Freesurfer

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Re: [Freesurfer] Choroid Plexus in ventricles
by Tracy A. Butler 13 Sep '12

13 Sep '12

Hi. Thanks for the response below. Does the fact that choroid plexus varies so much in intensity mean that Freesurfer does not always accurately measure CP volume? Do you think we should do some manual tracing to confirm Freesurfer results? Thanks, Tracy From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Wed, Sep 12, 2012 at 7:14 PM Subject: Re: [Freesurfer] Choroid Plexus in ventricles To: Hugh Wang <wangxiuyuan85(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Hi Hugh it depends on the dataset. It's a bit mysterious to me why sometimes the choroid is so bright and other times not. I've definitely seen it in the inf lat ventricles. We included choroid to avoid confusing it with hippocampus so I doubt we labeled any in the 3rd or 4th ventricles. cheers Bruce On Wed, 12 Sep 2012, Hugh Wang wrote: Dear Freesurfer Users, When masking out the ventricles and choroid plexus from aparg+aseg, I found there were choroid plexus volumes in lateral ventricles, but nothing in inferior lateral ventricles or 3rd/4th ventricle. Did I miss those tiny volumes or the Freesurfer didn't segment choroid plexus into that detail? Thanks! Best, Hugh P.S. I used Freesurfer 5.1 on a 64bit CentOS platform

2 1

multicenter morphometric analysis
by Heath Pardoe 13 Sep '12

13 Sep '12

Hi all, I was wondering if there was a consensus view on the optimal way to approach morphometric analysis (cortical thickness, volumetry & associated analyses) of MRI data acquired on multiple scanners. >From VBM literature & our own experience it appears that comparing MRI scans of patients from one scanner with controls scanned on another is a bad idea, because there are systematic differences that will manifest as very significant GM volume/concentration/density differences following statistical analysis when these differences are unlikely to really exist ie. we get a lot of false positives. Definitive findings on similar analyses using cortical thickness mapping seem harder to come by. There's the Han study from 2006 and Dickerson 2008 but both of these seem to be empirical analyses of mean absolute error or related measures rather than pitting scanner 1 subjects against scanner 2 subjects in a statistical analysis (please correct me if I haven't looked hard enough). Wonderlick et al 2009 is closer in terms of statistical analysis but these were done on one scanner so don't really address the multicenter issue. To my mind it seems likely that cortical thickness analysis would have the same problem as VBM and would require controls to be scanned on the same scanners as patients to account for inter-scanner variability. Does anyone have any opinions on this? Or, even better, any data so we can tell how much of a problem this is? In a related question, the ADNI study uses a phantom to correct an image for gradient nonlinearities in different scanners, and then pools this corrected data from multiple scanners into each control or patient group, and subsequent morphometric analyses are done without worrying about the multi-site issue. Does anyone have an opinion on the validity of this approach? I guess one way to investigate it would be to look at vertex-wise across-subject variance in coregistered cortical thickness maps both with and without the phantom-based correction procedure; if the variance was lower in the phantom-corrected variance map this would provide good evidence that it's worth the effort of undertaking this procedure. I would be keen to do this analysis but unless I'm mistaken the ADNI website only provides images that have already been processed to correct for gradient nonlinearities. An alternative approach that has been proposed is to scan a group of the same controls on multiple scanners to characterise between-scanner differences. The practicality of this approach breaks down as the number of centers increases. Again I would be interested to hear if anyone has experience in using this approach compared to others. In summary, there seem to be three ways to overcome inter-scanner variance: 1. scan different controls at each site 2. scan a phantom at each site (and probably scan controls too anyway) 3. scan the same group of controls at all sites I would be interested in hearing which approach people think is best, and why. Thanks if you're still reading! Best wishes Heath

3 4

Re: [Freesurfer] mris_preproc --fsgd
by spaeth＠nmr.mgh.harvard.edu 13 Sep '12

13 Sep '12

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(a)nmr.mgh.harvard.edu> > Date: Wed, September 12, 2012 4:58 pm > To: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

2 1

Testing Freesurfer Installation- Errors
by Melissa Lancaster 13 Sep '12

13 Sep '12

Hi, It seemed I had successful installed Freesufer, but when I went to run the tests I got errors with both tkmedit and tksurfer. when typing <tkmedit bert orig.mgz> I got the following error: Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in tkmedit.bin: could not open display: when typing <tksurfer bert rh pial> I got the following error: GLUT: Fatal Error in tksurfer.bin: could not open display: Any advice? Thanks, Melissa Melissa A. Lancaster, M.S. Clinical Psychology Doctoral Student Rosalind Franklin University of Medicine and Science

2 3

Choroid Plexus in ventricles
by Hugh Wang 12 Sep '12

12 Sep '12

Dear Freesurfer Users, When masking out the ventricles and choroid plexus from aparg+aseg, I found there were choroid plexus volumes in lateral ventricles, but nothing in inferior lateral ventricles or 3rd/4th ventricle. Did I miss those tiny volumes or the Freesurfer didn't segment choroid plexus into that detail? Thanks! Best, Hugh P.S. I used Freesurfer 5.1 on a 64bit CentOS platform

2 1

head motion values
by New Fei Ho 12 Sep '12

12 Sep '12

Hi, I would like to compare the mean head motion between two groups. Just to clarify the values found in the mcprextreg file: 1. Do the six columns represent translationX, translationY, translationZ and rotationX, rotationY, rotationZ? 2. Are the values found in each time-point (i) absolute, i.e. the absolute difference in displacement between this time-point and the middle time-point, or (ii) relative i.e. difference between consecutive time-points? Thanks, Newfei

2 1

mris_preproc --fsgd
by spaeth＠nmr.mgh.harvard.edu 12 Sep '12

12 Sep '12

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

2 1

picking peculiar points
by Borzello, Mia 12 Sep '12

12 Sep '12

Hi, I'm picking points for a coregistration using tkmedit, but oddly all of the R coordinates have been 0. For example, one point is [0 -14 73.5]. Does this seem right? Thanks in advance, Mia

2 2

terrible movement; salvagable?
by Anthony Dick 12 Sep '12

12 Sep '12

I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data. My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Developmental Science Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu

2 3

error with the cut plane in tksurfer
by Hye Young Heo 11 Sep '12

11 Sep '12

Hello, I am trying to cut the occipital plane, but I get the crashes and the error message, " tksufer.bin:tnl/t_vertex.c:407: update_input_ptrs: Assertion 'a[j].inputstride == vptr-> stride' failed. Abort(core dumped)" Anybody did figure it out and fix? Any advice would be most appreciated. Hye-Young.

2 1

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