Hi Alice, I would check out whether autocorrection of the defects in
that area were done properly. You create a segmentation of the defects
with defect-seg. It might not be in 5.0, so I've attached it. It might
not work properly in 5.0. If so, you'll have to download 5.2 (you can
have two different versions at the same time, just make sure to only run
defect-seg from 5.2).
doug
On 03/17/2013 09:16 PM, Alice Burnett wrote:
Hi FreeSurfer experts,
I have been working with a dataset we have run through FreeSurfer 5.0
and am interested in the medial orbitofrontal region (Desikan atlas).
We have an unexpected surface area finding, so we want to rule out any
systematic error in the generation of the area measurements. We
followed the wiki instructions for processing and checked and edited
all images as necessary, so the pial and white surface placement looks
OK. I'm wondering, would you have any particular recommendations for
QA checking the mOFC or things we should be looking out for?
Thanks so much!
Alice
This e-mail and any attachments to it (the "Communication") are,
unless otherwise stated, confidential, may contain copyright material
and is for the use only of the intended recipient. If you receive the
Communication in error, please notify the sender immediately by return
e-mail, delete the Communication and the return e-mail, and do not
read, copy, retransmit or otherwise deal with it. Any views expressed
in the Communication are those of the individual sender only, unless
expressly stated to be those of Murdoch Childrens Research Institute
(MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does
not accept liability in connection with the integrity of or errors in
the Communication, computer virus, data corruption, interference or
delay arising from or in respect of the Communication.
P Please consider the environment before printing this email
______________________________________________________________________
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
______________________________________________________________________
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
#!/bin/csh -f
# defect-seg
# Creates segmentations and annotations for defect visualization
set VERSION = '$Id: defect-seg,v 1.5 2012/12/10 21:17:00 greve Exp $';
set subject = ();
set PrintHelp = 0;
set DoLH = 1;
set DoRH = 1;
set DoMapToFsaverage = 0;
set cmdargs = ($argv);
if($#argv == 0) goto usage_exit;
set n = `echo $argv | egrep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
set n = `echo $argv | egrep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
set StartTime = `date`;
set tSecStart = `date '+%s'`;
cd $SUBJECTS_DIR/$subject
set LF = $SUBJECTS_DIR/$subject/scripts/defect-seg.log
if(-e $LF) mv $LF $LF.bak
echo "Logfile is $LF"
echo $0 | tee -a $LF
echo $cmdargs | tee -a $LF
echo $VERSION | tee -a $LF
date | tee -a $LF
uname -a | tee -a $LF
pwd | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR "| tee -a $LF
#-----------------------------------------
set HemiList = ();
if($DoLH) set HemiList = ($HemiList lh);
if($DoRH) set HemiList = ($HemiList rh);
foreach hemi ($HemiList)
# Create a text summary of the defects
set tmpsum = /tmp/defect-seg.$$.$hemi.sum
set cmd = (mri_surfcluster \
--in surf/$hemi.defect_labels --thmin .5 --hemi $hemi \
--surf orig.nofix --subject $subject --sum $tmpsum)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
set sum = scripts/$hemi.defect.summary
rm -f $sum
echo "# List of defects corrected by automatic topology fixer" >> $sum
echo "# $VERSION" >> $sum
echo "# subject $subject" >> $sum
echo "# hemi $hemi" >> $sum
echo "# $SUBJECTS_DIR" >> $sum
echo "# DefectNo Vertex NVertices" >> $sum
grep -v \# $tmpsum | awk '{print sprintf(" %3d \t %8d \t %4d",$1,$3,$8)}'
>> $sum
# Create a volume segmentation of the defects
# Load with $FREESURFER_HOME/DefectLUT.txt
set cmd = (mri_surf2vol --identity $subject --surf orig.nofix \
--template mri/orig.mgz --surfval surf/$hemi.defect_labels \
--hemi $hemi --o mri/surface.defects.mgz)
if($hemi == lh) set cmd = ($cmd --add 1000)
if($hemi == rh) then
set cmd = ($cmd --add 2000)
if($DoLH && $DoRH) set cmd = ($cmd --merge mri/surface.defects.mgz)
endif
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Create an annotation on the nofix (unfixed) surface
set cmd = (mris_seg2annot --seg surf/$hemi.defect_labels \
--ctab $DefectLUT --s $subject --h $hemi \
--o $hemi.defects.nofix.annot --surf orig.nofix)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Map the defect labels to the fixed surface
set cmd = (mri_surf2surf --s $subject --sval surf/$hemi.defect_labels \
--tval surf/$hemi.defect_labels.fix.mgz --hemi $hemi \
--srcsurfreg orig.nofix --trgsurfreg orig --mapmethod nnf)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Binarize
set cmd = (mri_binarize --i surf/$hemi.defect_labels.fix.mgz \
--o surf/$hemi.defect_labels.fix.bin.mgz --min 0.5)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Create an annotation on the fixed surface
set cmd = (mris_seg2annot --seg surf/$hemi.defect_labels.fix.mgz \
--ctab $DefectLUT --s $subject --h $hemi \
--o $hemi.defects.fix.annot)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Measure defect statistics
set cmd = (mri_segstats --annot $subject $hemi defects.fix \
--i $SUBJECTS_DIR/$subject/surf/$hemi.thickness \
--sum $SUBJECTS_DIR/$subject/stats/$hemi.defect.stats --excludeid 0)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
# Map to fsaverage space
if($DoMapToFsaverage) then
set cmd = (mri_surf2surf --hemi $hemi\
--srcsubject $subject \
--sval surf/$hemi.defect_labels.fix.mgz \
--trgsubject fsaverage \
--sval surf/$hemi.defect_labels.fix.fsaverage.mgz )
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1
endif
end
#-----------------------------------------
echo "" | tee -a $LF
echo "" | tee -a $LF
set tSecEnd = `date '+%s'`;
@ tSecRun = $tSecEnd - $tSecStart;
set tRunHours = `echo $tSecRun/3600|bc -l`
set tRunHours = `printf %5.2f $tRunHours`
echo "Started at $StartTime " |& tee -a $LF
echo "Ended at `date`" |& tee -a $LF
echo "defect-seg-Run-Time-Sec $tSecRun" |& tee -a $LF
date | tee -a $LF
echo "defect-seg done" | tee -a $LF
exit 0
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "--s":
if ( $#argv < 1) goto arg1err;
set subject = $argv[1]; shift;
breaksw
case "--lh-only":
set DoLH = 1;
set DoRH = 0;
breaksw
case "--rh-only":
set DoLH = 0;
set DoRH = 1;
breaksw
case "--fsaverage":
set DoMapToFsaverage = 1;
breaksw
case "--debug":
set verbose = 1;
set echo = 1;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#subject == 0) then
echo "ERROR: must spec a subject id"
exit 1;
endif
if(! -e $SUBJECTS_DIR/$subject) then
echo "ERROR: cannot find $subject"
exit 1;
endif
set DefectLUT = $FREESURFER_HOME/DefectLUT.txt
if(! -e $DefectLUT) then
echo "ERROR: cannot find $DefectLUT"
exit 1;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
arg2err:
echo "ERROR: flag $flag requires two arguments"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "defect-seg"
echo " --s subject"
echo " --lh-only"
echo " --rh-only"
echo ""
echo " --version : print version and exit"
echo " --help : print help and exit"
echo ""
if($PrintHelp) \
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;
#---- Everything below here is printed out as part of help -----#
BEGINHELP
This program creates some files that allows the user to visualize
and evaluate the surface defects that were automatically detected
and fixed by the topology correction program.
Creates:
scripts/?h.defects.summary
mri/surface.defects.mgz
surf/?h.defect_labels.fix.mgz
surf/?h.defect_labels.fix.bin.mgz
label/?h.defects.nofix.annot
label/?h.defects.fix.annot
stats/?h.defects.stats
# ----------------------------------------------------------
# List of defects, their numberic ID, and number of vertices,
# something like below
less scripts/lh.defects.summary
# List of defects corrected by automatic topology fixer
# subject 001_2
# hemi lh
# /space/sleep/2/users/cephalon/subjects/
# DefectNo Vertex NVertices
1 133379 36
2 130681 32
3 125634 65
# ----------------------------------------------------------
# See summary of defects:
less stats/lh.defects.stats
# This gives the area and average thickness over all defects
# asegstats2table can be run on this file to get a table
# of defects for multiple subjects
# asegstats2table --stats=lh.defect.stats -t group.lh.defect.dat ...
# Note: the output will say that it is "volume" but it is
# really "Area_2mm", ie, area in square mm
# ----------------------------------------------------------
# Visualize defects as a segmentation with left hemi surfaces
tkmedit subject orig.mgz -lh-defects
# The lh.orig.nofix is yellow
# The lh.white is green (aux surface)
# Defects show up as purple segmentations
# (defect number in segmentation name)
# wm.mgz automatically loaded as aux volume
# Visualize defects as a segmentation with right hemi surfaces
tkmedit subject orig.mgz -rh-defects
# ----------------------------------------------------------
# Visualize defects as an annotation
tksurfer 001_1 lh smoothwm.nofix -annot defects.nofix.annot
tksurfer 001_1 lh white -annot defects.fix.annot
# Defects show up as purple annotation
# (defect number in segmentation name)
# ----------------------------------------------------------
# Analyze defects across subjects
mris_preproc --out lh.defects.mgh --target fsaverage --hemi lh \
--meas defect_labels.fix.bin.mgz --fsgd your.fsgd
mri_glmfit --y lh.defects.mgh --surf fsaverage lh --no-prune \
--glmdir glm.lh.sm05 --fwhm 5 --fsgd your.fsgd
tksurfer fsaverage lh inflated -annot aparc.annot \
-ov glm.lh.sm05/osgm/sig.mgh -t lh.defects.mgh
_______________________________________________
Freesurfer mailing list
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.
