External Email - Use Caution Thank you very much. After the updata that you suggested, this error occurs: 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 > <dgr...@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 >>> <sdellipi...@gmail.com <mailto:sdellipi...@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 >>>> <dgr...@mgh.harvard.edu <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>On Behalf Of Stefano Delli >>>>> Pizzi >>>>> Sent: Saturday, February 3, 2024 2:33 PM >>>>> To: freesurfer@nmr.mgh.harvard.edu <mailto: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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be >>>>> https://secure-web.cisco.com/1VUSnXA-R8aMmePagKn7c5OTQLfckoVClegdJjwKCmfUWGs2PmA7bmD07BZN49m2NDPf6uY_ttaXKYvrRHqbtionPdA1hD4bPFRe8ncLlsGCIoKwpm0jKVmYXF0cxFDJregFcnAhbzjh0IIL2edgTk8-mrIrvpxwk59eF3EtsL63yrPSf1a5jds73CL5khujr1C1u6D9ZuDkiTdTEzzjXCyO-HRsPN5Qo_b4FOlImreAWWNLedmPC6yF7xR8YrwsCvsF1AXT8BkNxAS3loGM4aiQclLZTBluWIgsdcX1vU2J9pdPu04w5MGInUBJVyU0DIxpYhJWRSCv9ISY6kJCDNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> >>>>> <https://secure-web.cisco.com/1RGtmPM0hlMCo8Zjca56xbEFgG_xp75QgnTr8BS72v1bhOvgOaZ56wxierTWw6aBChhoVApCZZnLHEwoaPJUXDZjLIYQWnIhWYIKA-kNGVofBqirV7YvFc0TzAvadQSe0ANpIPTirgyFhqWIsN01-V7zxPFtlAKU7-jnQRLOGaOKtsYa2M5e8xaAqo1tCOHGrqCDXXK0uWOPpNk8LVSTl45asWLq7K0W8HiXtwSsMDXZn3Dg4abF6HqbH6riW2Hup5GFRBxuLunNBo-tObZ41fwyGjQtiw1Bsk6ZmGr4xEVZiHNPzZRSvZTm9qGlRUwD-3sa3qnKpcYAqISaE9OBjcA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to >>>> behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://secure-web.cisco.com/1RGtmPM0hlMCo8Zjca56xbEFgG_xp75QgnTr8BS72v1bhOvgOaZ56wxierTWw6aBChhoVApCZZnLHEwoaPJUXDZjLIYQWnIhWYIKA-kNGVofBqirV7YvFc0TzAvadQSe0ANpIPTirgyFhqWIsN01-V7zxPFtlAKU7-jnQRLOGaOKtsYa2M5e8xaAqo1tCOHGrqCDXXK0uWOPpNk8LVSTl45asWLq7K0W8HiXtwSsMDXZn3Dg4abF6HqbH6riW2Hup5GFRBxuLunNBo-tObZ41fwyGjQtiw1Bsk6ZmGr4xEVZiHNPzZRSvZTm9qGlRUwD-3sa3qnKpcYAqISaE9OBjcA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> The information in this e-mail is intended only for the person to whom it >>>> is addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at MailScanner has detected a possible fraud >>>> attempt from "secure-web.cisco.com" claiming to >>>> behttps://http://secure-web.cisco.com/16jogkVwEw3CL0eYdA7rGVXFGDl1ZMsrPX0oMaMfdAeanq7Qx2tly-ECBsssfxGeVF3vAE9OP2BQzN39xq4j4OzMAzGab3qd0NzpRWdzonQsE-3ISEkMr5-GP7klcun8QfJsiYsZ-z0gvxMWPiOxBLWPG64f4OaaBwewBIITc3glUWPNkKkTjfPtoV03XZbWWm38vQN7U0ZM8QB0Dl8EeqFvH45V7MDt0kB7xQaPmeqWX4EuahMLyvNpqgBFL5Tji5mu_TfZJIQjrApO72W90mzjfg57Wb95XHfKjp3yedRQYijfVtGzKx7oO6m-mrDw3LkGQvxH9i1e3AqvArAxB7Q/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>> >>>> <https://secure-web.cisco.com/1c9_PdX0MS4Dp1t3_S7ig7NDDRwU6Z42WDROfxYfWwU2LWpy7fLRlajLPdI24GmTLyeRwUxdtbRhdNGpJz0LxdLMfTUhTaZnYI7t6jg1S79ySiWtmHt47jqMUN7YzVP2rKqsFDJzJV4FAVcveIuD752QvvC6R1rRBHNNL21uJWZJhLdLIkvC_YULXyllF7INXeoFFDT-xAWnBpzOEoNlH4IwHXuXSEymB_l1j_H5VjENjjmP1Lr8Tf5tVAZwT4pBbjCVjR2uN-YcISFLtE7Z8CLOlLP4f-d8w6PQBj1aSDNNgQHNhPgOON5KVaykrQilv7_--OjpDE5aRIwRboA-unA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >>>> <MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be >>>> https://secure-web.cisco.com/1AbSpKWS3Wqx7Evqkn45FQpmKLYzlJqjsawI-wNV89JRP3bYSoS9Pa46VtfqA11hbJ1fUXWyzev8Pq8r97MLe5y98_0BqkHUWsZez4ceth52YGxgy5b0zXgd6K1dvJJpgtq8tFdIN0bmRRYlqjQDU332e5bYwczTUiua28cmrAKBpxCBqa53zZnFq4mmLaLuN6wDUCXHTDdXIytDNq4qUnQ41q1OE5ifiF6YExWBGshcb-qhRyGPcvWwxeyKSLjUK4NknuIKToXDZ1zAcLxzi4Cl61mFwbW-ZZt9eZMo9Z334xOhDpAPhaI2zKzTtQ6c4_LrLUyQc2Ob-g9aLRFWJLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >>>> >>>> <https://secure-web.cisco.com/1c9_PdX0MS4Dp1t3_S7ig7NDDRwU6Z42WDROfxYfWwU2LWpy7fLRlajLPdI24GmTLyeRwUxdtbRhdNGpJz0LxdLMfTUhTaZnYI7t6jg1S79ySiWtmHt47jqMUN7YzVP2rKqsFDJzJV4FAVcveIuD752QvvC6R1rRBHNNL21uJWZJhLdLIkvC_YULXyllF7INXeoFFDT-xAWnBpzOEoNlH4IwHXuXSEymB_l1j_H5VjENjjmP1Lr8Tf5tVAZwT4pBbjCVjR2uN-YcISFLtE7Z8CLOlLP4f-d8w6PQBj1aSDNNgQHNhPgOON5KVaykrQilv7_--OjpDE5aRIwRboA-unA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> >>>> . >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://secure-web.cisco.com/1VUSnXA-R8aMmePagKn7c5OTQLfckoVClegdJjwKCmfUWGs2PmA7bmD07BZN49m2NDPf6uY_ttaXKYvrRHqbtionPdA1hD4bPFRe8ncLlsGCIoKwpm0jKVmYXF0cxFDJregFcnAhbzjh0IIL2edgTk8-mrIrvpxwk59eF3EtsL63yrPSf1a5jds73CL5khujr1C1u6D9ZuDkiTdTEzzjXCyO-HRsPN5Qo_b4FOlImreAWWNLedmPC6yF7xR8YrwsCvsF1AXT8BkNxAS3loGM4aiQclLZTBluWIgsdcX1vU2J9pdPu04w5MGInUBJVyU0DIxpYhJWRSCv9ISY6kJCDNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1VUSnXA-R8aMmePagKn7c5OTQLfckoVClegdJjwKCmfUWGs2PmA7bmD07BZN49m2NDPf6uY_ttaXKYvrRHqbtionPdA1hD4bPFRe8ncLlsGCIoKwpm0jKVmYXF0cxFDJregFcnAhbzjh0IIL2edgTk8-mrIrvpxwk59eF3EtsL63yrPSf1a5jds73CL5khujr1C1u6D9ZuDkiTdTEzzjXCyO-HRsPN5Qo_b4FOlImreAWWNLedmPC6yF7xR8YrwsCvsF1AXT8BkNxAS3loGM4aiQclLZTBluWIgsdcX1vU2J9pdPu04w5MGInUBJVyU0DIxpYhJWRSCv9ISY6kJCDNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > <rawfunc2surf-sess.txt><rawfunc2tal-sess.txt><preproc-sess.txt>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1VUSnXA-R8aMmePagKn7c5OTQLfckoVClegdJjwKCmfUWGs2PmA7bmD07BZN49m2NDPf6uY_ttaXKYvrRHqbtionPdA1hD4bPFRe8ncLlsGCIoKwpm0jKVmYXF0cxFDJregFcnAhbzjh0IIL2edgTk8-mrIrvpxwk59eF3EtsL63yrPSf1a5jds73CL5khujr1C1u6D9ZuDkiTdTEzzjXCyO-HRsPN5Qo_b4FOlImreAWWNLedmPC6yF7xR8YrwsCvsF1AXT8BkNxAS3loGM4aiQclLZTBluWIgsdcX1vU2J9pdPu04w5MGInUBJVyU0DIxpYhJWRSCv9ISY6kJCDNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General Brigham > Compliance HelpLine at > https://secure-web.cisco.com/1AbSpKWS3Wqx7Evqkn45FQpmKLYzlJqjsawI-wNV89JRP3bYSoS9Pa46VtfqA11hbJ1fUXWyzev8Pq8r97MLe5y98_0BqkHUWsZez4ceth52YGxgy5b0zXgd6K1dvJJpgtq8tFdIN0bmRRYlqjQDU332e5bYwczTUiua28cmrAKBpxCBqa53zZnFq4mmLaLuN6wDUCXHTDdXIytDNq4qUnQ41q1OE5ifiF6YExWBGshcb-qhRyGPcvWwxeyKSLjUK4NknuIKToXDZ1zAcLxzi4Cl61mFwbW-ZZt9eZMo9Z334xOhDpAPhaI2zKzTtQ6c4_LrLUyQc2Ob-g9aLRFWJLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1AbSpKWS3Wqx7Evqkn45FQpmKLYzlJqjsawI-wNV89JRP3bYSoS9Pa46VtfqA11hbJ1fUXWyzev8Pq8r97MLe5y98_0BqkHUWsZez4ceth52YGxgy5b0zXgd6K1dvJJpgtq8tFdIN0bmRRYlqjQDU332e5bYwczTUiua28cmrAKBpxCBqa53zZnFq4mmLaLuN6wDUCXHTDdXIytDNq4qUnQ41q1OE5ifiF6YExWBGshcb-qhRyGPcvWwxeyKSLjUK4NknuIKToXDZ1zAcLxzi4Cl61mFwbW-ZZt9eZMo9Z334xOhDpAPhaI2zKzTtQ6c4_LrLUyQc2Ob-g9aLRFWJLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > .
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
