Nope, that's a bug. I've attached a new version. Copy and make it executable cp $FREESURFER_HOME/bin chmod a+x $FREESURFER_HOME/bin/reg-feat2anat Then try again
On 11/11/2020 11:55 PM, Walsh, Erin wrote:
External Email - Use Caution
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 https://secure-web.cisco.com/1H9mU-9s00zN3P3mT0enoWLpI-9zwcO9lCds21sBQW9qoSPpMEcJ1KDcbQsvZ9iZ1Wu8IP-mx8SyKgy5jTrUhqaifkxwjnbydCn313Or34EBuAeIPcKmXUV4FKIUHu40DO-K4tlIsBBuqJiWGQHla8aFFqx48xIcSripk-6LwN6dWCO54xxItZWbucQGSL7YHt8zMgt1Q3RkeKUYYsXeQegOqzfQRPfegNd8CP99ch-E1mhfgNf4fhJuy-83sR_XTelccCwB8_-dAqbfuF2-8SA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68229.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_cmdlThank 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
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