It is trying to use the annotation when making the registration tif.
This is hard coded in your version of make_average_surface. I've
attached a new version. Run it with --no-annot. Let me know if it works
and I'll check it into our distribution
doug
On 10/02/2014 12:00 AM, Reza Rajimehr wrote:
Hi Doug,
Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was
no obvious error for that on the screen. Not sure if this happened because
of not having an annot file for mris_make_template. Here is what I saw on
the screen:
%%%%%%%%%%
/usr/local/freesurfer/bin/make_average_surface
--subjects F99 --out iter00 --template-only --surf-reg sphere
$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $
Wed Oct 1 23:00:55 EDT 2014
/home/reza/structurals
setenv SUBJECTS_DIR /home/reza/structurals/
output ddir is /home/reza/structurals/
uid=1000(reza) gid=1000(reza)
groups=1000(reza),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),108(lpadmin),124(sambashare)
====================
make_average_surface
====================
Wed Oct 1 23:00:56 EDT 2014
/home/reza/structurals
/usr/local/freesurfer/bin/make_average_surface
--subjects F99 --out iter00 --template-only --surf-reg sphere
input subjects: F99
output subject: iter00
mri_add_xform_to_header -c auto
/home/reza/structurals//iter00/mri/mni305.cor.mgz
/home/reza/structurals//iter00/mri/mni305.cor.mgz
INFO: extension is mgz
#@# Making lh registration template ---------
/home/reza/structurals/iter00
mris_make_template -norot -annot aparc lh sphere F99 lh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...
processing subject F99 (1 of 1)
reading spherical surface /home/reza/structurals//F99/surf/lh.sphere...
could not read annot file
/home/reza/structurals//F99/surf/../label/lh.aparc.annot
No such file or directory
mris_make_template: could not read annot file aparc
No such file or directory
ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif
ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif
ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif
%%%%%%%%%%
Reza
Hi Reza, I think that this should work.
doug
set subjectlist = (subject1 subject2 ...)
1. Create a template from a single subject
make_average_surface --subjects $subjectlist[1] \
--out iter00 --template-only --surf-reg sphere.reg
2. Register each subject to this template, including first
subject. Each of these may take 30 min, so, if you have a lot of
subjects, you may want to submit each job to the cluster.
foreach subject ($subjectlist)
# Create subject/surf/iter00.sphere.reg, --no-annot for monkey
surfreg --s $subject --t iter00 --no-annot
end
3. Create a new template from all subjects using the new registration
make_average_surface --subjects $subjectlist \
--out iter01 --template-only --surf-reg iter00.sphere.reg
4. Register each subject to this new template
foreach subject ($subjectlist)
# Create subject/surf/iter01.sphere.reg, --no-annot for monkey
surfreg --s $subject --t iter01 --no-annot
end
5. Return to step 3. Iterate 4 or 5 times to remove the dependence on
the first subject.
When using mri_surf2surf or mris_preproc, spec --surfreg
iterXX.sphere.reg. For mris_preproc also spec --targ iterXX
_______________________________________________
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: 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/
#! /bin/tcsh -f
#
# make_average_surface
#
# Creates average surfaces and curvatures from a set of subjects.
#
# --help option will show usage
#
# Original Author: Doug Greve
# CVS Revision Info:
# $Author: greve $
# $Date: 2012/01/15 22:58:00 $
# $Revision: 1.58 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#
# uncomment this to increase number of allowable open files to maximum:
#limit descriptors unlimited
set VERSION = '$Id: make_average_surface,v 1.58 2012/01/15 22:58:00 greve Exp
$';
setenv FIX_VERTEX_AREA
set PrintHelp = 0;
set UseSymLink = 1;
set sdout = ();
set inputargs = ($argv);
if ( $?SUBJECTS) then
set SUBJECTS=($SUBJECTS)
endif
if ( $?SUBJECTS_DIR) then
set SUBJECTS_DIR=($SUBJECTS_DIR)
endif
set average_subject=average
set sphere_reg=sphere.reg
set transform_fname=""
set XFORM_FLAG=""
set ico_no=7
set DoXHemi = 0;
set topdir = ();
set DoTemplateOnly = 0;
set hemilist = ();
set measlist = (sulc curv thickness area volume inflated.H)
set UseAnnot = 1;
# these should match latest declarations in recon-all
set DESIKAN_GCS = curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
set DESTRIEUX_GCS = destrieux.simple.2009-07-29.gcs
# note: SUBJECTS can be set by --subjects
# SUBJECTS_DIR can be set by --sdir
# average_subject can be set by --out
# sphere_reg can be set by --surf-reg
# transform_fname can be set by --xform (default is no file specified)
# XFORM_FLAG appends -X to transform_fname if --xform is specified
if($#argv == 0) then
# zero args is allowed only if SUBJECTS env var is declared
if ( ! $?SUBJECTS) then
goto usage_exit;
endif
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
# This will put the data under $sdout (SUBJECTS_DIR by default)
set ddir = ${sdout}/${average_subject}
mkdir -p ${ddir} \
${ddir}/surf \
${ddir}/mri \
${ddir}/mri/transforms \
${ddir}/scripts \
${ddir}/label \
${ddir}/stats
cd $sdout/${average_subject}
set LF = ${ddir}/scripts/make_average_surface.log
if(-e $LF) mv $LF $LF.bak
echo "" | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo $0 $inputargs | tee -a $LF
echo "" | tee -a $LF
echo $VERSION | tee -a $LF
date | tee -a $LF
pwd | tee -a $LF
echo "output ddir is $sdout" | tee -a $LF
id | tee -a $LF
set tSecStart = `date '+%s'`;
#
# Begin script guts...
#
echo ==================== | tee -a $LF
echo make_average_surface | tee -a $LF
echo ==================== | tee -a $LF
date | tee -a $LF
pwd | tee -a $LF
echo $0 | tee -a $LF
echo $inputargs | tee -a $LF
echo input subjects: ${SUBJECTS} | tee -a $LF
echo output subject: ${average_subject} | tee -a $LF
# Copy MNI 305 to output mri dir
set mni305 = $FREESURFER_HOME/average/mni305.cor.mgz
if(! -e $mni305) then
echo "ERROR: cannot find $mni305"
exit 1;
endif
cp $mni305 $sdout/${average_subject}/mri
# Set the MNI305 xfm fname to 'auto'
set mnivol = $sdout/${average_subject}/mri/mni305.cor.mgz
set cmd = (mri_add_xform_to_header -c auto $mnivol $mnivol)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Create a file with the list of subjects (will not include xhemi)
set subjlistfile = /tmp/subjlistfile.$$
rm -f $subjlistfile
foreach s ($SUBJECTS)
echo $s >> $subjlistfile
end
cp $subjlistfile list.subjects.txt
set subjlistfile = $SUBJECTS_DIR/$average_subject/list.subjects.txt
# Include cross-hemi registration
if($DoXHemi) then
set tmp = ();
foreach s ($SUBJECTS)
set tmp = ($tmp $s $s/xhemi)
end
set SUBJECTS = ($tmp);
endif
#------------------------------------------------------------
# Make the lh and rh template first so that other jobs can be started
foreach hemi ($hemilist)
echo "" | tee -a $LF
# ------------------------------------------------------------------
echo "#@# Making $hemi registration template ---------" | tee -a $LF
set atlas = $hemi.reg.template.tif
set cmd = (mris_make_template -norot aparc \
$hemi $sphere_reg $SUBJECTS $atlas)
if($UseAnnot) set cmd = ($cmd -annot)
pwd | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit(1);
end
#------------------------------------------------------------
# Now do everything else
foreach hemi ($hemilist)
if($DoTemplateOnly) continue;
echo "" | tee -a $LF
cd $sdout/$average_subject
#--------------------------------------------------------------
foreach s (white pial orig)
echo "#@# Making average $hemi.$s surface ---------------------" | tee -a
$LF
date | tee -a $LF
set cmd = (mris_make_average_surface $XFORM_FLAG \
-i $ico_no -o $s -sdir-out $sdout\
${hemi} \
${s} ${sphere_reg} \
${average_subject} \
$SUBJECTS )
pwd | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) then
echo "mris_average_surface failed" | tee -a $LF
exit 1;
endif
echo "" | tee -a $LF
echo "" | tee -a $LF
end # loop over surfaces
#--------------------------------------------------------------
# Create sphere and sphere.reg
# mris_make_average_surface creates its own sphere.reg,
# so delete it and copy ico
rm -f surf/$hemi.$sphere_reg
if($ico_no == 7) then
# for historical reasons, use ?h.sphere.reg for ico7
set icoreg = ${FREESURFER_HOME}/average/surf/${hemi}.sphere.reg
else
set icoreg = ${FREESURFER_HOME}/average/surf/${hemi}.sphere.ico$ico_no.reg
endif
cp $icoreg surf/$hemi.sphere
# Create a link to sphere.reg (want to do this? or reg to fsaverage?)
if($UseSymLink) then
cd surf
ln -s $hemi.sphere $hemi.sphere.reg
ln -s $hemi.sphere $hemi.$average_subject.sphere.reg
cd ..
else
cp surf/$hemi.sphere surf/$hemi.sphere.reg
cp surf/$hemi.sphere surf/$hemi.$average_subject.sphere.reg
endif
echo "---------------------------------------------------" | tee -a $LF
echo "" | tee -a $LF
#--------------------------------------------------------------
echo "#@# Smoothing, inflating, etc $hemi ----------------" | tee -a $LF
cd $sdout/${average_subject}/surf
pwd | tee -a $LF
# Smooth white to get smoothwm (should average the indiv smoothwms?)
set cmd = (mris_smooth -nw -n 5 ./${hemi}.white ./${hemi}.smoothwm)
echo $cmd |& tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
echo "" | tee -a $LF
# Inflate the smoothwm
set niters = "-n 15";
if($ico_no <= 5) set niters = "-n 2";
set cmd = (mris_inflate -dist .01 -f .001 -no-save-sulc $niters
./${hemi}.smoothwm ./${hemi}.inflated)
echo $cmd |& tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
echo "" | tee -a $LF
cd $sdout/$average_subject
# Create average annot
foreach annot (aparc aparc.a2009s)
set cmd = (annot2std --o label/$hemi.$annot.annot --$hemi \
--f $subjlistfile --t $average_subject --a $annot \
--srcsurfreg $sphere_reg --trgsurfreg sphere.reg)
if($DoXHemi) set cmd = ($cmd --xhemi)
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1
end
# Create cortex label from Christophe's medial wall
set annot = $ddir/label/$hemi.aparc.a2009s.annot
if(! -e $annot) then
echo "ERROR: cannto find $annot" |& tee -a $LF
exit 1;
endif
# Create tmpdir
set tmpdir = $ddir/make_cortex_label.tmp.$$
rm -rf $tmpdir
mkdir -p $tmpdir
# Unload all of Christophe's labels into tmpdir
set cmd = (mri_annotation2label --subject $average_subject \
--hemi $hemi --outdir $tmpdir --annotation aparc.a2009s)
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
set MW = $tmpdir/$hemi.Unknown.label
if(! -e $MW) set MW = $tmpdir/$hemi.Medial_wall.label
if(! -e $MW) then
echo "ERROR: cannot find $hemi.Unknown.label or $hemi.Medial_wall.label"
exit 1;
endif
mv $MW $ddir/label/$hemi.Medial_wall.label # Move medial wall out of dir
# Create the cortex label with all the remaining labels
set ctxlabel = $ddir/label/$hemi.cortex.label
set cmd = (mri_mergelabels -o $ctxlabel -d $tmpdir)
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
rm -rf $tmpdir; # Cleanup
# Create average surface measures
foreach meas ($measlist)
set measout = $ddir/surf/stack.$hemi.$meas.mgh
set cmd = (mris_preproc --out $measout --f $subjlistfile \
--target $average_subject --hemi $hemi --meas $meas \
--srcsurfreg $sphere_reg --log $ddir/scripts/mris_preproc.$hemi.$meas.log)
if($DoXHemi) set cmd = ($cmd --xhemi)
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1
# Compute average across subject
set avgmeas = $ddir/surf/$hemi.$meas.avg.mgh
if($meas == area) set avgmeas = $ddir/surf/$hemi.white.avg.area.mgh; #
backcompat
set cmd = (mri_concat $measout --mean --o $avgmeas)
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1
# Compute std across subject
set stdmeas = $ddir/surf/std.$hemi.$meas.mgh
set cmd = (mri_concat $measout --std --o $stdmeas)
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1
# Convert avg to curv
set tval = $ddir/surf/$hemi.$meas
set cmd = (mri_surf2surf --sval $avgmeas --s $average_subject \
--tval $tval --trg_type curv --hemi $hemi)
pwd | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1
# Delete temporary stuff
if($meas != area) rm $avgmeas
end # meas
end # hemi
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 "make_average_surface-Run-Time-Hours $tRunHours" |& tee -a $LF
date | tee -a $LF
echo "make_average_surface done" | tee -a $LF
echo ""
exit 0
###############################################
############--------------##################
parse_args:
set cmdline = ($argv);
set getting_subjects = 0;
while( $#argv != 0 )
set flag = $argv[1];
if (! $getting_subjects) then
shift;
endif
switch($flag)
case "--help":
set PrintHelp = 1;
goto usage_exit;
exit 0;
case "--version":
echo $VERSION
exit 0;
case "--s":
case "--subjects":
if ( $#argv == 0) goto arg1moreerr;
set SUBJECTS = $argv[1]; shift;
# loop on getting variable number of subject names
set getting_subjects = 1; # see 'default:' case
breaksw
case "--fsgd":
if ( $#argv == 0) goto arg1err;
set fsgdf = $argv[1]; shift;
if(! -e $fsgdf) then
echo "ERROR: cannot find $fsgdf";
exit 1;
endif
set sl = `cat $fsgdf | awk '{if($1 == "Input") print $2}'`;
set SUBJECTS = ($sl);
breaksw
case "--out":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if ( $#argv == 0) goto arg1err;
set average_subject = $argv[1]; shift;
breaksw
case "--surfreg":
case "--surf-reg":
case "--surf_reg":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if ( $#argv == 0) goto arg1err;
set sphere_reg = $argv[1]; shift;
breaksw
case "--topdir":
case "--sd-out":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if( $#argv < 1) goto arg1err;
set sdout = $argv[1]; shift;
breaksw
case "--sd":
case "--sdir":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if ( $#argv == 0) goto arg1err;
set SUBJECTS_DIR = $argv[1]; shift;
setenv SUBJECTS_DIR $SUBJECTS_DIR
breaksw
case "--xform":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if ( $#argv == 0) goto arg1err;
set transform_fname = $argv[1]; shift;
set XFORM_FLAG = "-X $transform_fname";
breaksw
case "--ico":
case "--i":
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if ( $#argv == 0) goto arg1err;
set ico_no = $argv[1]; shift;
breaksw
case "--meas"
if ( $getting_subjects ) then
# got em all, from --subjects variable arg loop
set getting_subjects = 0;
shift;
endif
if($#argv < 1) goto arg1err;
set measlist = ($measlist $argv[1]); shift;
breaksw
case "--symlink":
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
set UseSymLink = 1;
breaksw
case "--no-annot":
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
set UseAnnot = 0;
breaksw
case "--no-symlink":
case "--no-link":
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
set UseSymLink = 0;
breaksw
case "--nocleanup":
# This has no effect, but needed for compat with make_average_volume
set cleanup = 0;
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--debug":
case "--echo":
set echo = 1;
set verbose = 1;
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--template-only":
set DoTemplateOnly = 1;
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--xhemi":
set DoXHemi = 1;
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--lh":
set hemilist = (lh)
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--rh":
set hemilist = (rh)
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--lhrh":
set hemilist = (lh rh)
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
case "--no-xhemi":
set DoXHemi = 0;
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
# These are flags passed to make_average_subject, but dont apply here
case "--no-surf":
case "--no-vol":
case "--force":
case "--link":
case "--keep-all-orig":
if ( $getting_subjects ) then
set getting_subjects = 0;
# got em all, from --subjects variable arg loop
endif
breaksw
default:
if ( $getting_subjects ) then
# loop on getting variable number of subjects,
# until a new flag is found, or no more args
set SUBJECTS = ( $SUBJECTS $argv[1] ); shift;
set getting_subjects = 1;
else
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
endif
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if (! $?SUBJECTS) then
echo "ERROR: no subjects declared!"
echo "Either declare subjects in SUBJECTS variable,"
echo "or declare using --subjects argument."
exit 1
endif
if (! $?SUBJECTS_DIR) then
echo "ERROR: SUBJECTS_DIR is not declared!"
echo "Either set the SUBJECTS_DIR environment variable,"
echo "or declare using --sdir argument, the root directory"
echo "for subject data files."
exit 1
endif
if(! -e $SUBJECTS_DIR ) then
echo "ERROR: SUBJECTS_DIR $SUBJECTS_DIR does not exist."
exit 1;
endif
if(! $?FREESURFER_HOME ) then
echo "ERROR: environment variable FREESURFER_HOME not set."
exit 1;
endif
if(! -e $FREESURFER_HOME ) then
echo "ERROR: FREESURFER_HOME $FREESURFER_HOME does not exist."
exit 1;
endif
if($#sdout == 0) set sdout = $SUBJECTS_DIR;
if($#hemilist == 0) set hemilist = (lh rh)
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
arg1moreerr:
echo "ERROR: flag $flag requires one or more arguments"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "USAGE: make_average_surface"
echo ""
echo "Required Arguments"
echo " --subjects <subj1> <subj2> ... <subjN>"
echo " : or declare subjects in SUBJECTS env var"
echo " --fsgd fsgdfile : get subject list from fsgd"
echo ""
echo "Optional Arguments"
echo " --out <average subject name> : default name is 'average'"
echo " --sdir <SUBJECTS_DIR to use instead of the one in the env>"
echo " --sd : same as --sdir"
echo " --sd-out topdir : put data here"
echo " --xform <transform_fname> : filename of transform file"
echo " --ico <number> : specify icosahedron number, default is 7 (ic7.tri)"
echo " --surf-reg <surface name> : alternative registration surface"
echo " --lh : only do left hemi (default is to do both)"
echo " --rh : only do right hemi (default is to do both)"
echo " default: sphere.reg"
echo " --force : overwrite existing average subject data"
echo " --no-annot : do not use annotation when making template tif"
echo " --template-only : useful when creating iterative atlases"
echo ""
echo " --help : short descriptive help"
echo " --no-symlink : do not use symbolic links (just copy files)"
echo " --no-lik : same as --no-symlink"
echo " --version : script version info"
echo " --echo : enable command echo, for debug"
echo " --debug : same as --echo"
echo ""
echo "See also: recon-all, make_final_surfaces, morph_subject"
echo ""
if(! $PrintHelp) exit 1;
echo Version: $VERSION
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
Creates average surfaces and curvatures from a set of subjects.
Calls mris_average_curvature, mris_make_average_surface, mris_smooth,
mris_inflate, and mris_curvature.
EXAMPLE
make_average_surface --out avgsubject --subjects subj1 subj2 subj3 subj4
will create $SUBJECTS_DIR/avgsubject with average surfaces for orig,
white, pial, inflated for each hemi.
SEE ALSO
make_average_subject, make_average_volume
GETTING HELP
Run recon-all --help for extensive text on the reconstruction process.
Or, send email to freesurfer@nmr.mgh.harvard.edu.
Also see http://surfer.nmr.mgh.harvard.edu.
_______________________________________________
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.
