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" greve@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, spaeth@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"greve@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, spaeth@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 greve@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 greve@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