Freesurfer

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30089 discussions

Re: [Freesurfer] ico4 parcellation and mri_segstats
by Douglas N Greve 14 Sep '12

14 Sep '12

It looks like there are several (102 to be exact) that do not have any voxels in your parcellation. Eg, #82: 82 82 ic4.tri_vertex_82 0 So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. doug On 09/10/2012 10:56 AM, Linda Douw wrote: > Hi Doug, > Output and sumfile are attached. Any ideas? > Linda > >> Message: 10 >> Date: Mon, 13 Aug 2012 15:55:13 -0400 >> From: Douglas N Greve<greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID:<50295BA1.8090307(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Linda, can you send the terminal output for mri_segstats? Can you >> also send the summary file? >> doug >> >> On 08/13/2012 10:59 AM, Linda Douw wrote: >>> Hi Doug, >>> >>> I first parcellate fsaverage5 using ico4 (all my functional data are >>> morphed to fsaverage5 surface): >>> >>> mris_make_face_parcellation /fsaverage5/rh.inflated >>> $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot >>> >>> Then I extract the waveforms using mri_segstats >>> >>> mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot >>> fsaverage5c rh ico4 --sum ico4_rh.sum >>> >>> Hope this clarifies the problem! >>> Linda >>> >>>> ------------------------------ >>>> >>>> Message: 25 >>>> Date: Fri, 10 Aug 2012 11:18:38 -0400 >>>> From: Douglas N Greve<greve(a)nmr.mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> Message-ID:<5025264E.3030801(a)nmr.mgh.harvard.edu> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> what are your command lines? >>>> doug >>>> >>>> On 08/09/2012 01:21 PM, Linda Douw wrote: >>>>> Dear Freesurfers, >>>>> >>>>> I'm trying to extract the average waveforms from all 2562 ROIs in an >>>>> annotation constructed using mris_make_face_parcellation with ico4. >>>>> However, I get only 2460 waveforms after doing mri_segstats, and the >>>>> summary files show that several ROIs are 'skipped' for some reason. Am >>>>> I >>>>> missing something? >>>>> >>>>> Thanks, >>>>> -- 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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T1w3D scan properties of pts with epilepsy
by Zuzana Nedelska 14 Sep '12

14 Sep '12

Hello: I have big file of pts with medial temporal lobe epilepsy (they usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes in amygdala). Pts are scanned with 'oblique' sequence, as it is perpendicular to long axis of hippocampus. Can these oblique sequences be used for FreeSurfer cortical reconstruction and subcort. volumes? I put some of them through 'recon-all' pipeline, which finished 'without errors'. In the 'stats' files (aseg.stats) of those subjects, I am missing volumetric values for left hippocampus and left amygdala. Patients are before surgery, so they have left structures for sure (even original dicom data are complete). The right hipo and amygdala volumes are stated in mm3 as expected. Why is that? Thanks for the advice.

3 2

Numerical result out of range error
by Blessy M 14 Sep '12

14 Sep '12

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

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

14 Sep '12

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>> > > 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> > > 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> > 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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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

1 0

Two questions about csd (cluster simulation data)
by Shanqing Cai 14 Sep '12

14 Sep '12

Hi, These might be old questions, but I couldn't find any entries related to them in the archives. 1) In the surface and volume csd files, what are the units of the "maxclustsize" columns? Are they mm^2 and mm^3 for surface and volume, respectively? Or are the voxel / vertex counts? 2) When mri_surfcluster uses a csd file to compute the cluster-wise correct p-values, how does it do that? Does it only use the maxclustsize? Or does it take other columns, such as maxsig, into account as well? Thanks! Best, Shanqing Cai

2 1

ERROR: You are trying to re-run an existing subject
by Carolina Valencia 14 Sep '12

14 Sep '12

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*

2 1

recon-all problem
by Eiran Vadim Harel 14 Sep '12

14 Sep '12

Hi all, Is there a change in the unpacking of the MPRAGE and DICOM files? The names of the files have changed. what file name should be put in the command: recon-all -i./file name -s subjectname Thanks, Eiran

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mris_anatomical_stats on multiple subjects
by Alexandra Tanner 14 Sep '12

14 Sep '12

Hi Doug and Freesurfers, I'm currently working on extracting thickness measurements from an ROI I manually created. I created my ROI label in tksurfer and applied the label to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats file, with the thickness measurement, from my label: mris_anatomical_stats -f something.stats -l something.label subjid ?h (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) This generated a stats file that gave me the average thickness for my ROI in my subject. I was wondering if there is a way to run the same command, but on multiple subjects at once, so as not to have to run this command on each individual subject. Any suggestions would be greatly appreciated! Best, Alex

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

13 Sep '12

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 > > > > >

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Re: [Freesurfer] head motion values
by Douglas N Greve 13 Sep '12

13 Sep '12

Hi New Fei, I did some digging and found the docs for the output (pasted below). Translations (displacement) are in mm, rotations are in degrees doug 1. n : time point 2. roll : rotation about the I-S axis (degrees CCW) 3. pitch : rotation about the R-L axis (degrees CCW) 4. yaw : rotation about the A-P axis (degrees CCW) 5. dS : displacement in the Superior direction (mm) 6. dL : displacement in the Left direction (mm) 7. dP : displacement in the Posterior direction (mm) 8. rmsold : RMS difference between input frame and reference frame 9. rmsnew : RMS difference between output frame and reference frame 10. trans : translation (mm) = sqrt(dS^2 + dL^2 + dP^2) On 09/13/2012 11:21 AM, New Fei Ho wrote: > Hi Doug, > > To explicitly clarify, does this mean > X: L-R > Y: Anterior-Posterior > Z: Inferior-Superior > > And are the values of translation/rotation in millimetres? > > Thanks, > New Fei > > >> If by XYZ you mean column, row, slice, then yes. The values are with >> respect to the middle time point (or whatever you used as the template), >> it is not the relative difference. >> doug >> >> On 09/12/2012 05:37 PM, New Fei Ho wrote: >>> 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 >>> _______________________________________________ >>> 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 >> >> >> > -- 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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