could not determine file for /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI/XXX/rest/001/fmcpr.even

Stefano

Il giorno 5 mar 2024, alle ore 16:26, Douglas N. Greve <dgreve@mgh.harvard.edu> ha scritto:
I've made a patch to try to fix this. I've attached 3 files. Copy them to $FREESURFER/fsfast/bin. Make them executable by running
cd $FREESURFER/fsfast/bin
chmod a+x rawfunc2surf-sess rawfunc2tal-sess preproc-sess
Let me know if that works

On 3/5/2024 2:28 AM, Stefano Delli Pizzi wrote:
        External Email - Use Caution
Here -debug outputs

preproc-sess -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return

foreach grp ( $grpdefs )
foreach grp ( )

goto check_params ;
goto check_params

if ( $#SessList == 0 ) then
if ( 1 == 0 ) then

if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif

goto check_params_return ;
goto check_params_return

set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then

set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end

set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )

set errs = 0 ;
set errs = 0

set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( 091223sbj01m_tp1 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./091223sbj01m_tp1
if ( -d $stst ) then
if ( -d ./091223sbj01m_tp1 ) then
if ( ! -r $stst ) then
if ( ! -r ./091223sbj01m_tp1 ) then
pushd $stst > /dev/null ;
pushd ./091223sbj01m_tp1
set tmp = ( $tmp `$PWDCMD` ) ;
set tmp = ( `$PWDCMD` )
pwd
popd > /dev/null ;
popd
endif
endif
end
end
set nfound = ( $#tmp ) ;
set nfound = ( 1 )
if ( $nfound == 0 ) then
if ( 1 == 0 ) then
if ( $nfound > 1 ) then
if ( 1 > 1 ) then
set SessPath = ( $SessPath $tmp ) ;
set SessPath = ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
end
end

set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then

set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
endif
endif
end
end

echo $SessPath
echo /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1

exit $errs ;
exit 0
set echo = 1 ;
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 ( $#instem == 0 ) set instem = "f" ;
if ( 0 == 0 ) set instem = f
set instem = f

if ( $#fsd == 0 ) then
if ( 1 == 0 ) then

if ( $DoMC || $DoReg ) then
if ( 0 || 1 ) then
if ( $PerRun == 0 && $PerSess == 0 ) then
if ( 1 == 0 && 0 == 0 ) then
endif
endif

if ( $DoMC ) then
if ( 0 ) then

set mcoutstem = $instem ;
set mcoutstem = f
endif
endif

if ( $DoSTC ) then
if ( 1 ) then
if ( $#stcinstem == 0 ) set stcinstem = $mcoutstem
if ( 0 == 0 ) set stcinstem = f
set stcinstem = f
if ( $#stcoutstem == 0 ) then
if ( 0 == 0 ) then
if ( $#SliceOrder ) set stcoutstem = $stcinstem.$SliceOrder
if ( 1 ) set stcoutstem = f.up
set stcoutstem = f.up
if ( $#SliceDelayFile ) set stcoutstem = $stcinstem.sdf
if ( 0 ) set stcoutstem = f.sdf
endif
endif
else
else

if ( $ToSurf || $ToMNI305 || $ToCVS ) then
if ( 1 || 1 || 0 ) then
if ( $#fwhm == 0 ) then
if ( 1 == 0 ) then
set DoVolSmooth = 0 ;
set DoVolSmooth = 0
set DoSurfSmooth = 0 ;
set DoSurfSmooth = 0
set DoSmooth = 0 ;
set DoSmooth = 0
endif
endif

if ( $DoSmooth ) then
if ( 0 ) then

if ( $DoInorm && $#inormstem == 0 ) then
if ( 0 && 0 == 0 ) then

if ( ! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate ) then
if ( ! 0 && ! 1 && ! 0 && ! 1 && ! 1 ) then

if ( $#ProjFrac && $DoProjAvg ) then
if ( 0 && 0 ) then

if ( $UseB0DC && $#ProjFracExpKey ) then
if ( 0 && 0 ) then

if ( $#regfile == 0 ) then
if ( 0 == 0 ) then
if ( ! $UseB0DC ) set regfile = register.dof$RegDOF.lta
if ( ! 0 ) set regfile = register.dof6.lta
set regfile = register.dof6.lta
if ( $UseB0DC ) set regfile = register.dof$RegDOF.b0dc.lta
if ( 0 ) set regfile = register.dof6.b0dc.lta
endif
endif

if ( $#SliceDelayFile != 0 && $#SliceOrder != 0 ) then
if ( 0 != 0 && 1 != 0 ) then

goto check_params_return ;
goto check_params_return

if ( $nolog ) then
if ( 0 ) then

set logdir = log ;
set logdir = log
mkdir -p $logdir
mkdir -p log
if ( ! -e $logdir ) then
if ( ! -e log ) then

if ( $#SessList > 1 ) then
if ( 1 > 1 ) then

set sb = `basename $SessList`
set sb = `basename $SessList`
basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
set LF = $logdir/preproc-sess.$sb.log
set LF = log/preproc-sess.091223sbj01m_tp1.log
endif
endif
if ( -e $LF ) mv $LF $LF.old
if ( -e log/preproc-sess.091223sbj01m_tp1.log ) mv log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old
mv log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old
endif
endif
endif
endif
echo "--------------------------------------------------------------"
echo --------------------------------------------------------------
--------------------------------------------------------------
echo "preproc-sess logfile is $LF"
echo preproc-sess logfile is log/preproc-sess.091223sbj01m_tp1.log
preproc-sess logfile is log/preproc-sess.091223sbj01m_tp1.log
echo "--------------------------------------------------------------"
echo --------------------------------------------------------------
--------------------------------------------------------------

echo "preproc-sess log file" >> $LF
echo preproc-sess log file
echo $VERSION | tee -a $LF
echo FreeSurferEnv.csh 7.4.1
tee -a log/preproc-sess.091223sbj01m_tp1.log
FreeSurferEnv.csh 7.4.1
echo "$user" | tee -a $LF
echo stefano
tee -a log/preproc-sess.091223sbj01m_tp1.log
stefano
echo "setenv FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF
echo setenv FREESURFER_HOME /Applications/freesurfer/7.4.1
tee -a log/preproc-sess.091223sbj01m_tp1.log
setenv FREESURFER_HOME /Applications/freesurfer/7.4.1
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI
tee -a log/preproc-sess.091223sbj01m_tp1.log
setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI
uname -a | tee -a $LF
uname -a
tee -a log/preproc-sess.091223sbj01m_tp1.log
Darwin IMACSTEFANO01.local 21.6.0 Darwin Kernel Version 21.6.0: Mon Dec 19 20:44:01 PST 2022; root:xnu-8020.240.18~2/RELEASE_X86_64 x86_64
pwd | tee -a $LF
pwd
tee -a log/preproc-sess.091223sbj01m_tp1.log
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA
echo $0 | tee -a $LF
echo /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
tee -a log/preproc-sess.091223sbj01m_tp1.log
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
echo $inputargs | tee -a $LF
echo -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug
tee -a log/preproc-sess.091223sbj01m_tp1.log
-s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug
date | tee -a $LF
date
tee -a log/preproc-sess.091223sbj01m_tp1.log
Lun 26 Feb 2024 18:46:29 CET

echo "instem $instem " | tee -a $LF
echo instem f
tee -a log/preproc-sess.091223sbj01m_tp1.log
instem f
echo "mc $DoMC $mcinstem $mcoutstem " | tee -a $LF
echo mc 0 f
tee -a log/preproc-sess.091223sbj01m_tp1.log
mc 0 f
echo "stc $DoSTC $stcinstem $stcoutstem" | tee -a $LF
echo stc 1 f f.up
tee -a log/preproc-sess.091223sbj01m_tp1.log
stc 1 f f.up
echo "sm $DoVolSmooth $sminstem $smoutstem " | tee -a $LF
echo sm 0
tee -a log/preproc-sess.091223sbj01m_tp1.log
sm 0
echo "mask $DoMask $maskstem" | tee -a $LF
echo mask 1 brain
tee -a log/preproc-sess.091223sbj01m_tp1.log
mask 1 brain

set ProjectDir = `pwd` ;
set ProjectDir = `pwd`
pwd

set StartTime = `date` ;
set StartTime = `date`
date

foreach sess ( $SessList )
foreach sess ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
set sessparent = `dirname $sess` ;
set sessparent = `dirname $sess`
dirname /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1

if ( -w . && $nolog != 1 ) then
if ( -w . && 0 != 1 ) then
mkdir -p log
mkdir -p log
set LF = $ProjectDir/log/preproc-$sessid-$fsd.log
set LF = /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
rm -f $LF
rm -f /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
else
else

echo "preproc-sess" >> $LF
echo preproc-sess
echo $sessid >> $LF
echo 091223sbj01m_tp1
echo $VERSION >> $LF
echo FreeSurferEnv.csh 7.4.1
uname -a >> $LF
uname -a
date >> $LF
date
pwd >> $LF
pwd
echo $inputargs >> $LF
echo -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug
echo "ProjectDir $ProjectDir" >> $LF
echo ProjectDir /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA

if ( $DoTemplate ) then
if ( 1 ) then
set cmd = ( mktemplate-sess -s $sessid -d $sessparent -fsd $fsd -funcstem $instem )
set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f )
if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ;
if ( 0 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -rlf )
if ( $nolog ) set cmd = ( $cmd -nolog ) ;
if ( 0 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -nolog )
if ( $UpdateOnly ) set cmd = ( $cmd -update ) ;
if ( 1 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update )
set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update )
echo "$sessid Template -----------------------------" | & tee -a $LF
echo 091223sbj01m_tp1 Template -----------------------------
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
091223sbj01m_tp1 Template -----------------------------
echo $cmd | & tee -a $LF
echo mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update
$cmd | & tee -a $LF
mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log

Session: /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ----------------
Lun 26 Feb 2024 18:46:29 CET
Detected input format at nii.gz
091223sbj01m_tp1 Update not needed
Run: 001 ----------------
Lun 26 Feb 2024 18:46:30 CET
091223sbj01m_tp1 001 Update not needed
Run: 002 ----------------
Lun 26 Feb 2024 18:46:30 CET
091223sbj01m_tp1 002 Update not needed
Run: 003 ----------------
Lun 26 Feb 2024 18:46:30 CET
091223sbj01m_tp1 003 Update not needed
Lun 26 Feb 2024 18:46:30 CET
mktemplate-sess completed
if ( $status ) exit 1 ;
if ( 0 ) exit 1
endif
endif

if ( $DoReg ) then
if ( 1 ) then
set cmd = ( register-sess -s $sessid -d $sessparent -fsd $fsd -delete-dat )
set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat )
set cmd = ( $cmd -dof $RegDOF -$contrast )
set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold )
if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ;
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -rlf )
if ( $PerRun ) set cmd = ( $cmd -per-run )
if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run )
set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run )
if ( $PerSess ) set cmd = ( $cmd -per-session )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -per-session )
if ( $nolog ) set cmd = ( $cmd -nolog ) ;
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -nolog )
if ( $UpdateOnly ) set cmd = ( $cmd -update ) ;
if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update )
set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update )
if ( $UseB0DC ) set cmd = ( $cmd -b0dc )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -b0dc )
if ( $InitCoReg ) set cmd = ( $cmd -init-coreg )
if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg )
set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg )
if ( $InitFSL ) set cmd = ( $cmd -init-fsl )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-fsl )
if ( $InitSPM ) set cmd = ( $cmd -init-spm )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-spm )
if ( $InitHeader ) set cmd = ( $cmd -init-header )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-header )
if ( $#IntermediateFSD ) set cmd = ( $cmd -bbr-int $IntermediateFSD $IntermediateStem )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -bbr-int )
if ( $#BBRXopts ) set cmd = ( $cmd -bbr-xopts $BBRXopts )
if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -bbr-xopts )
echo "$sessid Registration -----------------------------" | & tee -a $LF
echo 091223sbj01m_tp1 Registration -----------------------------
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
091223sbj01m_tp1 Registration -----------------------------
echo $cmd | & tee -a $LF
echo register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg
$cmd | & tee -a $LF
register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
--------------------------------------------------------------
register-sess logfile is /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/register-sess.091223sbj01m_tp1.log
--------------------------------------------------------------
Lun 26 Feb 2024 18:46:30 CET

setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI
cd /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA
/Applications/freesurfer/7.4.1/fsfast/bin/register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Darwin IMACSTEFANO01.local 21.6.0 Darwin Kernel Version 21.6.0: Mon Dec 19 20:44:01 PST 2022; root:xnu-8020.240.18~2/RELEASE_X86_64 x86_64

Session: /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ----------------
Lun 26 Feb 2024 18:46:30 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
Run: 001 ----------------
Lun 26 Feb 2024 18:46:30 CET
Update not needed
Run: 002 ----------------
Lun 26 Feb 2024 18:46:30 CET
Update not needed
Run: 003 ----------------
Lun 26 Feb 2024 18:46:30 CET
Update not needed
Lun 26 Feb 2024 18:46:30 CET
register-sess completed
if ( $status ) exit 1 ;
if ( 0 ) exit 1
endif
endif

if ( $DoMask ) then
if ( 1 ) then
set cmd = ( mkbrainmask-sess -maskstem $maskstem )
set cmd = ( mkbrainmask-sess -maskstem brain )
set cmd = ( $cmd -fsd $fsd )
set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest )
set cmd = ( $cmd -s $sessid -d $sessparent )
set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA )
if ( $PerRun ) set cmd = ( $cmd -per-run )
if ( 1 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run )
set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run )
if ( $PerSess ) set cmd = ( $cmd -per-session )
if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -per-session )
if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ;
if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -rlf )
if ( $nolog ) set cmd = ( $cmd -nolog ) ;
if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -nolog )
if ( $UpdateOnly ) set cmd = ( $cmd -update ) ;
if ( 1 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update )
set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update )
if ( $UseB0DC ) set cmd = ( $cmd -b0dc )
if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update -b0dc )
if ( $RegDOF != 6 ) set cmd = ( $cmd -dof $RegDOF )
if ( 6 != 6 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update -dof 6 )
echo "$sessid Mask ------------------------" | & tee -a $LF
echo 091223sbj01m_tp1 Mask ------------------------
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
091223sbj01m_tp1 Mask ------------------------
echo $cmd | & tee -a $LF
echo mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update
$cmd | & tee -a $LF
mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
------------------------------------------------
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
Lun 26 Feb 2024 18:46:30 CET
091223sbj01m_tp1 Update not needed for session-level mask
091223sbj01m_tp1 Update not needed for run 001 mask
091223sbj01m_tp1 Update not needed for run 002 mask
091223sbj01m_tp1 Update not needed for run 003 mask
091223sbj01m_tp1 Update not needed for run 001 meanval
091223sbj01m_tp1 Update not needed for run 002 meanval
091223sbj01m_tp1 Update not needed for run 003 meanval
Lun 26 Feb 2024 18:46:31 CET
mkbrainmask-sess done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
endif
endif

if ( $DoMC ) then
if ( 0 ) then

if ( $DoSTC ) then
if ( 1 ) then
set cmd = ( stc-sess -i $stcinstem -o $stcoutstem -ngroups $nSliceGroups )
set cmd = ( stc-sess -i f -o f.up -ngroups 1 )
if ( $#SliceOrder ) set cmd = ( $cmd -so $SliceOrder )
if ( 1 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up )
set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up )
if ( $#SliceDelayFile ) set cmd = ( $cmd -sdf $SliceDelayFile )
if ( 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -sdf )
set cmd = ( $cmd -s $sessid -d $sessparent -fsd $fsd )
set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest )
if ( $#RunListFile != 0 ) set cmd = ( $cmd -rlf $RunListFile ) ;
if ( 0 != 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -rlf )
if ( $nolog ) set cmd = ( $cmd -nolog ) ;
if ( 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -nolog )
if ( $UpdateOnly ) set cmd = ( $cmd -update ) ;
if ( 1 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update )
set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update )
echo "$sessid STC -----------------------------" | & tee -a $LF
echo 091223sbj01m_tp1 STC -----------------------------
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
091223sbj01m_tp1 STC -----------------------------
echo $cmd | & tee -a $LF
echo stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update
$cmd | & tee -a $LF
stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
Lun 26 Feb 2024 18:46:31 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA
/Applications/freesurfer/7.4.1/fsfast/bin/stc-sess
-i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update
FreeSurferEnv.csh 7.4.1
IMACSTEFANO01.local
091223sbj01m_tp1 -----------------
Lun 26 Feb 2024 18:46:31 CET
-rw-r--r-- 1 stefano staff 19539533 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/f.up.nii.gz
-rwx------ 1 stefano staff 19504393 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/f.nii.gz
Update not needed
-rw-r--r-- 1 stefano staff 19734829 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/f.up.nii.gz
-rwx------ 1 stefano staff 19701816 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/f.nii.gz
Update not needed
-rw-r--r-- 1 stefano staff 20008834 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/f.up.nii.gz
-rwx------ 1 stefano staff 19975502 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/f.nii.gz
Update not needed
Started at Lun 26 Feb 2024 18:46:31 CET
Ended at Lun 26 Feb 2024 18:46:31 CET
stc-sess Done
if ( $status ) exit 1 ;
if ( 0 ) exit 1
endif
endif

if ( $ToSurf ) then
if ( 1 ) then
set cmd = ( rawfunc2surf-sess -fwhm $fwhm )
set cmd = ( rawfunc2surf-sess -fwhm 0 )
set cmd = ( $cmd -s $sessid -d $sessparent -fsd $fsd )
set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest )

if ( "$hemi" == lh || "$hemi" == rh ) set cmd = ( $cmd -hemi $hemi )
if ( lhrh == lh || lhrh == rh ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -hemi lhrh )
if ( $subject == self ) set cmd = ( $cmd -self )
if ( fsaverage == self ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -self )
if ( $subject != self ) set cmd = ( $cmd -trgsubject $subject )
if ( fsaverage != self ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage )
set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage )
if ( $#RunListFile != 0 ) set cmd = ( $cmd -rlf $RunListFile ) ;
if ( 0 != 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -rlf )
if ( $#SliceOrder ) set cmd = ( $cmd -stc $SliceOrder )
if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up )
set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up )
if ( $#SliceDelayFile ) set cmd = ( $cmd -sdf $SliceDelayFile )
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -sdf )
if ( $nolog ) set cmd = ( $cmd -nolog ) ;
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -nolog )
if ( $UpdateOnly ) set cmd = ( $cmd -update ) ;
if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update )
set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update )
if ( $UseB0DC ) set cmd = ( $cmd -b0dc )
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -b0dc )
if ( $RegDOF != 6 ) set cmd = ( $cmd -dof $RegDOF )
if ( 6 != 6 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -dof 6 )
if ( $PerRun ) set cmd = ( $cmd -per-run )
if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run )
set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run )
if ( $PerSess ) set cmd = ( $cmd -per-session )
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -per-session )
if ( $#ProjFrac ) set cmd = ( $cmd -projfrac $ProjFrac -expkey $ProjFracExpKey )
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -projfrac -expkey )
if ( $#volsurffwhm ) set cmd = ( $cmd -volsurffwhm $volsurffwhm )
if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -volsurffwhm )
if ( ! $UseCortexLabel ) set cmd = ( $cmd -no-cortex-label )
if ( ! 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -no-cortex-label )
echo "$sessid To Surface -----------------------------" | & tee -a $LF
echo 091223sbj01m_tp1 To Surface -----------------------------
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
091223sbj01m_tp1 To Surface -----------------------------
echo $cmd | & tee -a $LF
echo rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run
$cmd | & tee -a $LF
rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run
tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
instem fmcpr.up
outstem fmcpr.up.sm0.fsaverage.hemi
------------------------------
1/1 091223sbj01m_tp1
1/1 091223sbj01m_tp1 001 lh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.lh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 002 lh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.lh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 003 lh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.lh.pr.nii.gz does not need updating
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.lh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 001 rh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.rh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 002 rh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.rh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 003 rh ---------
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.rh.pr.nii.gz does not need updating
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.rh.pr.nii.gz does not need updating
1/1 091223sbj01m_tp1 001 lh ---------
Lun 26 Feb 2024 18:46:32 CET
ERROR: could not determine file for /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/fmcpr.up
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1
Il giorno 23 feb 2024, alle ore 18:32, Stefano Delli Pizzi <sdellipizzi@gmail.com> ha scritto:
Thank you!
I have already sent it to you (probabile to Yujing) some days ago. Were they not okay?
Could it be because I'm running data on MacOS?
If you do preprocessing with -nomc, does it work on your dataset? I've tried it with three different databases.
Regards
Stefano

Il giorno 23 feb 2024, alle ore 17:32, Douglas N. Greve <dgreve@mgh.harvard.edu> ha scritto:
I cannot reproduce this locally. If you still want help, attach logs. You can also try running it with -debug as the first option and capture the copious terminal output.

On 2/6/2024 8:39 AM, Huang, Yujing wrote:
Not sure where this happened. Does it produce any log files that you can share? Maybe both logs with and without the -nomc option.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>On Behalf Of Stefano Delli Pizzi
Sent: Saturday, February 3, 2024 2:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] if: Expression Syntax - preproc-sess

External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run preproc-sess with -nomc option
 
preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest 
-per-run -sliceorder up -force
if: Expression Syntax.
 
This error occurred before to create the file with slice timing correction
 
The error did not occur when I run the preproc-sess command line without the 
-nomc option.
 
I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one?
 
FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Platform: Darwin Kernel Version 21.6.0
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