Hi
I have looked at QAtools at
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools.
But there seem to be some trouble. I have fixed up the wrong file issue
but there is problem with my files being in the wrong order. Should I
try to reorder the files to reflect the new situation or is there
something wrong with my processing of recon-all.
Knut J
mri/transforms/talairach.xfm mri/rawavg.mgz
mri/rawavg.mgz mri/orig.mgz
mri/orig.mgz mri/nu.mgz
mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm
mri/nu.mgz mri/transforms/talairach.xfm
.......... .........
.......... .........
.......... .........
14 outputfiles_NOTOK
#!/bin/csh -ef
# original by Vasanth Pappu
set subjects = ();
set Details = 0;
set missing_outputfiles = 0;
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
# ---
echo "In output_file_checker"
if ($Details) echo "SUBJECTS_DIR is $SUBJECTS_DIR "
if ($Details) echo ""
#sleep 2;
foreach s ($subjects)
pushd $SUBJECTS_DIR/$s > /dev/null
# first find out the number of 0??.mgz files
#set zerozeroMGZfiles = `ls -1rt mri/orig/0??.mgz`
set zerozeroMGZfiles = `ls -1rt $SUBJECTS_DIR/$s/mri/orig/* | egrep
"0[0-9][0-9].mgz"`
# then attach rest of files
set files69 = (mri/rawavg.mgz mri/orig.mgz mri/nu.mgz
mri/transforms/talairach.auto.xfm mri/transforms/talairach.xfm mri/T1.mgz
mri/brainmask.auto.mgz mri/brainmask.mgz mri/transforms/talairach.lta
mri/norm.mgz mri/transforms/talairach.m3z
mri/transforms/talairach.m3z.inv.x.mgz mri/transforms/talairach.m3z.inv.y.mgz
mri/transforms/talairach.m3z.inv.z.mgz mri/nu_noneck.mgz
mri/transforms/talairach_with_skull.lta mri/aseg.auto.mgz mri/aseg.mgz
stats/aseg.stats mri/brain.mgz mri/brain.finalsurfs.mgz mri/wm.seg.mgz
mri/wm.asegedit.mgz mri/wm.mgz mri/filled.mgz scripts/ponscc.cut.log
surf/lh.orig.nofix surf/lh.smoothwm.nofix surf/lh.inflated.nofix
surf/lh.qsphere.nofix surf/lh.orig surf/lh.white surf/lh.curv surf/lh.area
surf/lh.pial surf/lh.thickness surf/lh.smoothwm surf/lh.sulc surf/lh.inflated
mri/lh.ribbon.mgz surf/lh.sphere surf/lh.sphere.reg surf/rh.sphere.reg
surf/lh.avg_curv label/lh.aparc.annot stats/lh.aparc.stats
label/lh.aparc.a2009s.annot surf/rh.orig.nofix surf/rh.smoothwm.nofix
surf/rh.inflated.nofix surf/rh.qsphere.nofix surf/rh.orig surf/rh.white
surf/rh.curv surf/rh.area surf/rh.pial surf/rh.thickness surf/rh.smoothwm
surf/rh.sulc surf/rh.inflated mri/rh.ribbon.mgz surf/rh.sphere
surf/rh.sphere.reg surf/rh.avg_curv label/rh.aparc.annot stats/rh.aparc.stats
label/rh.aparc.a2009s.annot mri/aparc+aseg.mgz)
# original output_file_order_file:
/space/boba/1/users/nrecon/scripts//output_file_order_file1
#set output_file_order_file =
/space/boba/1/users/nrecon/scripts/output_file_order_file1
echo "checking if output file order file is set..."
if( $?output_file_order_file ) then
set files_in_order = (`cat $output_file_order_file`);
else
echo "output_file_order_file not specified, using default order"
set files_in_order = (`echo $files69`)
endif
set files70plus = "${zerozeroMGZfiles} $files_in_order"
if ($Details) echo "checking these files: "
if ($Details) echo "${files70plus}"
# list the files/check to see all files exist
# check to see if all files exist
echo "check to see if all files exist..."
set commonOrder = ($files70plus)
foreach f ($commonOrder)
if (! -e $f) then
echo "$s missing output files"
if ($Details) echo "$s has no $f"
set missing_outputfiles = 1;
goto theend;
endif
end
set realOrder = `ls -1rt $files70plus`
# check if both lists are same size
if ($#realOrder == $#commonOrder) then
if ($Details) echo "found $#realOrder files ..."
else
echo "ERROR: some files are missing."
exit 1;
endif
# check list against common order
set ok = 1;
set x = 1;
set nextx = 2;
@ realOrder_plus1 = $#realOrder + 1;
if ($Details) echo "realOrder_plus1 is $realOrder_plus1"
#foreach x (`seq 1 $#realOrder`)
while ($x < $realOrder_plus1)
#if ($Details) echo "x is $x"
#sleep 1;
#echo "looking at commonOrder[$x] is $commonOrder[$x]"
if ($realOrder[$x] == $commonOrder[$x]) then
if ($Details) echo "$realOrder[$x] last modified `stat -c %y
$realOrder[$x]`"
@ x = $x + 1; @ nextx = $nextx + 1;
continue;
# some exceptions (files that are generated in the same step that may have
very close date stamps)
else if ($commonOrder[$x] == "mri/filled.mgz" && $realOrder[$x] ==
"scripts/ponscc.cut.log" && $commonOrder[$nextx] == "scripts/ponscc.cut.log" &&
$realOrder[$nextx] == "mri/filled.mgz") then
if ($Details) echo "$realOrder[$x] last modified `stat -c %y
$realOrder[$x]`"
if ($Details) echo "$realOrder[$nextx] last modified `stat -c %y
$realOrder[$nextx]`"
@ x = $x + 2; @ nextx = $nextx + 2;
continue;
else
if ($Details) echo "ERROR: order is not commmon order: stopped at
$realOrder[$x], should be $commonOrder[$x] ..."
@ a = $x - 2;
@ z = $x + 4;
if ($Details) echo "real order: common order:"
if ($Details) echo ".......... ........."
if ($Details) echo ".......... ........."
if ($Details) echo ".......... ........."
foreach az (`seq $a $z`)
if ($Details) echo "$realOrder[$az] $commonOrder[$az]"
end
if ($Details) echo ".......... ........."
if ($Details) echo ".......... ........."
if ($Details) echo ".......... ........."
set ok = 0;
break;
endif
@ x = $x + 1; @ nextx = $nextx + 1;
end
if ($ok) then
if ($Details) echo ""
if ($Details) echo "real file order agrees with common file order"
echo "$s outputfiles_OK"
else
echo "$s outputfiles_NOTOK"
endif
theend:
popd > /dev/null
end
exit 0;
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "-s":
case "-subjid":
if ( $#argv == 0) goto arg1err;
set proceed = 1;
while ( $#argv != 0 && $proceed )
set subjects = ($subjects $argv[1]); shift;
if ( $#argv != 0 ) then
set proceed = `echo "$argv[1]" | gawk '{ if (substr($1, 1, 1)
== "-") {print "0"} else {print "1"} }'`;
endif
end
breaksw
case "-sf":
if ( $#argv == 0) goto arg1err;
set subjects = `cat $argv[1]`; shift;
breaksw
case "-outputfileorderfile"
set output_file_order_file = $argv[1]; shift;
breaksw
case "-details":
set Details = 1;
breaksw
case "-summary":
set Details = 0;
breaksw
# ----
default:
echo ERROR: Flag $flag unlegal.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#subjects == 0) then
echo "USAGE ERROR: must specify a subjid"
exit 1;
endif
goto check_params_return;
############--------------##################
##############--------------##################
##############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
##############--------------##################
##############--------------##################
##############--------------##################
##############--------------##################
usage_err:
echo "USAGE: flags:"
echo " "
echo "-s"
echo "-subjid"
echo "-sf"
echo " a file of a list of subjects"
echo "-outputfileorderfile"
echo " the file which has the order of the output files"
echo "-details"
echo "-summary"
exit 1
##############--------------##################
##############--------------##################
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