Something very strange is going on. What platform are you using? What
version of FreeSurfer? Can you send me the fsgd file as an attachment
instead of pasting it into email?
doug
On 09/13/2012 03:58 PM, spa...@nmr.mgh.harvard.edu wrote:
> 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
>
>
--
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
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