[Freesurfer] Recon-all step estimate
Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ 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.
Re: [Freesurfer] Recon-all step estimate
the recon-all.cmd file I think gets written to the scripts dir with every command that is run Bruce On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ 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.
Re: [Freesurfer] Recon-all step estimate
Hi Pedro, Here's a script that (I think) will do what you're looking for: http://web.mit.edu/mwaskom/stuff/recon_status I hope it's useful Michael 2011/11/8 Bruce Fischl fis...@nmr.mgh.harvard.edu the recon-all.cmd file I think gets written to the scripts dir with every command that is run Bruce On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ 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. ___ 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.
Re: [Freesurfer] Recon-all step estimate
You can look at the touch files in the touch directory. I've attached a
script that I use called rastat that does this. When I was the main
recon-all programmer, each process would create a touch file when it
completed, but I don't know if newer versions continue to do so. You can
also look at recon-all-status.log
doug
Pedro Paulo de Magalhães Oliveira Junior wrote:
Is there any script that I can use to estimate which step recon-all
are in?
My idea is to have a progress indicator for recon-all and this script
would be very useful.
thanks
Pedro Paulo Jr
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--
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
#!/bin/tcsh -f
# rastat - get current status of recon-all processes
set VERSION = '$Id$';
set sd = ();
set subjectlist = ();
set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
foreach subject ($subjectlist)
if(! -e $sd/$subject) then
echo $subject CANNOT FIND
continue;
endif
set ralog = $sd/$subject/scripts/recon-all.log
if(! -e $ralog) then
echo $subject nolog
continue
endif
set d = $sd/$subject/scripts/recon-all.done
if(-e $d) then
set DoneDate = `grep DATE $d | sed 's/DATE //g'`
echo $subject done $DoneDate
continue
endif
set e = $sd/$subject/scripts/recon-all.error
if(-e $e) then
set ErrorDate = `grep DATE $e | sed 's/DATE //g'`
echo $subject error $ErrorDate
continue
endif
set isrs = (IsRunning.lh IsRunning.rh IsRunning.lh+rh)
set IsRunning = 0;
foreach isr0 ($isrs)
set isr = $sd/$subject/scripts/$isr0
if(! -e $isr) continue;
set IsRunning = 1;
set StartDate = `grep DATE $isr | sed 's/DATE //g'`
set Hemis = `grep HEMI $isr | sed 's/HEMI //g' | sed 's/lh rh/lh+rh/'`
set tmp = `ls -lt $sd/$subject/touch/*.touch | head -n 2 | tail -n 1`
#set tmp = `ls -l $subject/scripts/recon-all.env`
#set month = $tmp[6];
#set day = $tmp[7];
#set time = $tmp[8];
set dir = $tmp[9];
set cmd = `basename $dir .touch`
#echo $subject running $month $day $time $cmd
echo $subject running $Hemis $StartDate $cmd
end
if(! $IsRunning) echo $subject notsure
end
exit 0
###
--##
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case -s:
if($#argv 1) goto arg1err;
set subjectlist = ($subjectlist $argv[1]); shift;
while(1 $#argv)
set a = `echo $argv[1] | cut -c 1`
if($a == -) break;
set subjectlist = ($subjectlist $argv[1]); shift;
end
breaksw
case -cwd:
case -pwd:
set sd = `pwd`;
breaksw
case -debug:
set verbose = 1;
set echo = 1;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
--##
--##
check_params:
if($#subjectlist == 0) then
echo ERROR: need subjects
exit 1;
endif
if($#sd == 0) set sd = $SUBJECTS_DIR;
goto check_params_return;
--##
--##
arg1err:
echo ERROR: flag $flag requires one argument
exit 1
--##
--##
usage_exit:
echo
echo rastat
echo
echo
if(! $PrintHelp) exit 1;
echo $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
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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.
