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, spaeth@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"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
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-- 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
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-- 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