname -a tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log Linux localhost.localdomain 2.6.32-220.el6.x86_64 #1 SMP Tue Dec 6 19:48:22 GMT 2011 x86_64 x86_64 x86_64 GNU/Linux set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz if ( ! -e $refvolcor ) then if ( ! -e /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz ) then if ( $fslext == img ) then if ( nii.gz == img ) then mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null mri_info --o /tmp/reg-feat2anat.rasgood.8606 --ras_good /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ; set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` cat /tmp/reg-feat2anat.rasgood.8606 endif endif echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF echo example_func ras_good_flag 1 tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log example_func ras_good_flag 1 if ( $exf_ras_good ) then if ( 1 ) then echo "-------------------------------------------------------" | tee -a $LF echo ------------------------------------------------------- tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log ------------------------------------------------------- echo "Initializing exf2anat with header" | tee -a $LF echo Initializing exf2anat with header tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log Initializing exf2anat with header set cmd = ( $TKR --targ $refvolcor --mov $FeatDir/example_func.$fslext --reg $anat2exf_regdat.init --fslregout $exf2anat_init_fslmat --regheader ) set cmd = ( tkregister2_cmdl --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader ) if ( ! $debug ) set cmd = ( $cmd --noedit ) if ( ! 1 ) set cmd = ( tkregister2_cmdl --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit ) echo $cmd | tee -a $LF echo tkregister2_cmdl --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister2_cmdl --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader $cmd | tee -a $LF tkregister2_cmdl --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz movable volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz reg file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.init LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz 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/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz Tmov: -------------------- -1.875 0.000 0.000 120.000; 0.000 0.000 4.000 -72.000; 0.000 -1.875 0.000 120.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 -0.074 0.997 -0.161; 0.000 -0.997 -0.074 2.052; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 -0.074 0.997 -0.161; 0.000 -0.997 -0.074 2.052; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 -0.074 0.997 -0.161; 0.000 -0.997 -0.074 2.052; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -14.0625, ref det = -1 if ( $status ) exit 1 ; if ( 0 ) exit 1 else else set outvol = $FeatDir/reg/freesurfer/tmp/exf-in-anat set outvol = /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat if ( ! $UseSPM ) then if ( ! 0 ) then set cmd = ( fslregister --s $subject --reg $anat2exf_regdat --mov $tempvol --dof $dof --bins $bins --cost $cost --fslmat $exf2anat_fslmat --fsvol $anatvol --maxangle $maxangle --initfslmat $exf2anat_init_fslmat --tmp $FeatDir/reg/freesurfer/tmp --out $outvol.$fslext ) set cmd = ( fslregister --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz ) if ( $DoBETFunc ) set cmd = ( $cmd --betfunc ) if ( 0 ) set cmd = ( fslregister --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz --betfunc ) echo "" | tee -a $LF echo tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log echo $cmd | tee -a $LF tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log echo fslregister --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz fslregister --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz $cmd | tee -a $LF tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log fslregister --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz Log file is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log Sun Jun 8 11:36:05 EDT 2014 --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp --out /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ localhost.localdomain Linux localhost.localdomain 2.6.32-220.el6.x86_64 #1 SMP Tue Dec 6 19:48:22 GMT 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/brain1 mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/P121/mri/ERROR: /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/P121/mri/ERROR: /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /home/brain1 mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.997259, 0.0739863) k_ras = (0, -0.0739863, 0.997259) keeping frame 0 writing to /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/movvol.fslregister.nii... Mov determinant is -14.0625 Sun Jun 8 11:36:06 EDT 2014 /home/brain1 flirt.fsl -ref /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.init.fsl.mat ** ERROR (nifti_image_read): failed to find header file for '/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Sun Jun 8 11:36:06 EDT 2014 /home/brain1 flirt.fsl -ref /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat -init /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/outvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for '/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Sun Jun 8 11:36:06 EDT 2014 /home/brain1 mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/outvol.fslregister.nii /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/outvol.fslregister.nii /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz niiRead(): error opening file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/outvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp/outvol.fslregister.nii... tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat cat: /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat: No such file or directory tmp: Subscript out of range. Started at Sun Jun 8 11:36:05 EDT 2014 Ended at Sun Jun 8 11:36:06 EDT 2014 fslregister Done To check results, run: tkregister2 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --surf orig if ( $status ) exit 1 ; if ( 0 ) exit 1 if ( $DoBBR ) then if ( 1 ) then cp $anat2exf_regdat $anat2exf_regdat.bbr.init cp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat.bbr.init cp: cannot stat `/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat': No such file or directory set cmd = ( bbregister --mov $tempvol --bold --$dof --init-reg $anat2exf_regdat --reg $anat2exf_regdat ) set cmd = ( bbregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --bold --6 --init-reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat ) echo "" | tee -a $LF echo tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log echo $cmd | tee -a $LF echo bbregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --bold --6 --init-reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log bbregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --bold --6 --init-reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat $cmd | tee -a $LF bbregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --bold --6 --init-reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log ERROR: cannot find /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat if ( $status ) exit 1 ; if ( 0 ) exit 1 endif endif else else cp $anat2exf_regdat $FeatDir/reg/freesurfer/register.dat cp /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/register.dat cp: cannot stat `/home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat': No such file or directory if ( $ReDoStandardReg ) then if ( 1 ) then set tmp = $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat set tmp = /usr/local/freesurfer/subjects/P121/mri/transforms/reg.mni152.2mm.dat if ( -e $tmp ) then if ( -e /usr/local/freesurfer/subjects/P121/mri/transforms/reg.mni152.2mm.dat ) then set cmd = ( fslregister --mov $stdbrain --s $subject --reg $anat2std_regdat --dof 12 ) set cmd = ( fslregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --dof 12 ) endif endif echo $cmd | tee -a $LF echo fslregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --dof 12 tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log fslregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --dof 12 $cmd | tee -a $LF fslregister --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --dof 12 tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log Log file is /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat.fslregister.log Sun Jun 8 11:36:06 EDT 2014 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --s P121 --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --dof 12 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ localhost.localdomain Linux localhost.localdomain 2.6.32-220.el6.x86_64 #1 SMP Tue Dec 6 19:48:22 GMT 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/brain1 mri_convert /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/refvol.fslregister.nii mri_convert /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1.49012e-08, -1) k_ras = (0, 1, 0) writing to /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/refvol.fslregister.nii... -------------------------------------- /home/brain1 mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii --frame 0 mri_convert /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii... Mov determinant is -8 /home/brain1 tkregister2_cmdl --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/reg0.8761.dat --regheader --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 --s P121 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii reg file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/reg0.8761.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/P121/mri/orig.mgz 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/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii 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 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -0.672; 0.000 0.000 1.000 25.105; 0.000 -1.000 -0.000 6.410; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -0.672; 0.000 0.000 1.000 25.105; 0.000 -1.000 -0.000 6.410; 0.000 0.000 0.000 1.000; Determinant 1 subject = P121 RegMat --------------------------- 1.000 0.000 0.000 -0.672; 0.000 0.000 1.000 25.105; 0.000 -1.000 -0.000 6.410; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Sun Jun 8 11:36:08 EDT 2014 /home/brain1 flirt.fsl -ref /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/refvol.fslregister.nii -in /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 Sun Jun 8 11:36:15 EDT 2014 /home/brain1 flirt.fsl -ref /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/refvol.fslregister.nii -in /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat.fsl.mat -init /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/tmp.fslregister.8761/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.767 -0.013 0.000 59.247; 0.012 -0.236 -0.697 205.879; 0.015 0.827 -0.191 40.346; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz reg file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/P121/mri/orig.mgz 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/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz 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 = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; Determinant 2.0944 subject = P121 RegMat --------------------------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: P Cleaning up Started at Sun Jun 8 11:36:06 EDT 2014 Ended at Sun Jun 8 11:36:31 EDT 2014 fslregister Done To check results, run: tkregister2 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --surf orig if ( $status ) exit 1 ; if ( 0 ) exit 1 set cmd = ( mri_matrix_multiply -im $anat2exf_regdat -iim $anat2std_regdat -om $exf2std_regdat ) set cmd = ( mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat ) echo $cmd | tee -a $LF echo mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat $cmd | tee -a $LF mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log mri_matrix_multiply: error opening file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat mri_matrix_multiply: exiting... if ( $status ) exit 1 ; if ( 0 ) exit 1 set cmd = ( $TKR --targ $stdbrain --mov $FeatDir/example_func.$fslext --reg $exf2std_regdat --fslregout $FeatDir/reg/freesurfer/example_func2standard.mat ) set cmd = ( tkregister2_cmdl --targ /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/example_func2standard.mat ) if ( ! $debug ) set cmd = ( $cmd --noedit ) if ( ! 1 ) set cmd = ( tkregister2_cmdl --targ /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/example_func2standard.mat --noedit ) echo $cmd | tee -a $LF echo tkregister2_cmdl --targ /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/example_func2standard.mat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister2_cmdl --targ /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/example_func2standard.mat $cmd | tee -a $LF tkregister2_cmdl --targ /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/example_func2standard.mat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log regio_read_register(): No such file or directory Could not open /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz movable volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz reg file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2std.register.dat if ( $status ) exit 1 ; if ( 0 ) exit 1 if ( $OverwriteExf2Std ) then if ( 0 ) then set cmd = ( mri_matrix_multiply -im $anat2std_regdat -iim $anat2exf_regdat -om $std2exf_regdat ) set cmd = ( mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2exf.register.dat ) echo $cmd | tee -a $LF echo mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2exf.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2exf.register.dat $cmd | tee -a $LF mri_matrix_multiply -im /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat -iim /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat -om /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2exf.register.dat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log mri_matrix_multiply: error opening file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat mri_matrix_multiply: exiting... if ( $status ) exit 1 ; if ( 0 ) exit 1 else else echo "-------------------------------------------------------" | tee -a $LF echo ------------------------------------------------------- tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log ------------------------------------------------------- set cmd = ( $TKR --s $subject --targ $refvolcor --mov $stdbrain --reg $anat2std_regdat --fslregout $std2anat_fslmat ) set cmd = ( tkregister2_cmdl --s P121 --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat ) if ( ! $debug ) set cmd = ( $cmd --noedit ) if ( ! 1 ) set cmd = ( tkregister2_cmdl --s P121 --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat --noedit ) echo $cmd | tee -a $LF echo tkregister2_cmdl --s P121 --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister2_cmdl --s P121 --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat $cmd | tee -a $LF tkregister2_cmdl --s P121 --targ /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat --fslregout /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/std2anat.fsl.mat tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz movable volume /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz reg file /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /usr/local/freesurfer/subjects/P121/mri/brainmask.mgz 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/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/standard.nii.gz 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 = 0, float2int = 0 ---- Input registration matrix -------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; Determinant 2.0944 subject = P121 RegMat --------------------------- 1.303 -0.019 -0.004 -0.608; -0.028 -0.379 1.330 -18.713; -0.017 -1.121 -0.307 -12.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 if ( $status ) exit 1 ; if ( 0 ) exit 1 set cmd = ( $TKR --s $subject --mov $tempvol ) set cmd = ( tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz ) set cmd = ( $cmd --reg $anat2exf_regdat ) set cmd = ( tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat ) set cmd = ( $cmd --fslreg $exf2anat_fslmat ) set cmd = ( tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat ) set cmd = ( $cmd --surf orig ) ; set cmd = ( tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig ) echo "" echo echo "To visually check your results, run:" | tee -a $LF echo To visually check your results, run: tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log To visually check your results, run: echo $cmd --tag | sed 's/_cmdl//g' | tee -a $LF echo tkregister2_cmdl --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag sed s/_cmdl//g tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log tkregister2 --s P121 --mov /home/brain1/fMRI/Homunculus/P121/Experiment.feat/example_func.nii.gz --reg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag echo "" echo echo "" echo if ( $cleanup == 0 ) then if ( 1 == 0 ) then rm -fr $FeatDir/reg/freesurfer/tmp rm -fr /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/tmp endif endif date | tee -a $LF date tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log Sun Jun 8 11:36:33 EDT 2014 echo "reg-feat2anat done" | tee -a $LF echo reg-feat2anat done tee -a /home/brain1/fMRI/Homunculus/P121/Experiment.feat/reg/freesurfer/reg-feat2anat.log reg-feat2anat done exit 0 ; exit 0