I've just created a new version of gtmstats2table (attached). This will take a
--volume flag to report the volume of the ROIs instead of the uptake
On 1/6/2021 6:00 PM, Julie Ottoy wrote:
External Email - Use Caution
Thank you Doug!
I have another question related to voxel size.
In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels.
However, is there a way to easily retrieve the volume (instead of NVoxels) for
each ROI within the gtm.stats file? I know that you should rescale by the pet
voxel size; however, I have a multi-site study with all different voxel sizes.
Or is there perhaps a way to apply the "aparcstats2table -meas volume" command
but get the same ROIs outputted as those in the gtm.stats file?
Thank you for the info!
Julie
On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
No, not a problem.
On 12/21/2020 12:52 PM, Julie Ottoy wrote:
External Email - Use Caution
Dear freesurfer team,
I am dealing with PET scans that were acquired at different sites. They do not
have uniform voxel size and dimensions. I was wondering if this would be an
issue for the sGTM and MG PETSurfer-PVC and/or for the "vol2surf --projfrac
0.5" and vertex-wise PET group-analyses. Should I resample to a uniform
voxelsize prior to these steps or does freesurfer take care of this issue
internally?
Thank you for the information.
Best regards
Julie
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#!/bin/tcsh -f
# gtmstats2table - sources
if(-e $FREESURFER_HOME/sources.csh) then
source $FREESURFER_HOME/sources.csh
endif
set VERSION = '$Id$';
set output = ();
set gtmdirlist = ();
set meas = uptake
set inputargs = ($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:
set StartTime = `date`;
set tSecStart = `date '+%s'`;
set year = `date +%Y`
set month = `date +%m`
set day = `date +%d`
set hour = `date +%H`
set min = `date +%M`
set outdir = `dirname $output`
mkdir -p $outdir
pushd $outdir > /dev/null
set outdir = `pwd`;
popd > /dev/null
#========================================================
rm -f $output
set stfile = $gtmdirlist[1]/gtm.stats.dat
set roilist = `cat $stfile | awk '{print $3}'`
echo "GTM $roilist" >> $output
@ nth = 0
foreach gtmdir ($gtmdirlist)
@ nth = $nth + 1
set stfile = $gtmdir/gtm.stats.dat
switch($meas)
case "uptake"
set st = `cat $stfile | awk '{print $7}'`
breaksw
case "voxels"
set st = `cat $stfile | awk '{print $5}'`
breaksw
case "volume"
set st0 = `cat $stfile | awk '{print $5}'`
set mask = $gtmdir/aux/mask.nii.gz
set cmd = (mri_info --voxvol $mask --o /tmp/gtmstats2table.$$.dat)
echo $cmd
$cmd
if($status) exit 1
set voxvol = `cat /tmp/gtmstats2table.$$.dat`
rm -f /tmp/gtmstats2table.$$.dat
set st = ()
foreach m ($st0)
set mst = `echo "$m*$voxvol" | bc -l `
set st = ($st $mst)
end
breaksw
endsw
echo "$nth $st" >> $output
end
#========================================================
# Done
echo "gtmstats2table Done"
exit 0
###############################################
############--------------##################
error_exit:
echo "ERROR:"
exit 1;
###############################################
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "--o":
if($#argv < 1) goto arg1err;
set output = $argv[1]; shift;
breaksw
case "--gtmdir":
case "--g":
if($#argv < 1) goto arg1err;
set gtmdir = $argv[1]; shift;
set gtmdirlist = ($gtmdirlist $gtmdir)
breaksw
case "--f":
if($#argv < 1) goto arg1err;
set gtmdirfile = $argv[1]; shift;
set gtmdirlist = ($gtmdirlist `cat $gtmdirfile`)
breaksw
case "--uptake":
set meas = uptake; # default
breaksw
case "--voxels":
set meas = voxels
breaksw
case "--volume":
set meas = volume
breaksw
case "--debug":
set verbose = 1;
set echo = 1;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#output == 0) then
echo "ERROR: must spec output"
exit 1;
endif
if($#gtmdirlist == 0) then
echo "ERROR: must spec list of gtmdirs"
exit 1;
endif
foreach gtmdir ($gtmdirlist)
set stfile = $gtmdir/gtm.stats.dat
if(! -e $stfile) then
echo "ERROR: cannot find $stfile"
exit 1;
endif
end
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 "gtmstats2table --o outputtable"
echo " --gtmdir gtmdir1 <--gtmdir gtmdir2>"
echo " --f file : file with a list of gtmdirs"
echo " --voxels : report the number of voxels in each ROI instead of uptake"
echo " --volume : report the volume (mm3) each ROI instead of uptake"
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
This script collects the GTM values (7th column) from the gtm.stats
file (output of mri_gtmpvc) and saves them in a white-space separated table
(similar to the output of asegstats2table and aparcstats2table). There
are two ways to specify the set of GTM directories to participate:
(1) provide a list on the command line with multiple --gtmdir options, eg,
--gtmdir cumi001/gtm.psf04 --gtmdir cumi002/gtm.psf04
(2) create a text file file with tall the gtmdirs, eg
echo cumi001/gtm.psf04 cumi002/gtm.psf04 > gtmdirlistfile
--f gtmdirlistfile
The output will be a table where the first row is the list of ROI
names. The subsequent rows will be for each input. The first column
will be the order number of the input (eg, 1, 2, 3, etc).
The output can be treated just like the outputs of asegstats2table and
aparcstats2table, eg,
mri_glmfit --table gtmstatstable --osgm --o glm.gtmstatstable
Alternatively, the number of voxels in each ROI or the volume of each ROI
can be reported by adding --voxels or --volume to the command line.
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