tkregister issue with reg-feat2anat {Disarmed} - Freesurfer

11 Nov 2020


      External Email - Use Caution
Greetings,
I am experiencing a similar tkregister2 issue described in this thread when attempting to run reg-feat2anat: https://secure-web.cisco.com/1H9mU-9s00zN3P3mT0enoWLpI-9zwcO9lCds21sBQW9qoSP...
I am using FSL version 5.0.10 and Freesurfer version 7. I have pasted the --debug output after my signature. I am wondering if there should be a call for tkregister2_cmdl_cmdl (as opposed to tkregister2_cmdl)?
set TKR = tkregister2_cmdl
set TKR = tkregister2_cmdl
if ( $usedev ) set TKR = $DEV/$TKR/$TKR
if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl
if ( ! $manual ) set TKR = $TKR"_cmdl"
if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl
set TKR = tkregister2_cmdl_cmdl
Thank you for any help you can provide!
Erin
--
Erin Walsh, Ph.D.
Assistant Professor
University of North Carolina-Chapel Hill
Department of Psychiatry
Chapel Hill, NC 27599-3367
erin_walsh@med.unc.edu
pronouns: she/her
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 )
case "--featdir":
case --featdir:
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set FeatDir = $argv[1] ; shift ;
set FeatDir = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.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 = BA0023_V1
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 /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.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 /proj/dichterlab/BATA/Analysis/FreeSurfer_7 ) then
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1 ) 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_cmdl
set TKR = tkregister2_cmdl
if ( $usedev ) set TKR = $DEV/$TKR/$TKR
if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl
if ( ! $manual ) set TKR = $TKR"_cmdl"
if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl
set TKR = tkregister2_cmdl_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 /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
FeatDir is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
mkdir -p $FeatDir/reg/freesurfer/tmp
mkdir -p /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/tmp
set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat
set exf2std_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat
if ( ! -e $exf2std_fslmat ) then
if ( ! -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat ) then
set exfbase = $FeatDir/example_func
set exfbase = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func
if ( -e $exfbase.nii.gz ) then
if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.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 /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii ) then
if ( -e $exfbase.img ) then
if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.img ) then
if ( $#fslext == 0 ) then
if ( 1 == 0 ) then
set tempvol = $FeatDir/example_func.$fslext
set tempvol = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
echo "template volume is $tempvol"
echo template volume is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
template volume is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
set anat2exf_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat
set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat
set anat2std_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2std.register.dat
set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat
set std2anat_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2anat.fsl.mat
set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_init_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat
set exf2anat_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.fsl.mat
set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat
set std2exf_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2exf.register.dat
set exf2std_regdat = $FeatDir/reg/freesurfer/exf2std.register.dat
set exf2std_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2std.register.dat
set segregdat = $FeatDir/reg/freesurfer/reg.bbr.dat
set segregdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg.bbr.dat
set stdbrain = $FeatDir/reg/standard.$fslext
set stdbrain = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/standard.nii.gz
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/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 = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log ) mv /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log.bak
echo log file is $LF
echo log file is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
log file is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
date | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
date
Wed Nov 11 18:22:53 EST 2020
pwd | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
pwd
/proj/dichterlab/BATA/Scripts/Hammer/Hammer_Activation/Censoring_Pipeline/Freesurfer
echo $0 | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo /nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat
/nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat
echo $cmdargs | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo --debug --feat /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat --subject BA0023_V1
--debug --feat /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat --subject BA0023_V1
uname -a | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
uname -a
Linux c1125.ll.unc.edu 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
set refvolcor = /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
if ( ! -e $refvolcor ) then
if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz ) then
if ( $fslext == img ) then
if ( nii.gz == img ) then
mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null
mri_info --o /tmp/reg-feat2anat.rasgood.36869 --ras_good /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ;
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$`
cat /tmp/reg-feat2anat.rasgood.36869
endif
endif
echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo example_func ras_good_flag 1
example_func ras_good_flag 1
if ( $exf_ras_good ) then
if ( 1 ) then
echo "-------------------------------------------------------" | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo -------------------------------------------------------
-------------------------------------------------------
echo "Initializing exf2anat with header" | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo Initializing exf2anat with header
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_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader )
if ( ! $debug ) set cmd = ( $cmd --noedit )
if ( ! 1 ) set cmd = ( tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit )
echo $cmd | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
echo tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader
tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader
$cmd | tee -a $LF
tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader
tkregister2_cmdl_cmdl: Command not found.
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1