Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

recon-all error
by hhal5293＠uni.sydney.edu.au 17 Sep '12

17 Sep '12

Hello, I am relatively new to FreeSurfer, so this may be a silly question, but when i run any of the recon-all commands such as: recon-all -autorecon-pial -subjid SMART001bT1 OR recon-all -s SMART001bT1 -autorecon2 -autorecon3 OR recon-all -s SMART001bT1 I keep getting this error: if: Expression Syntax Anyone know what may be causing this? Kind Regards, Harry

2 3

Re: [Freesurfer] Numerical result out of range error
by Blessy M 17 Sep '12

17 Sep '12

No, the cerebellum is not attached. On Fri, Sep 14, 2012 at 1:42 PM, Blessy M <blessam(a)gmail.com> wrote: > I have a MPRAGE scan, with slight atrophy on right side of brain. > Recon-all is crashing (see error below). Can anyone help me with this, so I > can get a reasonably parcellated brain? > > > *CORRECTING DEFECT 6 (vertices=151, convex hull=90) > After retessellation of defect 6, euler #=-52 (54998,159712,104662) : > difference with theory (-57) = -5 > > CORRECTING DEFECT 7 (vertices=27939, convex hull=5437) > normal vector of length zero at vertex 60965 with 0 faces > vertex 60965 has 0 face > Numerical result out of range > Linux compute-0-4.local 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT > 2010 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s . exited with ERRORS at Sat Sep 1 02:01:53 EDT 2012* > > > thanks > > Blessy >

2 4

Freeview display errors - Ubuntu 12.04
by Richard Binney 17 Sep '12

17 Sep '12

Hi Freesurfers, I've recently moved onto Ubuntu 12.04. The Freesurfer installation has required me to download various libraries and create many symbolic links to have it working. Further more I've had to set the doublebufferflag=1 (whatever that is) in order for tkmedit and freeview to work (they otherwise were tranparent display boxes). Still though I'm having some issues with freeview. It struggles with rendering the tracts generated in dpath from TRACULA. the tracts will disappear when the 3D box is moved and they are displayed in the wrong colors until you change opacity or another random parameter. Has anyone else experienced this and had any success resolving it? Are there any libraries or other general settings that need to be changed? Any help would be appreciated. On a side note I'm finding that freesurfer displays are also at the forefront, meaning they block terminals and other things I'm also working with. Any help to resolve this would be great too. Thanks Richard

1 1

Intracranial volume discrepancies
by Nikhil Chandra 17 Sep '12

17 Sep '12

Hi everyone, We have run FreeSurfer on roughly 60 subjects for a study, and are noticing some strange discrepancies for intracranial volume in aseg.stats for 8 of them. Here is a subset of what we see in one of the "bad" aseg.stats files: # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 559928.546875, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 769545.059854, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1263234.600914, mm^3 Here, the total volume of WM plus GM is 1,329,473.606729 mm^3, which exceeds the intracranial volume by 66,239.005815. This does not make sense - how can the volume of brain matter exceed the volume of the space that encompasses it? Does FreeSurfer generate a mask of the estimated intracranial volume? We would like to superimpose it over the T1 to see how accurate the estimation is for these cases. Also, does the mask (if it exists) include the cerebellum? Thank you for your help, Nikhil Chandra

2 1

Re: [Freesurfer] mris_preproc --fsgd
by spaeth＠nmr.mgh.harvard.edu 17 Sep '12

17 Sep '12

Good news, I recreated the FSGD file from scratch on a linux workstation using the exact same syntax and list of inputs and re-ran the mri_preproc and it worked this time. The original file that I was having issues with was also created on a linux workstation, however I had copied the inputs from a document that I had created using a Mac. Perhaps the issue had something to do with that process. Thank you very much for your help in troubleshooting. Rosa > ---------------------------- Original Message ---------------------------- > Subject: Re: [Freesurfer] mris_preproc --fsgd > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Date: Thu, September 13, 2012 5:02 pm > To: freesurfer(a)nmr.mgh.harvard.edu > -------------------------------------------------------------------------- > > 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(a)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(a)nmr.mgh.harvard.edu> >>> Date: Thu, September 13, 2012 11:53 am >>> To: freesurfer(a)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(a)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(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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> >>> >> _______________________________________________ >> 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 > > > > >

1 0

How to map ROI to native space
by Kong, Li 17 Sep '12

17 Sep '12

Hi all, I have one problem about rending ROI from VBM onto Freesurfer average surface and extracting thickness in this ROI region. I have already extracted one cluster (my ROI ) from VBM_derived group difference t_statistic map. I got a lot of information from this mail list, especially Alex's mail (thanks!!). Now I got the steps for my analysis as following: 1) Mapping ROI.img from MNI space to the native space of each subject. (I don't know how to do this step) 2) Convert volumetric mask to a label (using mri_vol2surf and mri_cor2label). 3) Extract thickness in this label for each subject (using mris_anatomical_stats). I read Voets' paper about this topic, but he just wrote "first inverse-warping the VBM group difference t_statistic map to native space of each subject" and there was no detailed information how to do it. I saw a lot information about the topic of VBM and Freesurfer in the mail list, but I did not find the exact method for my problem. Anyone has idea about my problem?? Any help will be appreciated! Thanks in advance! Li

2 2

Re: [Freesurfer] problem with tksurfer
by Douglas N Greve 17 Sep '12

17 Sep '12

Yes, just add --trgsubject fsaverage doug On 09/15/2012 07:02 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > This is a separate question but related to the volume to surface > conversion. Is it possible to sample the sig.nii.gz file to the > fsaverage surface instead of the individual subject surfaces using the > mri_vol2surf? How should I change the command bellow to do that? I > want to be able to load data from different subjects to a common space > and see each subject's data as a different overlay on the same common > space. Is that possible in freesurfer? > > Thanks, > Maryam > > On Tue, Sep 11, 2012 at 11:06 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Maryam, I finally figured out what is going on. The bottom line > is that it is just a weird coincidence. The volume size is > 70*70*33=161700 which happens to be exactly how many vertices are > in the left hemisphere of this subject. When tksurfer sees this, > it thinks that each voxel must be a vertex and displays it as such > instead of sampling the volume onto surface which is why it looks > so strange. There is not a way to force tksurfer to treat the > overlay as a volume, but instead (and probably better), you can > sample the volume onto the surface, then load it as an overlay, eg > > mri_vol2surf --reg register.dof6.dat --hemi lh --mov sig.nii.gz > --o lh.sig.mgh --projfrac 0.5 > tksurfer teal_tiger_kcb lh inflated -curv -overlay lh.sig.mgh > > and the same thing with the right side. > > The chances that this kind of thing happens must be several > million to one! > doug > > > > > On 09/06/2012 05:26 PM, Maryam Vaziri Pashkam wrote: > > Hi Doug, > > I uploaded the tar file. It is called incorrect_lh_test.tar > > Thanks, > Maryam > > On Wed, Sep 5, 2012 at 10:04 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Can you upload a tarball of the subject and the sig.nii.gz > to our > file drop? > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > doug > > > > On 08/28/2012 10:18 AM, Maryam Vaziri Pashkam wrote: > > Hi Doug, > > Any other insight how I can solve this problem? > > Maryam > > On Fri, Aug 24, 2012 at 7:17 PM, Maryam Vaziri Pashkam > <mvaziri(a)fas.harvard.edu <mailto:mvaziri@fas.harvard.edu> > <mailto:mvaziri@fas.harvard.edu <mailto:mvaziri@fas.harvard.edu>> > <mailto:mvaziri@fas.harvard.edu <mailto:mvaziri@fas.harvard.edu> > > <mailto:mvaziri@fas.harvard.edu > <mailto:mvaziri@fas.harvard.edu>>>> wrote: > > It looks fine to me. I have attached the tiff > image of a > coronal > slice. So this means that the registration of the > surface > to the > anatomical is fine. This is strange. I tried the > tksurfer > with the > original surface and the overlay on the rh looks > fine and > the left > hemisphere has the same problem as on the inflated > surface. Any > other idea? > > M > > > On Fri, Aug 24, 2012 at 6:54 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > I don't understand your last paragraph. Does > the lh > surface > look ok, eg, when you run > > tkmedit teal_tiger_kcb orig.mgz -surfs > > doug > > > > > On 08/24/2012 06:37 PM, Maryam Vaziri Pashkam > wrote: > > Yes I have checked it multiple times. They > are the > same. > Here are the two lines: > > tksurfer teal_tiger_kcb rh inflated -curv > -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > tksurfer teal_tiger_kcb lh inflated -curv > -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > I have copy pasted the inflated anatomical > folder > of the > subject from another computer. Is it > possible that > some > specific files are not copied properly? I dont > know where > are the files that have the information for > registration > of the anatomical brain to the inflated > suface. My > guess > is that is where the problem is. What do > you think? > > > Maryam > > > > On Fri, Aug 24, 2012 at 6:19 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > Hi Maryam, it seems very strange that one > hemisphere > looks ok but > other looks bad. In fact, I'd say that > it cannot > happen. The > differences are not likely to be due to > version. Can > you double > check that the tksurfer commands for > the lh > and rh are > the same > (except for lh and rh, of course) > doug > > > > > On 08/22/2012 09:13 PM, Maryam Vaziri > Pashkam > wrote: > > Hi Doug, > > I am having a problem with > tksurfer overlay > function. I ran > one analysis in freesurfer 5.1 on > a mac > machine > and I cannot > properly load it on the surface. The > analysis was > performed in > the native space. When I use > tksurfer to > load the > analysis on > the surface using the overlay > function I > dont get > an error but > the output image just shows small > dots on the > surface instead > of patches of activity. It looks > like the > registration is not > correct. I checked the > registration on the > volume > and it looks > fine to me. This only happens with > one of my > subject and only > on his left hemisphere. I have > attached > two tif > images called > lhnative.tif and rhnative.tif that > show the > results. I also > ran the analysis on the surface > for both > left and > right > hemisphere, and it looks fine > (lhsurf.tif and > rhsurf.tif files > attached). > Any Idea how to solve this problem? My > guess is > that the error > is in the registration of > anatomical volume to > anatomical > surface in the left hemisphere of this > specific > subject, but I > dont know how to solve this issue. > > here is the code that I use to > load the > data on > the surface: > > tksurfer teal_tiger_kcb lh > inflated -curv > -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > Just a note that the recon-all was > performed in > freesurfer 4.5 > and the analysis on freesurfer > 5.1. Any chance > this might have > caused the error? > > Thanks, > Maryam > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended > only for > the person to > whom it is > addressed. If you believe this e-mail > was sent > to you > in error and > the e-mail > contains patient information, please > contact > the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to > you in error > but does not contain patient > information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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

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Re: [Freesurfer] mris_anatomical_stats on multiple subjects
by Garikoitz Lerma-Usabiaga (Gari) 17 Sep '12

17 Sep '12

Hi Li, there you go, Gari https://docs.google.com/open?id=0Byf71TWfovledFhJYWN2cGtHV00 On 2012-09-15, at 19:38, "Kong, Li" <Li.Kong(a)med.uni-heidelberg.de> wrote: > Hi Gari, > I saw your email to Alex about your method obtaining statistics from multiple subjects with Python script. Could you send the code to me? > > Thanks > > Li > > > > > > > ………………………………………………………………… > Li Kong > PhD candidate > Section of Geriatric Psychiatry > University of Heidelberg, Germany > E-mail: li.kong(a)med.uni-heidelberg.de > Tel:+49-62215638526<tel:+49-62215638526> (O)

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Fwd: white matter and pial surface don't track sulcus
by Darren Gitelman 16 Sep '12

16 Sep '12

Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?actio… I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

2 1

Re: [Freesurfer] ERROR: You are trying to re-run an existing subject
by Douglas N Greve 14 Sep '12

14 Sep '12

When you run recon-all -s HPTU_vol11_2012 -i pacsfiles/MPRAGE.Ser1.Img0.dcm Does the folder or file called $SUBJECTS_DIR/HPTU_vol11_2012 already exist? doug On 09/14/2012 05:00 PM, Carolina Valencia wrote: > first rename folder *dicom* to *pacsfiles* > then run > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/HPTU_vol11_2012$ > recon-all -s HPTU_vol11_2012 -i pacsfiles/MPRAGE.Ser1.Img0.dcm > then with a bulk rename files program rename *MPRAGE*.Ser1.Img0.dcm > ... to *T13D*.Ser1.Img0.dcm... > then run > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/HPTU_vol11_2012$ > recon-all -s HPTU_vol11_2012 -i pacsfiles/T13D.Ser1.Img0.dcm > > I usually use tab in order to doesn't make mistakes and typos. > > Thanks, > > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > what did you rename it to and what is your command line after you > rename it? > > > On 09/14/2012 04:48 PM, Carolina Valencia wrote: > > As I said in the first email I tried the suggestions in the > message, rename the files, folders, eliminate the folders, > starts from scratch etc and again with your answer, I rename > the folder of dicom, and rename the MPRAGE files and anything > works, still the same message. > Thank you, > > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > The error output below tells you what to do. If the > subject folder > (HPTU_vol11_2012) already exists. Since it has your dicom > data in > it, you should not delete it. Instead, rename that > directory and > keep your command-line (changing the -i path to point to > the new > dicom file but keeping the same subject name), or change > the name > of the subject. > doug > > > > > On 09/14/2012 03:44 PM, Carolina Valencia wrote: > > the directory exists and trying without / doesn't > change anything, > any advice? > One week ago, I was processing with the same command > line with > other subjects without problems, > > 2012/9/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > And before you run this, does > $SUBJECTS_DIR/HPTU_vol11_2012 exist? > BTW, try it without a slash at the end of the name. > doug > > > On 09/14/2012 02:09 PM, Carolina Valencia wrote: > > > Sure! > > cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$ > recon-all -s HPTU_vol11_2012/ -i > HPTU_vol11_2012/dicom/MPRAGE.Ser1.Img0.dcm > > 2012/9/14 Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > What is your command line? > doug > > > > On 09/14/2012 12:23 PM, Carolina Valencia > wrote: > > Hi Freesurfer users: > > > > I'm trying to run recon-all command in a single subject and > > I don't know why always there is an error message about the > names, I > > tried the suggestionsin the message, rename the files, folders, > > eliminate the folders etc > > But I don't succeed to star to running my data. > > Many thanks, > > > > > > ERROR: You are trying to re-run an existing subject with > (possibly) > > new input data (-i). If this is truly new input data, you > should delete > > the subject folder and re-run, or specify a different > subject name. > > If you are just continuing an analysis of an existing > subject, then > > omit all -i flags. > > > > -- > > -- > > *Carolina Valencia Muñoz* > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended > only > for the > person to > whom it is > addressed. If you believe this e-mail was > sent to > you in > error and > the e-mail > contains patient information, please > contact the > Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, > please > contact the > sender and properly > dispose of the e-mail. > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- -- > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- 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

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Freesurfer September 2012