Greetings,

I am experiencing a similar tkregister2 issue described in this thread when attempting to run reg-feat2anat: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg68229.html

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

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

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

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

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

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

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

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

set fslext = nii.gz ;

set fslext = nii.gz

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

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: Command not found.

if ( $status ) exit 1 ;

if ( 1 ) exit 1

exit 1