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Commit 47af6b0f authored by Matthew Webster's avatar Matthew Webster
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This commit was manufactured by cvs2svn to create tag 'FinalFive'. 

Sprout from master 2018-06-07 15:04:24 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'remove unnecessary ext'
Delete:
    eddy_correct
    regscript
    remove_vols
parent 835c7815
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eddy_correct deleted 100755 → 0
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View file @ 835c7815
#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
Usage() {
echo ""
echo "Usage: eddy_correct <4dinput> <4doutput> <reference_no>"
echo ""
exit 1
}
[ "$3" = "" ] && Usage
input=`${FSLDIR}/bin/remove_ext ${1}`
output=`${FSLDIR}/bin/remove_ext ${2}`
ref=${3}
if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
echo "Input does not exist or is not in a supported format"
exit 1
fi
avwroi $input $output $ref 1
avwsplit $input
full_list=`${FSLDIR}/bin/imglob -oneperimage vol*`
for i in $full_list ; do
echo processing $i
echo processing $i >> ${output}.ecclog
${FSLDIR}/bin/flirt -in $i -ref $output -nosearch -o $i -paddingsize 1 >> ${output}.ecclog
done
avwmerge -t $output $full_list
/bin/rm vol*
regscript deleted 100755 → 0
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View file @ 835c7815
#!/bin/sh
# preprocessing for DTI images acquired at FMRIB
####################################################################
#This script performs registration of all the volumes
#in a given dti dataset to a reference non-diffusion-weighted image
#(scaling, translation along the PE direction and shearing)
#Brain Extraction is also performed
#with a fractional intensity treshold of 0.025
####################################################################
Usage() {
echo "REGSCRIPT - Preprocessing for DTI images acquired at FMRIB "
echo ""
echo "USAGE: regscript <username> <study_number> <output_dir> [number_acqs] [type_of_correction] [series_numb_dti] [zero_pad] [study_dir]"
echo ""
echo "default number_acqs is 1"
echo ""
echo "The FID files should normally be in"
echo " ~username/scratch/MRdata/study_number/"
echo ""
echo "type_of_correction (optional):"
echo " mc - correct for eddy currents and motion (default)"
echo " bvecs will only be rotated if number_acqs is 1"
echo " as the amount of rotation corresponding to a given"
echo " volume for different acquisitions would not be the same"
echo " and it wouldn't be possible to simply average the data"
echo " ed - correct only for eddy currents (3 degrees of freedom)"
echo ""
echo "series_numb_dti (optional)- default is 2"
echo " e.g. series_2.1 - non-DW image (nodif)"
echo " series_2.2 - DTI (acquisition 1)"
echo " series_2.3 - DTI (acquisition 2) ..."
echo ""
echo "zero_pad (optional) - default is off"
echo " set it on to run load_varian"
echo " with the option -hkspad "
echo " you might wish to try this if the"
echo " half k-space reconstruction has failed"
echo ""
echo "Indicate study_dir if the files are in a different directory"
echo ""
echo "OUTPUTS"
echo "-----------------------------------------------------------------------"
echo " non-DWI: nodif"
echo " DTI after registration: data (if number_acqs equal to 1)"
echo " data1, data2... (several repetitions)"
echo " Brain mask: nodif_brain_mask"
echo " T1-structural (optional - only if series_numb_dti is 2): struct"
echo " T2-structural (optional - only if series_numb_dti is 2): T2-weighted"
echo " Diffusion directions: bvals and bvecs"
echo ""
exit 1
}
#===================================================================
correct_bvs() {
#===================================================================
# Arg_1 = fid directory - to read procpar file
fid_dir=$1
matlab -nodisplay -nojvm -nosplash 1> matlab.out1 2>&1 <<EOF
addpath('/usr/people/dtiuser/etc/FMRIB_bvals_bvecs/');
rotate_bvecs($number_acqs,$n_vols,'$fid_dir');
exit
EOF
rm matlab.out1 -f;
}
#===================================================================
[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ "$3" = "" ] && Usage
username=$1
study_number=$2
output_dir=`pwd`/$3
if [ $# -ge 4 ]; then
number_acqs=$4
echo Assuming number_acqs is $number_acqs
else
number_acqs=1;
echo Assuming number_acqs is 1
fi
if [ $# -ge 5 ]; then
type_cor=$5
else
type_cor='mc'
fi
if [ $# -ge 6 ]; then
series_numb=$6
echo series_numb_dti is $series_numb
else
series_numb=2;
echo series_numb_dti is $series_numb
fi
option='-hks'
if [ $# -ge 7 ]; then
check=$7
check_option=`echo $check`
case $check_option
in
on) option='-hkspad';;
off) option='-hks';;
*) option='-hks';;
esac
fi
echo load_varian will run with option $option
if [ $# -ge 8 ]; then
study_dir=$8
else
study_dir=/usr/people/${username}/scratch/MRdata
fi
nodiffid=${study_dir}/${study_number}/series_${series_numb}.1
dtifid=${study_dir}/${study_number}/series_${series_numb}.
structfid=${study_dir}/${study_number}/series_3.1
T2fid=${study_dir}/${study_number}/series_4.1
if [ ! -e $output_dir ]; then
mkdir $output_dir
fi
cd $output_dir
echo output_dir is $output_dir
cp ~dtiuser/etc/dof3 .
#Load FID files
if [ -e ${nodiffid}.fid ]; then
echo Loading nodif
load_varian $nodiffid $output_dir/nodif -auto -float -buo $option
else
echo $nodiffid.fid: FID not found
exit;
fi
nvols_nodif=`fslval $output_dir/nodif dim4`
if [ $nvols_nodif -gt 1 ]; then
echo nodif has more than 1 volume - file name will be changed to data
echo first volume will be saved as nodif
immv nodif dti1
fslroi dti1 nodif 0 1
count=1
image_numb=2
scan_numb=2
else
count=0
image_numb=1
scan_numb=2
fi
while [ $count -lt $number_acqs ]; do
if [ -e ${dtifid}${scan_numb}.fid ]; then
echo Loading dti${image_numb}
load_varian ${dtifid}${scan_numb}.fid ${output_dir}/dti${image_numb} -auto -float -buo -egrv $option
else
echo ${dtifid}${image_numb}.fid: file not found
exit;
fi
count=`expr $count + 1`;
image_numb=`expr $image_numb + 1`;
scan_numb=`expr $scan_numb + 1`;
done
scan_numb=`expr $scan_numb - 1`;
if [ $series_numb -eq 2 ]; then
if [ -e ${structfid}.fid ]; then
echo Loading structural
load_varian ${structfid} ${output_dir}/struct -auto -float
fi
if [ -e ${T2fid}.fid ]; then
echo Loading T2-weighted
load_varian $T2fid ${output_dir}/T2_weighted -auto -float
fi
fi
#Registers each volume in dti to the reference image nodif
nvols=`fslval dti1 dim4`;
echo $nvols gradient directions
count_acqs=0
#checking if the # of slices is the same
ns_nodif=`fslval nodif dim3`;
ns_dti=`fslval dti1 dim3`;
if [ $ns_nodif != $ns_dti ]; then
rm nodif* -f
dim1=`fslval dti1 dim1`;
dim2=`fslval dti1 dim2`;
fslroi dti1 nodif 0 $dim1 0 $dim2 0 $ns_dti 0 1
fi
correc=`echo $type_cor`;
case $correc
in
mc) echo Correcting for eddy currents and motion
if [ ! -e matrices ]; then
mkdir matrices
fi
while [ $count_acqs -lt $number_acqs ]; do
tmp_acqs=`expr $count_acqs + 1`;
fslsplit dti${tmp_acqs}
if [ $nvols -lt 9 ]; then
count=0
while [ ${count} != ${nvols} ];do
echo FLIRT on volume ${count}
flirt -in vol000$count -ref nodif -out rvol000$count -nosearch -omat matrices/mat
avscale matrices/mat vol000$count >matrices/tmp
head -n 4 matrices/tmp | tail -n 3 > matrices/MAT000${count}${tmp_acqs}
count=`expr $count + 1`;
done
else
count=0
while [ $count != 10 ];do
echo FLIRT on volume ${count}
flirt -in vol000$count -ref nodif -out rvol000$count -nosearch -omat matrices/mat
avscale matrices/mat vol000$count >matrices/tmp
head -n 4 matrices/tmp | tail -n 3 > matrices/MAT000${count}${tmp_acqs}
imrm vol000${count}
count=`expr $count + 1`;
done
while [ ${count} != ${nvols} ];do
echo FLIRT on volume ${count}
flirt -in vol00${count} -ref nodif -out rvol00${count} -nosearch -omat matrices/mat
avscale matrices/mat vol00$count >matrices/tmp
head -n 4 matrices/tmp | tail -n 3 > matrices/MAT00${count}${tmp_acqs}
rm -f matrices/mat
rm -f matrices/tmp
imrm vol000${count}
count=`expr $count + 1`;
done
fi
#Clean up unecessary files
rm vol* -f
rm dti${tmp_acqs}* -f
if [ $number_acqs -eq 1 ]
then
echo creating file: data
fslmerge -t data `$FSLDIR/bin/imglob rvol0*`
else
echo creating file: data${tmp_acqs}
fslmerge -t data${tmp_acqs} `$FSLDIR/bin/imglob rvol00*`
fi
#Clean up unecessary files
rm rvol* -f
count_acqs=`expr $count_acqs + 1`;
done
rm -f matrices/mat;
rm -f matrices/tmp;;
ed) echo Correcting only for eddy currents
while [ $count_acqs -lt $number_acqs ]; do
tmp_acqs=`expr $count_acqs + 1`;
fslsplit dti${tmp_acqs}
if [ $nvols -lt 9 ]; then
count=0
while [ ${count} != ${nvols} ];do
echo FLIRT on volume ${count}
flirt -schedule dof3 -in vol000$count -ref nodif -out rvol000$count -nosearch
count=`expr $count + 1`;
done
else
count=0
while [ $count != 10 ];do
echo FLIRT on volume ${count}
flirt -schedule dof3 -in vol000$count -ref nodif -out rvol000$count -nosearch
count=`expr $count + 1`;
done
while [ ${count} != ${nvols} ];do
echo FLIRT on volume ${count}
flirt -schedule dof3 -in vol00${count} -ref nodif -out rvol00${count} -nosearch
count=`expr $count + 1`;
done
fi
#Clean up unecessary files
rm vol* -f
rm dti${tmp_acqs}* -f
if [ $number_acqs -eq 1 ]
then
echo creating file: data
fslmerge -t data `$FSLDIR/bin/imglob rvol*`
else
echo creating file: data${tmp_acqs}
echo `$FSLDIR/bin/imglob rvol*`
fslmerge -t data${tmp_acqs} `$FSLDIR/bin/imglob rvol*`
fi
#Clean up unecessary files
rm rvol* -f
count_acqs=`expr $count_acqs + 1`;
done;;
*) echo Type_of_correction must be either mc or ed
exit;;
esac
#Brain Extraction
echo BE
bet nodif mask -f 0.025 -m
immv mask_mask nodif_brain_mask
rm mask.* -f
rm dof3 -f
#Copy relevant bvals and bvecs file
n_vols=`echo $nvols`;
case $n_vols
in
7) cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvals_6 bvals;
cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvecs_6 bvecs;
filename='gdata7';;
13) cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvals_12 bvals;
cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvecs_12 bvecs;
filename='gdata13';;
63) cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvals_60 bvals;
cp ~dtiuser/etc/FMRIB_bvals_bvecs/bvecs_60 bvecs;
filename='gdata63';;
*) echo 'bvals and bvecs not available for that # of directions';
exit;;
esac
#The bvecs will only be rotated for 1 acquisition
#The amount of rotation corresponding to a given volume for
#different acquisitions would be different and it wouldn't be possible
#to simply average the data
if [ $number_acqs -eq 1 ]; then
echo Rotating bvecs using matrices produced by Flirt
case $correc
in
mc)
if [ $nvols_nodif -gt 1 ]; then
fid_direc='$nodiffid';
else
fid_direc='${dtifid}${scan_numb}.fid';
fi
correct_bvs $fid_direc;;
*) exit;;
esac
fi
echo Done!
remove_vols deleted 100755 → 0
+ 0
− 81
View file @ 835c7815
#!/bin/sh
# preprocessing for DTI images acquired at FMRIB
Usage() {
echo "REMOVE_VOLS - Remove dodgy volumes from DTI data acquired at FMRIB "
echo ""
echo "USAGE: remove_vols <input_file> <output_file> <dodgyvols> "
echo ""
echo "example: remove_vols data data_rv 4 19 35"
echo ""
echo "Note that the first volume is 0 and not 1"
echo ""
exit 1
}
[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ "$3" = "" ] && Usage
input_file=$1
output_file=$2
current_dir=`pwd`
if [ ! `imtest $input_file` ]; then
echo Cant find $input_file
exit
fi
if [ ! -e bvals ]; then
echo Cant find bvals
exit
fi
if [ ! -e bvecs ]; then
echo Cant find bvecs
exit
fi
fslsplit $input_file
vol=0
num_vols=`expr $# - 2`
t=""
rm dodgy_vols -f
printf $t >dodgy_vols
while [ $vol -lt $num_vols ]; do
printf $t>tmp1
printf $t>tmp2
v=$3
shift
if [ `imtest vol000${v}` ]; then
imrm vol000${v}
fi
if [ `imtest vol00${v}` ]; then
imrm vol00${v}
fi
echo $v > tmp1
cat dodgy_vols tmp1 > tmp2
cat tmp2 > dodgy_vols
rm tmp* -f
vol=`expr $vol + 1`
done
echo Removing dodgy volumes from bvals and bvecs
matlab -nodisplay -nojvm -nosplash 1> matlab.out1 2>&1 <<EOF
addpath('/usr/people/dtiuser/etc/FMRIB_bvals_bvecs/');
remove_vols('$current_dir');
exit
EOF
rm matlab.out1 -f
echo "Merging Volumes"
fslmerge -t $output_file `$FSLDIR/bin/imglob vol*`
rm vol* -f
rm dodgy_vols -f
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