Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Fixing incorrect segmentation and pial surface
by Brenna Day 03 Sep '13

03 Sep '13

Hi, I have a file where the pial surface is excluding some of the gray matter. I edited wm.mgz and added control points to brainmask.mgz, this fixed some of the pial surface errors but not all. After looking at the aseg closer there is a section of incorrectly labeled wm near the pial surface errors. Voxels which look like they should be labeled at wm are labeled as left-putamen in the aseg. Is there a way to fix this other than manual edits to the aseg? I'm using v5.0.0 and the aim is to run mri_segstats with the segmented brain and a matched PIB scan, so I do need the segmentation and the pial surface to be quite correct. I've attached some screenshots of the problematic area, it runs through coronal slices 96-106 and 118-124. Thanks for any help you can give. Regards, Brenna [image: Inline image 1][image: Inline image 2][image: Inline image 3]

2 1

FW: No brain tissue after recon-all all
by pablo najt 03 Sep '13

03 Sep '13

Hi Doug, Thank you very much for your output about my output files. Yes, I understand that these images are skull stripped. But since there are possibilities of error in the skull stripping process I was concern about extra no brain tissue being included in the output. I think the location of the tissue I was referring was mistaken. To make it clearer I have circled (in red) the specific area in the images attached I have concerns about not being brain tissue. I noticed that this repeats in several other of my subjects and I wanted to make sure it is fine. Best,Pablo > Date: Tue, 3 Sep 2013 09:50:06 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] No brain tissue after recon-all all > > > Hi Pablo, this is a skull stripped image. In the human brain there is no > brain tissue ventral to the orbital frontal areaso any tissue there has > been stripped away. > doug > > > On 09/02/2013 12:49 AM, pablo najt wrote: > > > > Dear FS experts, > > I have a doubt about a potential registration problem after running > > recon-all -all. I noticed that one of the image outcome when opened > > with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to > > orbitofrontal areas. I have attached snapshots to illustrate the image. > > I would greatly appreciate your output on this since I have no > > experience with FS and I am not sure what to expect. I would like to > > enquire whether I should be concerned about this image or if this is > > not a problem. > > > > Many thanks, > > Pablo > > > > > > _______________________________________________ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. >

2 2

trying to understand mri_surf2surf
by David Romano 03 Sep '13

03 Sep '13

Hi everyone, In an earlier post, I had asked how to transform the white surface of one subject to the white surface of another subject, and Bruce Fischl suggested mri_surf2surf should be able to do this. After looking over the website material related to mri_surf2surf, I find I'm not sure how mri_surf2surf works, and so am still not sure how to proceed. As a starting point, suppose we have the file lh.sphere.reg for each of two subjects, A and B, and consider, say, vertex 1 of subject A. Here is what I understand: This vertex maps to a point P on the sphere that has coordinates given in subjects A's lh.sphere.reg file. The point P is contained in some closed triangle T from B's mesh, as that mesh appears in B's lh.sphere.reg file. This triangle is formed from three points on the sphere that correspond to three vertices that appear in B's lh.white file. These three vertices thus form a triangle T' in B's native volume space, and thus the point P contained in T corresponds to a point P' in B's native volume space that is contained in T'. So here is my question: How would I used mri_surf2surf to find the coordinates (in B's native volume space) of the point P'? Thanks in advance for you help in clarifying this for me. Best regards, David Romano

2 3

Re: [Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter"
by Douglas N Greve 03 Sep '13

03 Sep '13

It is not finding what it needs in this folder /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh Can you check that it exists and that it has the same files in it that the corresponding folders from other sessions has? If it does not, check that you have space and permissions there and then try rerunning selxavg3-sess doug On 09/03/2013 10:35 AM, Kathryn Devaney wrote: > Hi Doug, > > Same error - here's the debug output (pasted below & in attached text > file). > > Thanks, > Katie > > > kdevaney@frontal: [227] > circlet/connectivity_average_labels/ROI_average_labels/ funcroi-sess > -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi ROI_rh_antTPJ.roi > -update 10:27am > ------------------------------------------- > /srv/mind3/r2/users/fspace2/120723EC > Tue Sep 3 10:27:48 EDT 2013 > set: Variable name must begin with a letter. > kdevaney@frontal: [228] > circlet/connectivity_average_labels/ROI_average_labels/ funcroi-sess > -debug -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi > ROI_rh_antTPJ.roi -update > set echo = 1 ; > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 7 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -s > shift > > switch ( $flag ) > switch ( -s ) > if ( $#argv == 0 ) goto arg1err ; > if ( 6 == 0 ) goto arg1err > set SessList = ( $SessList $argv[1] ) ; shift ; > set SessList = ( 120723EC ) > shift > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -d > shift > > switch ( $flag ) > switch ( -d ) > if ( $#argv == 0 ) goto arg1err ; > if ( 4 == 0 ) goto arg1err > if ( ! -d $argv[1] ) then > if ( ! -d /srv/mind3/r2/users/fspace2 ) then > if ( ! -r $argv[1] ) then > if ( ! -r /srv/mind3/r2/users/fspace2 ) then > set srchdir = $argv[1] ; shift ; > set srchdir = /srv/mind3/r2/users/fspace2 > shift > set SearchPathList = ( $SearchPathList $srchdir ) ; > set SearchPathList = ( /srv/mind3/r2/users/fspace2 ) > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 3 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -roi > shift > > switch ( $flag ) > switch ( -roi ) > > end > end > while ( $#argv != 0 ) > while ( 2 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = ROI_rh_antTPJ.roi > shift > > switch ( $flag ) > switch ( ROI_rh_antTPJ.roi ) > > end > end > while ( $#argv != 0 ) > while ( 1 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -update > shift > > switch ( $flag ) > switch ( -update ) > > end > end > while ( $#argv != 0 ) > while ( 0 != 0 ) > goto parse_args_return ; > goto parse_args_return > > foreach grp ( $grpdefs ) > foreach grp ( ) > > goto check_params ; > goto check_params > > if ( $#SessList == 0 ) then > if ( 1 == 0 ) then > > if ( $#SearchPathList == 0 ) then > if ( 1 == 0 ) then > > goto check_params_return ; > goto check_params_return > > > set UniqueList = ( ) ; > set UniqueList = ( ) > foreach d ( $SearchPathList ) > foreach d ( /srv/mind3/r2/users/fspace2 ) > if ( ! -e $d ) then > if ( ! -e /srv/mind3/r2/users/fspace2 ) then > > set IsUnique = 1 ; > set IsUnique = 1 > foreach u ( $UniqueList ) > foreach u ( ) > if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; > if ( 1 ) set UniqueList = ( /srv/mind3/r2/users/fspace2 ) > set UniqueList = ( /srv/mind3/r2/users/fspace2 ) > end > end > > set SearchPathList = ( $UniqueList ) ; > set SearchPathList = ( /srv/mind3/r2/users/fspace2 ) > > set errs = 0 ; > set errs = 0 > > > set SessPath = ( ) ; > set SessPath = ( ) > foreach sess ( $SessList ) > foreach sess ( 120723EC ) > set tmp = ( ) ; > set tmp = ( ) > foreach d ( $SearchPathList ) > foreach d ( /srv/mind3/r2/users/fspace2 ) > set stst = $d/$sess > set stst = /srv/mind3/r2/users/fspace2/120723EC > if ( -d $stst ) then > if ( -d /srv/mind3/r2/users/fspace2/120723EC ) then > if ( ! -r $stst ) then > if ( ! -r /srv/mind3/r2/users/fspace2/120723EC ) then > pushd $stst > /dev/null ; > pushd /srv/mind3/r2/users/fspace2/120723EC > set tmp = ( $tmp `$PWDCMD` ) ; > set tmp = ( `$PWDCMD` ) > pwd > popd > /dev/null ; > popd > endif > endif > end > end > set nfound = ( $#tmp ) ; > set nfound = ( 1 ) > if ( $nfound == 0 ) then > if ( 1 == 0 ) then > if ( $nfound > 1 ) then > if ( 1 > 1 ) then > set SessPath = ( $SessPath $tmp ) ; > set SessPath = ( /srv/mind3/r2/users/fspace2/120723EC ) > end > end > > > set UniqueList = ( ) ; > set UniqueList = ( ) > foreach s ( $SessPath ) > foreach s ( /srv/mind3/r2/users/fspace2/120723EC ) > set IsUnique = 1 ; > set IsUnique = 1 > foreach u ( $UniqueList ) > foreach u ( ) > if ( ! $IsUnique && ! $AllowRedundant ) then > if ( ! 1 && ! 0 ) then > > set UniqueList = ( $UniqueList $s ) ; > set UniqueList = ( /srv/mind3/r2/users/fspace2/120723EC ) > endif > endif > end > end > > > echo $SessPath > echo /srv/mind3/r2/users/fspace2/120723EC > > exit $errs ; > exit 0 > set echo = 1 ; > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 7 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -s > shift > > switch ( $flag ) > switch ( -s ) > case "-sf": > case -sf: > case "-d": > case -d: > case "-df": > case -df: > shift ; > shift > > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -d > shift > > switch ( $flag ) > switch ( -d ) > case "-df": > case -df: > shift ; > shift > > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 3 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -roi > shift > > switch ( $flag ) > switch ( -roi ) > if ( $#argv < 1 ) goto arg1err ; > if ( 2 < 1 ) goto arg1err > set roicfg = $argv[1] ; shift ; > set roicfg = ROI_rh_antTPJ.roi > shift > if ( ! -e $roicfg ) then > if ( ! -e ROI_rh_antTPJ.roi ) then > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 1 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = -update > shift > > switch ( $flag ) > switch ( -update ) > set UpdateOnly = 1 ; > set UpdateOnly = 1 > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 0 != 0 ) > > goto parse_args_return ; > goto parse_args_return > > goto check_params ; > goto check_params > > if ( $#SessList == 0 ) then > if ( 1 == 0 ) then > > > if ( $#roicfg == 0 ) then > if ( 1 == 0 ) then > set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'` > set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'` > awk {if($1 == "roiname") print $2} > cat ROI_rh_antTPJ.roi > set label = `cat $roicfg | awk '{if($1 == "label") print $2}'` > set label = `cat $roicfg | awk '{if($1 == "label") print $2}'` > awk {if($1 == "label") print $2} > cat ROI_rh_antTPJ.roi > set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'` > set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'` > awk {if($1 == "annot") print $2} > cat ROI_rh_antTPJ.roi > if ( $#annot ) then > if ( 0 ) then > set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'` > set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'` > awk {if($1 == "seg") print $2} > cat ROI_rh_antTPJ.roi > if ( $#segvol ) then > if ( 0 ) then > set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'` > set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'` > awk {if($1 == "fillthresh") print $2} > cat ROI_rh_antTPJ.roi > set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'` > set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'` > awk {if($1 == "analysis") print $2} > cat ROI_rh_antTPJ.roi > set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'` > set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'` > awk {if($1 == "contrast") print $2} > cat ROI_rh_antTPJ.roi > set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'` > set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'` > awk {if($1 == "sign") print $2} > cat ROI_rh_antTPJ.roi > set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'` > set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'` > awk {if($1 == "thresh") print $2} > cat ROI_rh_antTPJ.roi > set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'` > set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'` > awk {if($1 == "pct") print $2} > cat ROI_rh_antTPJ.roi > set map = `cat $roicfg | awk '{if($1 == "map") print $2}'` > set map = `cat $roicfg | awk '{if($1 == "map") print $2}'` > awk {if($1 == "map") print $2} > cat ROI_rh_antTPJ.roi > set frame = `cat $roicfg | awk '{if($1 == "frame") print $2}'` > set frame = `cat $roicfg | awk '{if($1 == "frame") print $2}'` > awk {if($1 == "frame") print $2} > cat ROI_rh_antTPJ.roi > > if ( ! -d $analysis ) then > if ( ! -d circlet.fsaverage.sm3.mc.rh ) then > > goto check_params_return ; > goto check_params_return > > set fsd = `getana -a $analysis -t fsd` > set fsd = `getana -a $analysis -t fsd` > getana -a circlet.fsaverage.sm3.mc.rh -t fsd > > set IsNative = `getana -a $analysis -t IsNative` > set IsNative = `getana -a $analysis -t IsNative` > getana -a circlet.fsaverage.sm3.mc.rh -t IsNative > set IsMNI305 = `getana -a $analysis -t IsMNI305` > set IsMNI305 = `getana -a $analysis -t IsMNI305` > getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305 > set IsSurface = `getana -a $analysis -t IsSurface` > set IsSurface = `getana -a $analysis -t IsSurface` > getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface > if ( $IsSurface ) then > if ( 1 ) then > set hemi = `getana -a $analysis -t hemi` > set hemi = `getana -a $analysis -t hemi` > getana -a circlet.fsaverage.sm3.mc.rh -t hemi > set anasubject = `getana -a $analysis -t subject` > set anasubject = `getana -a $analysis -t subject` > getana -a circlet.fsaverage.sm3.mc.rh -t subject > endif > endif > set RegDOF = `getana -a $analysis -t RegDOF` > set RegDOF = `getana -a $analysis -t RegDOF` > getana -a circlet.fsaverage.sm3.mc.rh -t RegDOF > > set cvol = ( ) ; > set cvol = ( ) > set labelfile = ( ) ; > set labelfile = ( ) > set segfile = ( ) ; > set segfile = ( ) > set annotfile = ( ) ; > set annotfile = ( ) > > > @ nthsess = 0 ; > @ nthsess = 0 > foreach sess ( $SessList ) > foreach sess ( /srv/mind3/r2/users/fspace2/120723EC ) > @ nthsess = $nthsess + 1 ; > @ nthsess = 0 + 1 > set sessbase = `basename $sess` ; > set sessbase = `basename $sess` > basename /srv/mind3/r2/users/fspace2/120723EC > set sessdir = `dirname $sess` ; > set sessdir = `dirname $sess` > dirname /srv/mind3/r2/users/fspace2/120723EC > > echo "-------------------------------------------" > echo ------------------------------------------- > ------------------------------------------- > echo "$sess " > echo /srv/mind3/r2/users/fspace2/120723EC > /srv/mind3/r2/users/fspace2/120723EC > date > date > Tue Sep 3 10:27:59 EDT 2013 > set subject = `cat $sess/subjectname` > set subject = `cat $sess/subjectname` > cat /srv/mind3/r2/users/fspace2/120723EC/subjectname > > set anadir = $sess/$fsd/$analysis > set anadir = > /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh > if ( ! -e $anadir ) then > if ( ! -e > /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh > ) then > set ext = `stem2fmt $anadir/meanfunc` > set ext = `stem2fmt $anadir/meanfunc` > stem2fmt > /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/meanfunc > > > > > if ( $#label ) then > if ( 1 ) then > > set labelfile = $SUBJECTS_DIR/$subject/label/$label > set labelfile = > /r2/users/fspace2/autorecon-subjects//ec51/label/allsubjs_rh_antTPJ.label > if ( ! -e $labelfile ) then > if ( ! -e > /r2/users/fspace2/autorecon-subjects//ec51/label/allsubjs_rh_antTPJ.label > ) then > endif > endif > > if ( $#segvol ) then > if ( 0 ) then > > if ( $#annot ) then > if ( 0 ) then > > > if ( $#contrast ) then > if ( 0 ) then > > > set roivol = $anadir/$roiname.$ext > set roivol = > /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.ERROR: > could not determine format for > /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/meanfunc > set: Variable name must begin with a letter. > kdevaney@frontal: [229] > circlet/connectivity_average_labels/ROI_average_labels/ > > On 9/3/13 10:11 AM, Douglas N Greve wrote: >> It looks like it is dying on this command. Can you run it? If you get >> the same error, run it with -debug as the first option and send me >> the terminal output >> >> funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi >> ROI_rh_antTPJ.roi -update >> >> >> On 08/30/2013 04:27 PM, Kathryn Devaney wrote: >>> Hi Doug, >>> >>> The -debug output is below and also in the attached text file - the >>> first line is the command. >>> >>> Thanks! >>> Katie >>> >>> kdevaney@frontal: [231] >>> circlet/connectivity_average_labels/ROI_average_labels/ >>> funcroi-table-sess -debug -o output.rh_antTPJ -roi ROI_rh_antTPJ.roi >>> -a circlet.fsaverage.sm3.mc.rh -c 3v4 -sf sessid -df sesspar >>> set echo = 1 ; >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 12 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -o >>> shift >>> >>> switch ( $flag ) >>> switch ( -o ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 11 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = output.rh_antTPJ >>> shift >>> >>> switch ( $flag ) >>> switch ( output.rh_antTPJ ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 10 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -roi >>> shift >>> >>> switch ( $flag ) >>> switch ( -roi ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 9 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = ROI_rh_antTPJ.roi >>> shift >>> >>> switch ( $flag ) >>> switch ( ROI_rh_antTPJ.roi ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 8 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -a >>> shift >>> >>> switch ( $flag ) >>> switch ( -a ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 7 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = circlet.fsaverage.sm3.mc.rh >>> shift >>> >>> switch ( $flag ) >>> switch ( circlet.fsaverage.sm3.mc.rh ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 6 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -c >>> shift >>> >>> switch ( $flag ) >>> switch ( -c ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 5 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = 3v4 >>> shift >>> >>> switch ( $flag ) >>> switch ( 3v4 ) >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 4 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -sf >>> shift >>> >>> switch ( $flag ) >>> switch ( -sf ) >>> if ( $#argv == 0 ) goto arg1err ; >>> if ( 3 == 0 ) goto arg1err >>> set grpdef = $argv[1] ; shift ; >>> set grpdef = sessid >>> shift >>> if ( ! -e $grpdef ) then >>> if ( ! -e sessid ) then >>> set grpdefs = ( $grpdefs $grpdef ) ; >>> set grpdefs = ( sessid ) >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 2 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -df >>> shift >>> >>> switch ( $flag ) >>> switch ( -df ) >>> if ( $#argv == 0 ) goto arg1err ; >>> if ( 1 == 0 ) goto arg1err >>> if ( ! -e $argv[1] ) then >>> if ( ! -e sesspar ) then >>> set srchdirfile = $argv[1] ; shift ; >>> set srchdirfile = sesspar >>> shift >>> set SearchPathList = ( $SearchPathList `cat $srchdirfile` ) ; >>> set SearchPathList = ( `cat $srchdirfile` ) >>> cat sesspar >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 0 != 0 ) >>> goto parse_args_return ; >>> goto parse_args_return >>> >>> foreach grp ( $grpdefs ) >>> foreach grp ( sessid ) >>> set SessList = ( $SessList `cat $grp` ) ; >>> set SessList = ( `cat $grp` ) >>> cat sessid >>> end >>> end >>> >>> goto check_params ; >>> goto check_params >>> >>> if ( $#SessList == 0 ) then >>> if ( 6 == 0 ) then >>> >>> if ( $#SearchPathList == 0 ) then >>> if ( 1 == 0 ) then >>> >>> goto check_params_return ; >>> goto check_params_return >>> >>> >>> set UniqueList = ( ) ; >>> set UniqueList = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> if ( ! -e $d ) then >>> if ( ! -e /r2/users/fspace2/ ) then >>> >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( ) >>> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; >>> if ( 1 ) set UniqueList = ( /r2/users/fspace2/ ) >>> set UniqueList = ( /r2/users/fspace2/ ) >>> end >>> end >>> >>> set SearchPathList = ( $UniqueList ) ; >>> set SearchPathList = ( /r2/users/fspace2/ ) >>> >>> set errs = 0 ; >>> set errs = 0 >>> >>> >>> set SessPath = ( ) ; >>> set SessPath = ( ) >>> foreach sess ( $SessList ) >>> foreach sess ( 120209UU 120314ST 120405CC_circlet 120723EC 120723NP >>> 120723QL ) >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120209UU >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120209UU ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120209UU ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120209UU >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU ) >>> end >>> end >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120314ST >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120314ST ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120314ST ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120314ST >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST ) >>> end >>> end >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120405CC_circlet >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120405CC_circlet ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120405CC_circlet ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120405CC_circlet >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) >>> end >>> end >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120723EC >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120723EC ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120723EC ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120723EC >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC ) >>> end >>> end >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120723NP >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120723NP ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120723NP ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120723NP >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP ) >>> end >>> end >>> set tmp = ( ) ; >>> set tmp = ( ) >>> foreach d ( $SearchPathList ) >>> foreach d ( /r2/users/fspace2/ ) >>> set stst = $d/$sess >>> set stst = /r2/users/fspace2//120723QL >>> if ( -d $stst ) then >>> if ( -d /r2/users/fspace2//120723QL ) then >>> if ( ! -r $stst ) then >>> if ( ! -r /r2/users/fspace2//120723QL ) then >>> pushd $stst > /dev/null ; >>> pushd /r2/users/fspace2//120723QL >>> set tmp = ( $tmp `$PWDCMD` ) ; >>> set tmp = ( `$PWDCMD` ) >>> pwd >>> popd > /dev/null ; >>> popd >>> endif >>> endif >>> end >>> end >>> set nfound = ( $#tmp ) ; >>> set nfound = ( 1 ) >>> if ( $nfound == 0 ) then >>> if ( 1 == 0 ) then >>> if ( $nfound > 1 ) then >>> if ( 1 > 1 ) then >>> set SessPath = ( $SessPath $tmp ) ; >>> set SessPath = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP >>> /srv/mind3/r2/users/fspace2/120723QL ) >>> end >>> end >>> >>> >>> set UniqueList = ( ) ; >>> set UniqueList = ( ) >>> foreach s ( $SessPath ) >>> foreach s ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP >>> /srv/mind3/r2/users/fspace2/120723QL ) >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( ) >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU ) >>> endif >>> endif >>> end >>> end >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( /srv/mind3/r2/users/fspace2/120209UU ) >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120314ST == >>> /srv/mind3/r2/users/fspace2/120209UU ) then >>> end >>> end >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST ) >>> endif >>> endif >>> end >>> end >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST ) >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120405CC_circlet == >>> /srv/mind3/r2/users/fspace2/120209UU ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120405CC_circlet == >>> /srv/mind3/r2/users/fspace2/120314ST ) then >>> end >>> end >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) >>> endif >>> endif >>> end >>> end >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723EC == >>> /srv/mind3/r2/users/fspace2/120209UU ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723EC == >>> /srv/mind3/r2/users/fspace2/120314ST ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723EC == >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) then >>> end >>> end >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC ) >>> endif >>> endif >>> end >>> end >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC ) >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723NP == >>> /srv/mind3/r2/users/fspace2/120209UU ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723NP == >>> /srv/mind3/r2/users/fspace2/120314ST ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723NP == >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723NP == >>> /srv/mind3/r2/users/fspace2/120723EC ) then >>> end >>> end >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP ) >>> endif >>> endif >>> end >>> end >>> set IsUnique = 1 ; >>> set IsUnique = 1 >>> foreach u ( $UniqueList ) >>> foreach u ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP ) >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723QL == >>> /srv/mind3/r2/users/fspace2/120209UU ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723QL == >>> /srv/mind3/r2/users/fspace2/120314ST ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723QL == >>> /srv/mind3/r2/users/fspace2/120405CC_circlet ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723QL == >>> /srv/mind3/r2/users/fspace2/120723EC ) then >>> end >>> end >>> if ( $s == $u ) then >>> if ( /srv/mind3/r2/users/fspace2/120723QL == >>> /srv/mind3/r2/users/fspace2/120723NP ) then >>> end >>> end >>> if ( ! $IsUnique && ! $AllowRedundant ) then >>> if ( ! 1 && ! 0 ) then >>> >>> set UniqueList = ( $UniqueList $s ) ; >>> set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP >>> /srv/mind3/r2/users/fspace2/120723QL ) >>> endif >>> endif >>> end >>> end >>> >>> >>> echo $SessPath >>> echo /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP >>> /srv/mind3/r2/users/fspace2/120723QL >>> >>> exit $errs ; >>> exit 0 >>> set echo = 1 ; >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 12 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -o >>> shift >>> >>> switch ( $flag ) >>> switch ( -o ) >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 11 < 1 ) goto arg1err >>> set outtable = $argv[1] ; shift ; >>> set outtable = output.rh_antTPJ >>> shift >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 10 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -roi >>> shift >>> >>> switch ( $flag ) >>> switch ( -roi ) >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 9 < 1 ) goto arg1err >>> set roicfg = $argv[1] ; shift ; >>> set roicfg = ROI_rh_antTPJ.roi >>> shift >>> if ( ! -e $roicfg ) then >>> if ( ! -e ROI_rh_antTPJ.roi ) then >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 8 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -a >>> shift >>> >>> switch ( $flag ) >>> switch ( -a ) >>> case "-analysis": >>> case -analysis: >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 7 < 1 ) goto arg1err >>> set analysis = $argv[1] ; shift ; >>> set analysis = circlet.fsaverage.sm3.mc.rh >>> shift >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 6 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -c >>> shift >>> >>> switch ( $flag ) >>> switch ( -c ) >>> case "-contrast": >>> case -contrast: >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 5 < 1 ) goto arg1err >>> set contrast = $argv[1] ; shift ; >>> set contrast = 3v4 >>> shift >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 4 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -sf >>> shift >>> >>> switch ( $flag ) >>> switch ( -sf ) >>> case "-df": >>> case -df: >>> case "-d": >>> case -d: >>> set sessargs = ( $sessargs $flag $argv[1] ) ; shift ; >>> set sessargs = ( -sf sessid ) >>> shift >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 2 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -df >>> shift >>> >>> switch ( $flag ) >>> switch ( -df ) >>> case "-d": >>> case -d: >>> set sessargs = ( $sessargs $flag $argv[1] ) ; shift ; >>> set sessargs = ( -sf sessid -df sesspar ) >>> shift >>> breaksw >>> breaksw >>> >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 0 != 0 ) >>> >>> goto parse_args_return ; >>> goto parse_args_return >>> >>> goto check_params ; >>> goto check_params >>> >>> if ( $#outtable == 0 ) then >>> if ( 1 == 0 ) then >>> >>> if ( $#roicfg == 0 ) then >>> if ( 1 == 0 ) then >>> set ROIname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'` >>> set ROIname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'` >>> awk {if($1 == "roiname") print $2} >>> cat ROI_rh_antTPJ.roi >>> set ROIanalysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'` >>> set ROIanalysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'` >>> awk {if($1 == "analysis") print $2} >>> cat ROI_rh_antTPJ.roi >>> set ROIIsNative = `getana -a $ROIanalysis -t IsNative` >>> set ROIIsNative = `getana -a $ROIanalysis -t IsNative` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsNative >>> set ROIIsMNI305 = `getana -a $ROIanalysis -t IsMNI305` >>> set ROIIsMNI305 = `getana -a $ROIanalysis -t IsMNI305` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305 >>> set ROIIsSurface = `getana -a $ROIanalysis -t IsSurface` >>> set ROIIsSurface = `getana -a $ROIanalysis -t IsSurface` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface >>> set ROIhemi = ( ) ; >>> set ROIhemi = ( ) >>> if ( $ROIIsSurface ) then >>> if ( 1 ) then >>> set ROIhemi = `getana -a $ROIanalysis -t hemi` >>> set ROIhemi = `getana -a $ROIanalysis -t hemi` >>> getana -a circlet.fsaverage.sm3.mc.rh -t hemi >>> endif >>> endif >>> set ROIfsd = `getana -a $ROIanalysis -t fsd` >>> set ROIfsd = `getana -a $ROIanalysis -t fsd` >>> getana -a circlet.fsaverage.sm3.mc.rh -t fsd >>> >>> if ( $measure == volume && $#analysis ) then >>> if ( mean == volume && 1 ) then >>> if ( $measure == volume && $#contrast ) then >>> if ( mean == volume && 1 ) then >>> >>> if ( $#analysis == 0 ) set analysis = $ROIanalysis >>> if ( 1 == 0 ) set analysis = circlet.fsaverage.sm3.mc.rh >>> >>> if ( $#contrast == 0 && $#map != 0 ) then >>> if ( 1 == 0 && 0 != 0 ) then >>> >>> if ( $#contrast ) then >>> if ( 1 ) then >>> set conlist = ( `getana -a $analysis -t contrasts` ) ; >>> set conlist = ( `getana -a $analysis -t contrasts` ) >>> getana -a circlet.fsaverage.sm3.mc.rh -t contrasts >>> set ConFound = 0 ; >>> set ConFound = 0 >>> foreach con ( $conlist ) >>> foreach con ( 12v0 12v7 1v0 2v0 34v0 34v12 3v0 3v4 4v0 56v0 56v12 >>> 56v34 5v0 6v0 7v0 ) >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 12v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 12v7 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 1v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 2v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 34v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 34v12 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 3v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 3v4 == 3v4 ) set ConFound = 1 >>> set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 4v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 56v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 56v12 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 56v34 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 5v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 6v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( $con == $contrast ) set ConFound = 1 ; >>> if ( 7v0 == 3v4 ) set ConFound = 1 >>> end >>> end >>> if ( ! $ConFound ) then >>> if ( ! 1 ) then >>> if ( $#map == 0 ) set map = ces ; >>> if ( 0 == 0 ) set map = ces >>> set map = ces >>> endif >>> endif >>> >>> set fsd = `getana -a $analysis -t fsd` >>> set fsd = `getana -a $analysis -t fsd` >>> getana -a circlet.fsaverage.sm3.mc.rh -t fsd >>> >>> set IsNative = `getana -a $analysis -t IsNative` >>> set IsNative = `getana -a $analysis -t IsNative` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsNative >>> set IsMNI305 = `getana -a $analysis -t IsMNI305` >>> set IsMNI305 = `getana -a $analysis -t IsMNI305` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305 >>> set IsSurface = `getana -a $analysis -t IsSurface` >>> set IsSurface = `getana -a $analysis -t IsSurface` >>> getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface >>> set hemi = ( ) ; >>> set hemi = ( ) >>> if ( $IsSurface ) then >>> if ( 1 ) then >>> set hemi = `getana -a $analysis -t hemi` >>> set hemi = `getana -a $analysis -t hemi` >>> getana -a circlet.fsaverage.sm3.mc.rh -t hemi >>> endif >>> endif >>> >>> if ( ( $IsNative && ! $ROIIsNative ) || ( $IsMNI305 && ! >>> $ROIIsMNI305 ) || ( $IsSurface && ! $ROIIsSurface ) ) then >>> if ( ( 0 && ! 0 ) || ( 0 && ! 0 ) || ( 1 && ! 1 ) ) then >>> >>> if ( $IsSurface && $hemi != $ROIhemi ) then >>> if ( 1 && rh != rh ) then >>> >>> goto check_params_return ; >>> goto check_params_return >>> >>> >>> if ( $#LF == 0 ) set LF = log/funcroi-table-sess.log >>> if ( 0 == 0 ) set LF = log/funcroi-table-sess.log >>> set LF = log/funcroi-table-sess.log >>> if ( -e $LF ) mv $LF $LF.old >>> if ( -e log/funcroi-table-sess.log ) mv log/funcroi-table-sess.log >>> log/funcroi-table-sess.log.old >>> mv log/funcroi-table-sess.log log/funcroi-table-sess.log.old >>> echo $LF >>> echo log/funcroi-table-sess.log >>> log/funcroi-table-sess.log >>> >>> echo "funcroi-table-sess log file" >> $LF >>> echo funcroi-table-sess log file >>> echo $VERSION >> $LF >>> echo $Id: funcroi-table-sess,v 1.3.2.3 2011/04/18 19:50:37 greve Exp $ >>> date >> $LF >>> date >>> uname -a >> $LF >>> uname -a >>> pwd >> $LF >>> pwd >>> echo $0 >> $LF >>> echo >>> /scratch/local/pkg/freesurfer/freesurfer-5.1.0/fsfast/bin/funcroi-table-sess >>> echo $inputargs >> $LF >>> echo -debug -o output.rh_antTPJ -roi ROI_rh_antTPJ.roi -a >>> circlet.fsaverage.sm3.mc.rh -c 3v4 -sf sessid -df sesspar >>> id >> $LF >>> id >>> >>> set StartTime = `date` ; >>> set StartTime = `date` >>> date >>> >>> set tmpdir = /tmp/tmp.funcroi-table-sess.$$ >>> set tmpdir = /tmp/tmp.funcroi-table-sess.4966 >>> mkdir -p $tmpdir >>> mkdir -p /tmp/tmp.funcroi-table-sess.4966 >>> >>> >>> set sess0list = ( ) ; >>> set sess0list = ( ) >>> set sumlist = ( ) ; >>> set sumlist = ( ) >>> set sessidlist = $tmpdir/sessid >>> set sessidlist = /tmp/tmp.funcroi-table-sess.4966/sessid >>> rm -f $sessidlist >>> rm -f /tmp/tmp.funcroi-table-sess.4966/sessid >>> echo "FirstRow" >> $sessidlist >>> echo FirstRow >>> foreach sess ( $SessList ) >>> foreach sess ( /srv/mind3/r2/users/fspace2/120209UU >>> /srv/mind3/r2/users/fspace2/120314ST >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> /srv/mind3/r2/users/fspace2/120723EC >>> /srv/mind3/r2/users/fspace2/120723NP >>> /srv/mind3/r2/users/fspace2/120723QL ) >>> set sessid = `basename $sess` ; >>> set sessid = `basename $sess` >>> basename /srv/mind3/r2/users/fspace2/120209UU >>> set sessdir = `dirname $sess` ; >>> set sessdir = `dirname $sess` >>> dirname /srv/mind3/r2/users/fspace2/120209UU >>> echo "$sessid" >> $sessidlist >>> echo 120209UU >>> >>> set ROIanadir = $sess/$ROIfsd/$ROIanalysis >>> set ROIanadir = >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $ROIanadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> >>> set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update ) >>> set cmd = ( funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 >>> -roi ROI_rh_antTPJ.roi -update ) >>> echo $cmd >>> echo funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> $cmd >>> funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> ------------------------------------------- >>> /srv/mind3/r2/users/fspace2/120209UU >>> Fri Aug 30 16:23:55 EDT 2013 >>> 120209UU Update not needed >>> Ended at Fri Aug 30 16:23:55 EDT 2013 >>> funcroi-sess completed >>> >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ >>> if ( $status ) then >>> if ( 0 ) then >>> >>> set anadir = $sess/$fsd/$analysis >>> set anadir = >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $anadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> if ( $#contrast ) then >>> if ( 1 ) then >>> set condir = $anadir/$contrast >>> set condir = >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4 >>> set mapfile = `stem2fname $condir/$map` ; >>> set mapfile = `stem2fname $condir/$map` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces >>> if ( $status ) then >>> if ( 0 ) then >>> >>> else >>> else >>> set sumdir = $tmpdir/$sessid >>> set sumdir = /tmp/tmp.funcroi-table-sess.4966/120209UU >>> mkdir -p $sumdir >>> mkdir -p /tmp/tmp.funcroi-table-sess.4966/120209UU >>> set sum = $sumdir/$ROIname.$frame.dat >>> set sum = /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> >>> set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i >>> $mapfile --sum $sum ) >>> set cmd = ( mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat ) >>> echo $cmd >>> echo mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> $cmd | tee -a $LF >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> tee -a log/funcroi-table-sess.log >>> >>> $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ >>> cwd >>> cmdline mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> sysname Linux >>> hostname frontal >>> machine x86_64 >>> user kdevaney >>> Loading >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> Loading >>> /srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> Voxel Volume is 1 mm^3 >>> Generating list of segmentation ids >>> Found 1 segmentations >>> Computing statistics for each segmentation >>> 0 1 809 809 >>> >>> Reporting on 1 segmentations >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ok = `grep -v \# $sum | wc -l` >>> set ok = `grep -v \# $sum | wc -l` >>> wc -l >>> grep -v # /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> if ( ! $ok ) then >>> if ( ! 1 ) then >>> >>> set sumlist = ( $sumlist $sum ) >>> set sumlist = ( >>> /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat ) >>> end >>> end >>> set sessid = `basename $sess` ; >>> set sessid = `basename $sess` >>> basename /srv/mind3/r2/users/fspace2/120314ST >>> set sessdir = `dirname $sess` ; >>> set sessdir = `dirname $sess` >>> dirname /srv/mind3/r2/users/fspace2/120314ST >>> echo "$sessid" >> $sessidlist >>> echo 120314ST >>> >>> set ROIanadir = $sess/$ROIfsd/$ROIanalysis >>> set ROIanadir = >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $ROIanadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> >>> set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update ) >>> set cmd = ( funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 >>> -roi ROI_rh_antTPJ.roi -update ) >>> echo $cmd >>> echo funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> $cmd >>> funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> ------------------------------------------- >>> /srv/mind3/r2/users/fspace2/120314ST >>> Fri Aug 30 16:23:55 EDT 2013 >>> 120314ST Update not needed >>> Ended at Fri Aug 30 16:23:55 EDT 2013 >>> funcroi-sess completed >>> >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ >>> if ( $status ) then >>> if ( 0 ) then >>> >>> set anadir = $sess/$fsd/$analysis >>> set anadir = >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $anadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> if ( $#contrast ) then >>> if ( 1 ) then >>> set condir = $anadir/$contrast >>> set condir = >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4 >>> set mapfile = `stem2fname $condir/$map` ; >>> set mapfile = `stem2fname $condir/$map` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces >>> if ( $status ) then >>> if ( 0 ) then >>> >>> else >>> else >>> set sumdir = $tmpdir/$sessid >>> set sumdir = /tmp/tmp.funcroi-table-sess.4966/120314ST >>> mkdir -p $sumdir >>> mkdir -p /tmp/tmp.funcroi-table-sess.4966/120314ST >>> set sum = $sumdir/$ROIname.$frame.dat >>> set sum = /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> >>> set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i >>> $mapfile --sum $sum ) >>> set cmd = ( mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat ) >>> echo $cmd >>> echo mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> $cmd | tee -a $LF >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> tee -a log/funcroi-table-sess.log >>> >>> $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ >>> cwd >>> cmdline mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> sysname Linux >>> hostname frontal >>> machine x86_64 >>> user kdevaney >>> Loading >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> Loading >>> /srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> Voxel Volume is 1 mm^3 >>> Generating list of segmentation ids >>> Found 1 segmentations >>> Computing statistics for each segmentation >>> 0 1 784 784 >>> >>> Reporting on 1 segmentations >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ok = `grep -v \# $sum | wc -l` >>> set ok = `grep -v \# $sum | wc -l` >>> wc -l >>> grep -v # /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> if ( ! $ok ) then >>> if ( ! 1 ) then >>> >>> set sumlist = ( $sumlist $sum ) >>> set sumlist = ( >>> /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat ) >>> end >>> end >>> set sessid = `basename $sess` ; >>> set sessid = `basename $sess` >>> basename /srv/mind3/r2/users/fspace2/120405CC_circlet >>> set sessdir = `dirname $sess` ; >>> set sessdir = `dirname $sess` >>> dirname /srv/mind3/r2/users/fspace2/120405CC_circlet >>> echo "$sessid" >> $sessidlist >>> echo 120405CC_circlet >>> >>> set ROIanadir = $sess/$ROIfsd/$ROIanalysis >>> set ROIanadir = >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $ROIanadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> >>> set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update ) >>> set cmd = ( funcroi-sess -s 120405CC_circlet -d >>> /srv/mind3/r2/users/fspace2 -roi ROI_rh_antTPJ.roi -update ) >>> echo $cmd >>> echo funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 >>> -roi ROI_rh_antTPJ.roi -update >>> funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> $cmd >>> funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> ------------------------------------------- >>> /srv/mind3/r2/users/fspace2/120405CC_circlet >>> Fri Aug 30 16:23:55 EDT 2013 >>> 120405CC_circlet Update not needed >>> Ended at Fri Aug 30 16:23:55 EDT 2013 >>> funcroi-sess completed >>> >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ >>> if ( $status ) then >>> if ( 0 ) then >>> >>> set anadir = $sess/$fsd/$analysis >>> set anadir = >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $anadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> if ( $#contrast ) then >>> if ( 1 ) then >>> set condir = $anadir/$contrast >>> set condir = >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4 >>> set mapfile = `stem2fname $condir/$map` ; >>> set mapfile = `stem2fname $condir/$map` >>> stem2fname >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces >>> if ( $status ) then >>> if ( 0 ) then >>> >>> else >>> else >>> set sumdir = $tmpdir/$sessid >>> set sumdir = /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet >>> mkdir -p $sumdir >>> mkdir -p /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet >>> set sum = $sumdir/$ROIname.$frame.dat >>> set sum = >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> >>> set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i >>> $mapfile --sum $sum ) >>> set cmd = ( mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat ) >>> echo $cmd >>> echo mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> $cmd | tee -a $LF >>> mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> tee -a log/funcroi-table-sess.log >>> >>> $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ >>> cwd >>> cmdline mri_segstats --seg >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> --frame 0 --id 1 --i >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> --sum >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> sysname Linux >>> hostname frontal >>> machine x86_64 >>> user kdevaney >>> Loading >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz >>> Loading >>> /srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz >>> Voxel Volume is 1 mm^3 >>> Generating list of segmentation ids >>> Found 1 segmentations >>> Computing statistics for each segmentation >>> 0 1 801 801 >>> >>> Reporting on 1 segmentations >>> if ( $status ) exit 1 ; >>> if ( 0 ) exit 1 >>> >>> set ok = `grep -v \# $sum | wc -l` >>> set ok = `grep -v \# $sum | wc -l` >>> wc -l >>> grep -v # >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat >>> if ( ! $ok ) then >>> if ( ! 1 ) then >>> >>> set sumlist = ( $sumlist $sum ) >>> set sumlist = ( >>> /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat >>> /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat >>> /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat ) >>> end >>> end >>> set sessid = `basename $sess` ; >>> set sessid = `basename $sess` >>> basename /srv/mind3/r2/users/fspace2/120723EC >>> set sessdir = `dirname $sess` ; >>> set sessdir = `dirname $sess` >>> dirname /srv/mind3/r2/users/fspace2/120723EC >>> echo "$sessid" >> $sessidlist >>> echo 120723EC >>> >>> set ROIanadir = $sess/$ROIfsd/$ROIanalysis >>> set ROIanadir = >>> /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> if ( ! -e $ROIanadir ) then >>> if ( ! -e >>> /srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh >>> ) then >>> >>> >>> set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update ) >>> set cmd = ( funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 >>> -roi ROI_rh_antTPJ.roi -update ) >>> echo $cmd >>> echo funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> $cmd >>> funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi >>> ROI_rh_antTPJ.roi -update >>> ------------------------------------------- >>> /srv/mind3/r2/users/fspace2/120723EC >>> Fri Aug 30 16:23:56 EDT 2013 >>> set: Variable name must begin with a letter. >>> if ( $status ) exit 1 ; >>> if ( 1 ) exit 1 >>> exit 1 >>> >>> >>> On 8/30/13 2:09 PM, Douglas N Greve wrote: >>>> Hi Katie, can you run it with -debug as the first arg and send me the >>>> copious terminal output? >>>> doug >>>> >>>> >>>> On 08/30/2013 01:53 PM, Kathryn Devaney wrote: >>>>> Hi Doug& Surfers, >>>>> >>>>> I'm having this same issue. I'm running funcroi-table-sess on two >>>>> analyses (lh and rh). There was no 'log' folder in my working >>>>> directory, >>>>> so I created it. Everythingran fine for the lh, but when I try to >>>>> run >>>>> it in the rh I get >>>>> >>>>> set: Variable name must begin with a letter >>>>> >>>>> Here's the output of 'bugr' on my machine: >>>>> >>>>> --------------------------------------------------------------------- >>>>> >>>>> FREESURFER_HOME: /scratch/local/pkg/freesurfer/freesurfer-5.1.0 >>>>> >>>>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >>>>> >>>>> RedHat release: Fedora release 17 (Beefy Miracle) >>>>> >>>>> Kernel info: Linux 3.6.3-1.fc17.x86_64 x86_64 >>>>> >>>>> --------------------------------------------------------------------- >>>>> >>>>> Let me know if you'd like me to send the terminal output of >>>>> funcroi-table-sess -debug >>>>> >>>>> Thanks! >>>>> Katie >>>>> >>>>> >>>>> >>>>> On 8/19/13 4:05 PM, Douglas N Greve wrote: >>>>>> Is there a folder called "log" in the directly you are running it >>>>>> from? >>>>>> If not, try creating one. If so, then >>>>>> run it with -debug as the first arg and send me the terminal output. >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 08/19/2013 02:07 PM, Joseph Andreano wrote: >>>>>>> Hi All, >>>>>>> >>>>>>> I'm trying to use funcroi-table-sess, but whenever I send this >>>>>>> command: >>>>>>> >>>>>>> funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305 >>>>>>> -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat >>>>>>> >>>>>>> I get this error: >>>>>>> >>>>>>> set: Variable name must begin with a letter >>>>>>> >>>>>>> So far as I can tell, all the variables in that command begin >>>>>>> with a >>>>>>> letter. Any idea what the problem might be? >>>>>>> >>>>>>> >>>>>>> _________________________________ >>>>>>> >>>>>>> Joseph M. Andreano, PhD >>>>>>> Postdoctoral Researcher >>>>>>> Interdisciplinary Affective >>>>>>> Science Laboratory >>>>>>> Massachusetts General Hospital >>>>>>> _________________________________ >>>>>>> _______________________________________________ >>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

recon-all exited with errors
by Troebinger, Luzia 03 Sep '13

03 Sep '13

Hi all, I posted a message regarding this problem a while ago, but still not resolved. Basically, freesurfer exits with errors in the final (autorecon-3) stages, because of what must be a problem with the symbolic link lh.EC_average. The link is created as should be, but I get an error message saying the file lh.EC_average/surf/lh.sphere.reg doesn't exist. I checked that the path to the subjects directory is correct, and that the file in question exists, and both was the case. I am running out of ideas of how to fix this - does anyone know what might be going wrong? Best Luzia

2 1

Converting fsaveraged EPI to volume
by Marcel Falkiewicz 03 Sep '13

03 Sep '13

Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds? Thanks in advance, Marcel

5 18

mri_vol2surf projection of white matter results
by Robert Schulz 03 Sep '13

03 Sep '13

Dear Freesurfers, I transferred the white matter binary mask (derived from aseg, volume) to FSL and performed probabilistic tractography in it. Now I'd like to project the 'outer' white matter results (vol) onto the white surface. To test for the acuracy of this approach, I tried to project the white matter mask (binarized, volume) itself on the surface, proper projection should give only 1s (ones) on the surface, which holds true for the majority of vertices. I used the following command: mri_vol2surf --mov whitevolume.mgz --reg struct2freesurfer.dat --projdist-max 0 3 0.1 --interp nearest --hemi rh --out ... Is there a way to optimize this? The binarized white matter data (volume) is just below the white matter surface in most cases, sometimes, voxels are also above the surface. If I try trilinear I get values far away from 1 (hence values which are not included in the primary data (=binarized mask). Looking forward to your suggestions. Thank you very much, Best Robert -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

1 0

mri_vol2surf projection of white matter results
by Robert Schulz 03 Sep '13

03 Sep '13

2 1

mri_surf2surf to fsaverageX introduces offset
by Franz Liem 03 Sep '13

03 Sep '13

Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 118611 > num faces : 237218 > num strips : 0 > surface area: 77595.6 > AvgVtxArea 0.654202 > AvgVtxDist 0.885026 > StdVtxDist 0.251941 > ctr : (-33.3535, -11.9536, 42.7693) > vertex locs : surfaceRAS > talairch.xfm: > 1.045 -0.093 -0.014 1.081; > 0.099 1.095 0.070 -4.263; > 0.010 -0.083 1.290 -41.092; > 0.000 0.000 0.000 1.000; > surfaceRAS to talaraiched surfaceRAS: > 1.045 -0.093 -0.014 1.177; > 0.099 1.095 0.070 13.377; > 0.010 -0.083 1.290 -49.756; > 0.000 0.000 0.000 1.000; > talairached surfaceRAS to surfaceRAS: > 0.949 0.081 0.006 -1.900; > -0.085 0.902 -0.050 -14.449; > -0.013 0.058 0.772 37.650; > 0.000 0.000 0.000 1.000; > volume geometry: > extent : (256, 256, 256) > voxel : ( 1.0000, 1.0000, 1.0000) > x_(ras) : (-1.0000, -0.0000, 0.0000) > y_(ras) : (-0.0000, 0.0000, -1.0000) > z_(ras) : ( 0.0000, 1.0000, -0.0000) > c_(ras) : ( 0.0989, 0.9660, 0.9027) > ... mris_info lh.white.ico6 > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 40962 > num faces : 81920 > num strips : 0 > surface area: 75477.4 > AvgVtxArea 1.842620 > AvgVtxDist 1.573724 > StdVtxDist 0.523314 > ctr : (-33.3983, -12.0872, 42.7743) > vertex locs : surfaceRAS > volume geometry info is either not contained or not valid. > ...

3 11

Re: [Freesurfer] apply fnirt transformation on a surface
by Bruce Fischl 03 Sep '13

03 Sep '13

thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > >

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