Yes, it still has 22 subjects. The only difference between yesterday and
today was that I individually ran mris_preproc on subjects 005, 006, 007,
and 010 to test whether any of those files were corrupt or missing. All 4
successfully ran mri_surf2surf, however this morning when I ran
mris_preproc again with the --debug option, only subjects 005 and 006 were
successful. Does this mean that I will just have to specify each of my
subjects individually with the --s flag in mris_preproc and then run the
glmfit with the FSGD file?
Thanks,
Rosa
> ---------------------------- Original Message ----------------------------
> Subject: Re: [Freesurfer] mris_preproc --fsgd
> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> Date: Thu, September 13, 2012 11:53 am
> To: freesurfer@nmr.mgh.harvard.edu
> --------------------------------------------------------------------------
>
> Are you sure that oa_txeffect_verum.fsgd has more than two subjects? This
> run seems different than the one you sent yesterday which only found one
> subject.
> doug
>
>
>
> On 09/13/2012 08:48 AM, spa...@nmr.mgh.harvard.edu wrote:
>> Thanks Doug, here is the preproc log using the debug option:
>>
>> nmr. set echo = 1 ;
>> set debug = 1 ;
>> set debug = 1
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 10 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>> set flag = --fsgd
>> shift
>>
>> switch ( $flag )
>> switch ( --fsgd )
>> if ( $#argv == 0 ) goto arg1err ;
>> if ( 9 == 0 ) goto arg1err
>> set fsgdf = $argv[1] ; shift ;
>> set fsgdf = oa_txeffect_verum.fsgd
>> shift
>> if ( ! -e $fsgdf ) then
>> if ( ! -e oa_txeffect_verum.fsgd ) then
>> set sl = `cat $fsgdf | awk '{if($1 == "Input") print $2}'` ;
>> set sl = `cat $fsgdf | awk '{if($1 == "Input") print $2}'`
>> cat oa_txeffect_verum.fsgd
>> awk {if($1 == "Input") print $2}
>> set subjlist = ( $subjlist $sl ) ;
>> set subjlist = ( FSrecon_oaeaa005 FSrecon_oaeaa006 )
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 8 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>> set flag = --target
>> shift
>>
>> switch ( $flag )
>> switch ( --target )
>> if ( $#argv == 0 ) goto arg1err ;
>> if ( 7 == 0 ) goto arg1err
>> set target = $argv[1] ; shift ;
>> set target = fsaverage
>> shift
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 6 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>> set flag = --hemi
>> shift
>>
>> switch ( $flag )
>> switch ( --hemi )
>> if ( $#argv == 0 ) goto arg1err ;
>> if ( 5 == 0 ) goto arg1err
>> set srchemi = $argv[1] ; shift ;
>> set srchemi = rh
>> shift
>> set trghemi = $srchemi ;
>> set trghemi = rh
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 4 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>> set flag = --meas
>> shift
>>
>> switch ( $flag )
>> switch ( --meas )
>> if ( $#argv< 1 ) goto arg1err ;
>> if ( 3< 1 ) goto arg1err
>> set meas = $argv[1] ; shift ;
>> set meas = thickness
>> shift
>> set srcsurf = 1 ;
>> set srcsurf = 1
>> set srcfmt = curv ;
>> set srcfmt = curv
>> set MeasIn = 1 ;
>> set MeasIn = 1
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 2 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>> set flag = --out
>> shift
>>
>> switch ( $flag )
>> switch ( --out )
>> if ( $#argv == 0 ) goto arg1err ;
>> if ( 1 == 0 ) goto arg1err
>> set outpath = $argv[1] ; shift ;
>> set outpath = rh.oa_txeffect_verum.thickness.00.mgh
>> shift
>>
>> set outstem = `fname2stem $outpath`
>> set outstem = `fname2stem $outpath`
>> fname2stem rh.oa_txeffect_verum.thickness.00.mgh
>> if ( $status ) then
>> if ( 0 ) then
>> breaksw
>> breaksw
>>
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 0 != 0 )
>>
>> goto parse_args_return ;
>> goto parse_args_return
>>
>>
>> goto handle_fsfast ;
>> goto handle_fsfast
>>
>> if ( $#SessFile ) then
>> if ( 0 ) then
>>
>> goto handle_fsfast_return ;
>> goto handle_fsfast_return
>>
>>
>> goto check_params ;
>> goto check_params
>>
>> if ( $#subjlistfile&& $#ivplist ) then
>> if ( 0&& 0 ) then
>> if ( $#subjlistfile&& $#fsgdf ) then
>> if ( 0&& 1 ) then
>> if ( $#ivplist&& $#fsgdf ) then
>> if ( 0&& 1 ) then
>> if ( $#subjlist == 0 ) then
>> if ( 2 == 0 ) then
>> if ( $#srchemi == 0 ) then
>> if ( 1 == 0 ) then
>> if ( $#trghemi == 0 ) then
>> if ( 1 == 0 ) then
>> if ( $#outpath == 0&& ! $CacheOutOnly ) then
>> if ( 1 == 0&& ! 0 ) then
>> if ( $#target == 0 ) then
>> if ( 1 == 0 ) then
>> if ( ! -e $SUBJECTS_DIR ) then
>> if ( ! -e /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912/ )
>> then
>> if ( ! -e $SUBJECTS_DIR/$target ) then
>> if ( ! -e
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//fsaverage )
>> then
>> if ( $srcsurf == 0&& $srcvol == 0&& $#sval == 0 ) then
>> if ( 1 == 0&& 0 == 0&& 0 == 0 ) then
>> if ( $srcsurf&& $srcvol ) then
>> if ( 1&& 0 ) then
>> if ( $srcsurf&& $#projfrac != 0 ) then
>> if ( 1&& 0 != 0 ) then
>> if ( $catmean&& $catstd ) then
>> if ( 0&& 0 ) then
>> if ( $#meas&& $#isplist ) then
>> if ( 1&& 0 ) then
>> if ( $MeasIn&& $CacheIn ) then
>> if ( 1&& 0 ) then
>> if ( $#ivplist != 0 ) then
>> if ( 0 != 0 ) then
>> if ( $#isplist != 0 ) then
>> if ( 0 != 0 ) then
>> if ( $paireddiff ) then
>> if ( 0 ) then
>>
>> if ( ! -e $SUBJECTS_DIR ) then
>> if ( ! -e /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912/ )
>> then
>>
>>
>> if ( $DoXHemi ) then
>> if ( 0 ) then
>>
>> echo "nsubjects = $#subjlist" ;
>> echo nsubjects = 2
>> nsubjects = 2
>> @ nthsubj = 1 ;
>> @ nthsubj = 1
>> foreach subj ( $subjlist )
>> foreach subj ( FSrecon_oaeaa005 FSrecon_oaeaa006 )
>> set subjpath = $SUBJECTS_DIR/$subj
>> set subjpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005
>> if ( ! -e $subjpath ) then
>> if ( ! -e
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005
>> ) then
>> if ( $#meas ) then
>> if ( 1 ) then
>> if ( ! $CacheIn ) set measpath = $subjpath/$surfdir/$srchemi.$meas
>> if ( ! 0 ) set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> if ( $CacheIn ) set measpath = $subjpath/$surfdir/$srchemi.$meas.mgh
>> if ( 0 ) set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness.mgh
>> if ( ! -e $measpath ) then
>> if ( ! -e
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> ) then
>> endif
>> endif
>> if ( $#ivplist != 0 ) then
>> if ( 0 != 0 ) then
>> @ nthsubj = $nthsubj + 1 ;
>> @ nthsubj = 1 + 1
>> end
>> end
>> set subjpath = $SUBJECTS_DIR/$subj
>> set subjpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006
>> if ( ! -e $subjpath ) then
>> if ( ! -e
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006
>> ) then
>> if ( $#meas ) then
>> if ( 1 ) then
>> if ( ! $CacheIn ) set measpath = $subjpath/$surfdir/$srchemi.$meas
>> if ( ! 0 ) set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> if ( $CacheIn ) set measpath = $subjpath/$surfdir/$srchemi.$meas.mgh
>> if ( 0 ) set measpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness.mgh
>> if ( ! -e $measpath ) then
>> if ( ! -e
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> ) then
>> endif
>> endif
>> if ( $#ivplist != 0 ) then
>> if ( 0 != 0 ) then
>> @ nthsubj = $nthsubj + 1 ;
>> @ nthsubj = 2 + 1
>> end
>> end
>>
>> if ( $#fwhmsrc&& $#niterssrc ) then
>> if ( 0&& 0 ) then
>>
>> if ( $#fwhmtarg&& $#niterstarg ) then
>> if ( 0&& 0 ) then
>>
>> if ( $#projfrac&& $#projfracmax ) then
>> if ( 0&& 0 ) then
>>
>> goto check_params_return ;
>> goto check_params_return
>>
>> set nsubjects = $#subjlist ;
>> set nsubjects = 2
>> if ( $srcsurf ) set geom = surface
>> if ( 1 ) set geom = surface
>> set geom = surface
>> if ( $srcvol ) set geom = volume
>> if ( 0 ) set geom = volume
>>
>> if ( ! $CacheOutOnly ) then
>> if ( ! 0 ) then
>>
>> isanalyze $outpath> & /dev/null
>> isanalyze rh.oa_txeffect_verum.thickness.00.mgh
>> if ( $status ) then
>> if ( 0 ) then
>> isnifti $outpath> & /dev/null
>> isnifti rh.oa_txeffect_verum.thickness.00.mgh
>> if ( $status ) then
>> if ( 0 ) then
>>
>> set outdir = `dirname $outpath` ;
>> set outdir = `dirname $outpath`
>> dirname rh.oa_txeffect_verum.thickness.00.mgh
>> mkdir -p $outdir
>> mkdir -p .
>> if ( $status ) then
>> if ( 0 ) then
>> endif
>> endif
>>
>>
>> if ( $#tmpdir == 0 ) set tmpdir = $outdir/tmp.mris_preproc.$$
>> if ( 0 == 0 ) set tmpdir = ./tmp.mris_preproc.10777
>> set tmpdir = ./tmp.mris_preproc.10777
>> echo tmpdir is $tmpdir
>> echo tmpdir is ./tmp.mris_preproc.10777
>> tmpdir is ./tmp.mris_preproc.10777
>> pwd
>> pwd
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912
>> mkdir -p $tmpdir
>> mkdir -p ./tmp.mris_preproc.10777
>> if ( $status ) then
>> if ( 0 ) then
>>
>>
>> if ( ! $nolog ) then
>> if ( ! 0 ) then
>> if ( $#LF == 0 ) then
>> if ( 0 == 0 ) then
>> if ( ! $CacheOutOnly ) set LF = $outstem.mris_preproc.log
>> if ( ! 0 ) set LF = rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> set LF = rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> if ( $CacheOutOnly ) set LF = mris_preproc.$geom.$trghemi.log
>> if ( 0 ) set LF = mris_preproc.surface.rh.log
>> if ( -e $LF ) mv $LF $LF.bak
>> if ( -e rh.oa_txeffect_verum.thickness.00.mris_preproc.log ) mv
>> rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> rh.oa_txeffect_verum.thickness.00.mris_preproc.log.bak
>> endif
>> endif
>> else
>> else
>>
>> echo "Log file is $LF"
>> echo Log file is rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Log file is rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>> date | tee -a $LF
>> date
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Thu Sep 13 08:39:56 EDT 2012
>> echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
>> echo setenv SUBJECTS_DIR
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912/
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> setenv SUBJECTS_DIR
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912/
>> echo "cd `pwd`" | tee -a $LF
>> echo cd `pwd`
>> pwd
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> cd /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912
>> echo $0 $cmdargs | tee -a $LF
>> echo /usr/local/freesurfer/stable5_1_0/bin/mris_preproc --debug --fsgd
>> oa_txeffect_verum.fsgd --target fsaverage --hemi rh --meas thickness
>> --out
>> rh.oa_txeffect_verum.thickness.00.mgh
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> /usr/local/freesurfer/stable5_1_0/bin/mris_preproc --debug --fsgd
>> oa_txeffect_verum.fsgd --target fsaverage --hemi rh --meas thickness
>> --out
>> rh.oa_txeffect_verum.thickness.00.mgh
>> echo "" | tee -a $LF
>> echo
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>> uname -a | tee -a $LF
>> uname -a
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Linux brownie 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 17:10:18 EDT 2012
>> x86_64 x86_64 x86_64 GNU/Linux
>> echo $VERSION | tee -a $LF
>> echo $Id: mris_preproc,v 1.59 2011/03/02 20:16:39 nicks Exp $
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> $Id: mris_preproc,v 1.59 2011/03/02 20:16:39 nicks Exp $
>> cat $FREESURFER_HOME/build-stamp.txt | tee -a $LF
>> cat /usr/local/freesurfer/stable5_1_0/build-stamp.txt
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514
>> echo "tmpdir is $tmpdir" | tee -a $LF
>> echo tmpdir is ./tmp.mris_preproc.10777
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> tmpdir is ./tmp.mris_preproc.10777
>> echo "Src $srchemi $SrcSurfReg" | tee -a $LF
>> echo Src rh sphere.reg
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Src rh sphere.reg
>> echo "Trg $trghemi $TrgSurfReg" | tee -a $LF
>> echo Trg rh sphere.reg
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Trg rh sphere.reg
>> echo "" | tee -a $LF
>> echo
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>>
>> set tvallist = ( ) ;
>> set tvallist = ( )
>> @ nthsubj = 0 ;
>> @ nthsubj = 0
>> foreach subj ( $subjlist )
>> foreach subj ( FSrecon_oaeaa005 FSrecon_oaeaa006 )
>> @ nthsubj = $nthsubj + 1 ;
>> @ nthsubj = 0 + 1
>> echo "\n\n" | tee -a $LF
>> echo \n\n
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>>
>>
>> echo "---------------------------------------------------" | tee -a $LF
>> echo ---------------------------------------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> ---------------------------------------------------
>> echo "#@# $nthsubj/$#subjlist $subj `date` --------------" | tee -a $LF
>> echo #@# 1/2 FSrecon_oaeaa005 `date` --------------
>> date
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> #@# 1/2 FSrecon_oaeaa005 Thu Sep 13 08:39:56 EDT 2012 --------------
>>
>> set subjpath = $SUBJECTS_DIR/$subj
>> set subjpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005
>>
>> if ( $CacheOutOnly&& $CacheOutUpdate ) then
>> if ( 0&& 0 ) then
>>
>> if ( $CacheIn ) then
>> if ( 0 ) then
>>
>>
>> if ( $srcvol ) then
>> if ( 0 ) then
>>
>>
>> if ( $#meas || $#sval ) then
>> if ( 1 || 0 ) then
>> set srcsurfpath = $subjpath/$surfdir/$srchemi.$meas
>> set srcsurfpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> else
>> else
>> endif
>> endif
>>
>> set subjtmp = `echo $subj | sed 's/\//./g'` ;
>> set subjtmp = `echo $subj | sed 's/\//./g'`
>> echo FSrecon_oaeaa005
>> sed s/\//./g
>> set tval = $tmpdir/$subjtmp.$nthsubj.mgh
>> set tval = ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> set cmd = ( mri_surf2surf )
>> set cmd = ( mri_surf2surf )
>> set cmd = ( $cmd --srcsubject $subj --srchemi $srchemi --srcsurfreg
>> $SrcSurfReg )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg )
>> set cmd = ( $cmd --trgsubject $target --trghemi $trghemi --trgsurfreg
>> $TrgSurfReg )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg )
>> set cmd = ( $cmd --tval $tval )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh )
>> if ( $#sval == 0 ) then
>> if ( 0 == 0 ) then
>> set cmd = ( $cmd --sval $srcsurfpath )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> )
>> else
>> else
>> if ( $jac ) set cmd = ( $cmd --jac )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --jac )
>> if ( $#srcfmt ) set cmd = ( $cmd --sfmt $srcfmt )
>> if ( 1 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv )
>> if ( $synth&& ! $srcvol ) set cmd = ( $cmd --synth )
>> if ( 0&& ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --synth )
>> if ( $#fwhmsrc ) set cmd = ( $cmd --fwhm-src $fwhmsrc )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --fwhm-src )
>> if ( $#niterssrc ) set cmd = ( $cmd --nsmooth-in $niterssrc )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --nsmooth-in )
>> if ( $reshape ) set cmd = ( $cmd --reshape ) ;
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --reshape )
>> if ( ! $reshape ) set cmd = ( $cmd --noreshape ) ;
>> if ( ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape )
>> if ( ! $hash ) set cmd = ( $cmd --nohash ) ;
>> if ( ! 1 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --nohash )
>> if ( $SmoothCortexOnly ) set cmd = ( $cmd --cortex )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --cortex )
>> if ( ! $SmoothCortexOnly ) set cmd = ( $cmd --no-cortex )
>> if ( ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex )
>> echo "-----------------------" | tee -a $LF
>> echo -----------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> -----------------------
>> echo $cmd | tee -a $LF
>> echo mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> if ( $RunIt ) $cmd |& tee -a $LF
>> if ( 1 ) mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi rh --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Source registration surface changed to sphere.reg
>> Target registration surface changed to sphere.reg
>> srcsubject = FSrecon_oaeaa005
>> srcval =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> srctype = curv
>> trgsubject = fsaverage
>> trgval = ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> trgtype =
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> srchemi = rh
>> trghemi = rh
>> frame = 0
>> fwhm-in = 0
>> fwhm-out = 0
>> label-src = (null)
>> label-trg = (null)
>> OKToRevFaceOrder = 1
>> Reading source surface reg
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.sphere.reg
>> Loading source data
>> Reading curvature file
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa005/surf/rh.thickness
>> Reading target surface reg
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//fsaverage/surf/rh.sphere.reg
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (163842)
>>
>> surf2surf_nnfr: building target hash (res=16).
>> Surf2Surf: Reverse Loop (136669)
>> Reverse Loop had 22984 hits
>> Surf2Surf: Dividing by number of hits (163842)
>> INFO: nSrcLost = 0
>> nTrg121 = 145198, nTrgMulti = 18644, MnTrgMultiHits = 2.23278
>> nSrc121 = 99095, nSrcLost = 0, nSrcMulti = 37574, MnSrcMultiHits =
>> 2.33489
>> Saving target data
>> Saving to ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> if ( $status ) exit 1 ;
>> if ( 0 ) exit 1
>> endif
>> endif
>>
>>
>> if ( $#CacheOutFile ) then
>> if ( 0 ) then
>>
>>
>> set tvallist = ( $tvallist $tval )
>> set tvallist = ( ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh )
>>
>> end
>> end
>> @ nthsubj = $nthsubj + 1 ;
>> @ nthsubj = 1 + 1
>> echo "\n\n" | tee -a $LF
>> echo \n\n
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>>
>>
>> echo "---------------------------------------------------" | tee -a $LF
>> echo ---------------------------------------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> ---------------------------------------------------
>> echo "#@# $nthsubj/$#subjlist $subj `date` --------------" | tee -a $LF
>> echo #@# 2/2 FSrecon_oaeaa006 `date` --------------
>> date
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> #@# 2/2 FSrecon_oaeaa006 Thu Sep 13 08:40:05 EDT 2012 --------------
>>
>> set subjpath = $SUBJECTS_DIR/$subj
>> set subjpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006
>>
>> if ( $CacheOutOnly&& $CacheOutUpdate ) then
>> if ( 0&& 0 ) then
>>
>> if ( $CacheIn ) then
>> if ( 0 ) then
>>
>>
>> if ( $srcvol ) then
>> if ( 0 ) then
>>
>>
>> if ( $#meas || $#sval ) then
>> if ( 1 || 0 ) then
>> set srcsurfpath = $subjpath/$surfdir/$srchemi.$meas
>> set srcsurfpath =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> else
>> else
>> endif
>> endif
>>
>> set subjtmp = `echo $subj | sed 's/\//./g'` ;
>> set subjtmp = `echo $subj | sed 's/\//./g'`
>> echo FSrecon_oaeaa006
>> sed s/\//./g
>> set tval = $tmpdir/$subjtmp.$nthsubj.mgh
>> set tval = ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh
>> set cmd = ( mri_surf2surf )
>> set cmd = ( mri_surf2surf )
>> set cmd = ( $cmd --srcsubject $subj --srchemi $srchemi --srcsurfreg
>> $SrcSurfReg )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg )
>> set cmd = ( $cmd --trgsubject $target --trghemi $trghemi --trgsurfreg
>> $TrgSurfReg )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg )
>> set cmd = ( $cmd --tval $tval )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh )
>> if ( $#sval == 0 ) then
>> if ( 0 == 0 ) then
>> set cmd = ( $cmd --sval $srcsurfpath )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> )
>> else
>> else
>> if ( $jac ) set cmd = ( $cmd --jac )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --jac )
>> if ( $#srcfmt ) set cmd = ( $cmd --sfmt $srcfmt )
>> if ( 1 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv )
>> if ( $synth&& ! $srcvol ) set cmd = ( $cmd --synth )
>> if ( 0&& ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --synth )
>> if ( $#fwhmsrc ) set cmd = ( $cmd --fwhm-src $fwhmsrc )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --fwhm-src )
>> if ( $#niterssrc ) set cmd = ( $cmd --nsmooth-in $niterssrc )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --nsmooth-in )
>> if ( $reshape ) set cmd = ( $cmd --reshape ) ;
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --reshape )
>> if ( ! $reshape ) set cmd = ( $cmd --noreshape ) ;
>> if ( ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape )
>> if ( ! $hash ) set cmd = ( $cmd --nohash ) ;
>> if ( ! 1 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --nohash )
>> if ( $SmoothCortexOnly ) set cmd = ( $cmd --cortex )
>> if ( 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi
>> rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --cortex )
>> if ( ! $SmoothCortexOnly ) set cmd = ( $cmd --no-cortex )
>> if ( ! 0 ) set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006
>> --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh
>> --trgsurfreg sphere.reg --tval
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex )
>> set cmd = ( mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex )
>> echo "-----------------------" | tee -a $LF
>> echo -----------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> -----------------------
>> echo $cmd | tee -a $LF
>> echo mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> if ( $RunIt ) $cmd |& tee -a $LF
>> if ( 1 ) mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh
>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg
>> sphere.reg --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> mri_surf2surf --srcsubject FSrecon_oaeaa006 --srchemi rh --srcsurfreg
>> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
>> --tval ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --sval
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> --sfmt curv --noreshape --no-cortex
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Source registration surface changed to sphere.reg
>> Target registration surface changed to sphere.reg
>> srcsubject = FSrecon_oaeaa006
>> srcval =
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> srctype = curv
>> trgsubject = fsaverage
>> trgval = ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh
>> trgtype =
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> srchemi = rh
>> trghemi = rh
>> frame = 0
>> fwhm-in = 0
>> fwhm-out = 0
>> label-src = (null)
>> label-trg = (null)
>> OKToRevFaceOrder = 1
>> Reading source surface reg
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.sphere.reg
>> Loading source data
>> Reading curvature file
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//FSrecon_oaeaa006/surf/rh.thickness
>> Reading target surface reg
>> /autofs/cluster/kong/2/oaeaa/structural/GroupAnalysis0912//fsaverage/surf/rh.sphere.reg
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (163842)
>>
>> surf2surf_nnfr: building target hash (res=16).
>> Surf2Surf: Reverse Loop (126029)
>> Reverse Loop had 19317 hits
>> Surf2Surf: Dividing by number of hits (163842)
>> INFO: nSrcLost = 0
>> nTrg121 = 148359, nTrgMulti = 15483, MnTrgMultiHits = 2.24763
>> nSrc121 = 85133, nSrcLost = 0, nSrcMulti = 40896, MnSrcMultiHits =
>> 2.39696
>> Saving target data
>> Saving to ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh
>> if ( $status ) exit 1 ;
>> if ( 0 ) exit 1
>> endif
>> endif
>>
>>
>> if ( $#CacheOutFile ) then
>> if ( 0 ) then
>>
>>
>> set tvallist = ( $tvallist $tval )
>> set tvallist = ( ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh )
>>
>> end
>> end
>>
>> echo "\n\n" | tee -a $LF
>> echo \n\n
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>>
>>
>>
>> if ( ! $CacheOutOnly ) then
>> if ( ! 0 ) then
>>
>> set cmd = ( mri_concat $tvallist --o $outpath )
>> set cmd = ( mri_concat ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh )
>> if ( $paireddiff ) set cmd = ( $cmd --paired-diff --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --paired-diff --prune )
>> if ( $paireddiffnorm ) set cmd = ( $cmd --paired-diff-norm --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --paired-diff-norm --prune )
>> if ( $paireddiffnorm1 ) set cmd = ( $cmd --paired-diff-norm1 --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --paired-diff-norm1 --prune )
>> if ( $paireddiffnorm2 ) set cmd = ( $cmd --paired-diff-norm2 --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --paired-diff-norm2 --prune )
>> if ( $catmean ) set cmd = ( $cmd --mean --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --mean --prune )
>> if ( $catstd ) set cmd = ( $cmd --std --prune ) ;
>> if ( 0 ) set cmd = ( mri_concat
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh --std --prune )
>> echo "-----------------------" | tee -a $LF
>> echo -----------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> -----------------------
>> echo $cmd | tee -a $LF
>> echo mri_concat ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> mri_concat ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh
>> if ( $RunIt ) $cmd |& tee -a $LF
>> if ( 1 ) mri_concat ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh
>> mri_concat ./tmp.mris_preproc.10777/FSrecon_oaeaa005.1.mgh
>> ./tmp.mris_preproc.10777/FSrecon_oaeaa006.2.mgh --o
>> rh.oa_txeffect_verum.thickness.00.mgh
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> ninputs = 2
>> Checking inputs
>> nframestot = 2
>> Allocing output
>> Done allocing
>> nframes = 2
>> Writing to rh.oa_txeffect_verum.thickness.00.mgh
>> if ( $status ) exit 1 ;
>> if ( 0 ) exit 1
>> echo "\n\n" | tee -a $LF
>> echo \n\n
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>>
>>
>>
>>
>>
>> if ( $#fwhmtarg || $#niterstarg ) then
>> if ( 0 || 0 ) then
>> endif
>> endif
>>
>> if ( $cleanup ) then
>> if ( 1 ) then
>> echo "Cleaning up" | tee -a $LF
>> echo Cleaning up
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Cleaning up
>> set cmd = ( rm -r $tmpdir )
>> set cmd = ( rm -r ./tmp.mris_preproc.10777 )
>> echo "-----------------------" | tee -a $LF
>> echo -----------------------
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> -----------------------
>> echo $cmd | tee -a $LF
>> echo rm -r ./tmp.mris_preproc.10777
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> rm -r ./tmp.mris_preproc.10777
>> $cmd |& tee -a $LF
>> rm -r ./tmp.mris_preproc.10777
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> if ( $status ) exit 1 ;
>> if ( 0 ) exit 1
>> endif
>> endif
>>
>>
>> date | tee -a $LF
>> date
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> Thu Sep 13 08:40:13 EDT 2012
>> echo "mris_preproc done" | tee -a $LF
>> echo mris_preproc done
>> tee -a rh.oa_txeffect_verum.thickness.00.mris_preproc.log
>> mris_preproc done
>>
>> exit 0
>> exit 0
>>
>>
>>
>>> ---------------------------- Original Message
>>> ----------------------------
>>> Subject: Re: [Freesurfer] mris_preproc --fsgd
>>> From: "Douglas N Greve"<gr...@nmr.mgh.harvard.edu>
>>> Date: Wed, September 12, 2012 4:58 pm
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> --------------------------------------------------------------------------
>>>
>>> Can you run it with --debug as the first option and send me the
>>> terminal
>>> output? It will be a lot, so capture it like this:
>>>
>>> mris_preproc ... |& tee proroc.log
>>>
>>> doug
>>>
>>> On 09/12/2012 04:43 PM, spa...@nmr.mgh.harvard.edu wrote:
>>>> Hi,
>>>>
>>>> I am trying to run mris_preproc on a set of 22 subjects (specified in
>>>> my
>>>> fsgd file), but the command only runs on the first subject listed in
>>>> my
>>>> fsgd file, and none of the subsequent subjects.
>>>>
>>>> I run the command:
>>>> mris_preproc --fsgd oa_txeffect_verum.fsgd --target fsaverage --hemi
>>>> lh
>>>> --meas thickness --out lh.oa_txeffect_verum.thickness.00.mgh
>>>>
>>>> And only the first subject listed in the fsgd file runs through
>>>> mris_surf2surf
>>>>
>>>> ---------------------------------------------------
>>>> #@# 1/1 FSrecon_oaeaa005 Wed Sep 12 16:02:41 EDT 2012 --------------
>>>> -----------------------
>>>> mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi lh --srcsurfreg
>>>> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
>>>> --tval ./tmp.mris_preproc.3029/FSrecon_oaeaa005.1.mgh --sval
>>>> FSrecon_oaeaa005/surf/lh.thickness --sfmt curv --noreshape --no-cortex
>>>>
>>>> I am able to run mris_preproc on each individual subject, specified
>>>> with
>>>> the flag --s FSrecon_oaeaa010 by running the following command:
>>>>
>>>> mris_preproc --s FSrecon_oaeaa010 --target fsaverage --hemi rh --meas
>>>> thickness --out rh.oa_txeffect_verum.thickness.00.mgh
>>>>
>>>> My fsgd file is:
>>>>
>>>> GroupDescriptorFile 1
>>>> Title Treatment Effect
>>>> MeasurementName thickness
>>>> Class groupVerum
>>>> Variables tx_effect
>>>> Input FSrecon_oaeaa005 groupVerum 1.58
>>>> Input FSrecon_oaeaa006 groupVerum 9.58
>>>> Input FSrecon_oaeaa007 groupVerum 2.08
>>>> Input FSrecon_oaeaa008 groupVerum -0.17
>>>> Input FSrecon_oaeaa010 groupVerum 1.08
>>>> Input FSrecon_oaeaa011 groupVerum 3.5
>>>> Input FSrecon_oaeaa013 groupVerum 1.58
>>>> Input FSrecon_oaeaa015 groupVerum 4
>>>> Input FSrecon_oaeaa016 groupVerum -0.17
>>>> Input FSrecon_oaeaa017 groupVerum 1
>>>> Input FSrecon_oaeaa021 groupVerum -1.83
>>>> Input FSrecon_oaeaa023 groupVerum 4.67
>>>> Input FSrecon_oaeaa026 groupVerum 1.83
>>>> Input FSrecon_oaeaa028 groupVerum 1.17
>>>> Input FSrecon_oaeaa029 groupVerum 0.5
>>>> Input FSrecon_oaeaa034 groupVerum -1
>>>> Input FSrecon_oaeaa037 groupVerum 1.25
>>>> Input FSrecon_oaeaa039 groupVerum -2.08
>>>> Input FSrecon_oaeaa040 groupVerum 2.67
>>>> Input FSrecon_oaeaa041 groupVerum 2
>>>> Input FSrecon_oaeaa043 groupVerum 4.5
>>>> Input FSrecon_oaeaa045 groupVerum -0.67
>>>>
>>>> Based on other data sets I have worked with using mris_preproc, it
>>>> seems
>>>> that the mri_surf2surf should be run on each subject listed in the
>>>> fsgd
>>>> file. Is the format of my fsgd file incorrect? If my fsgd file is not
>>>> the
>>>> issue, is there a work around so that I don't have to run each subject
>>>> through mris_preproc and mri_surf2surf individually?
>>>>
>>>> Thanks,
>>>>
>>>> Rosa
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
_______________________________________________
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
