Skip to content

Commit

Permalink
Work around issue with applywarp in FSL6
Browse files Browse the repository at this point in the history 
Applywarp now creates an output volume for each volume of
the reference image so it is essential that we use a 3D
image as the reference. We now create 'nativeref' for this purpose
  • Loading branch information
@mcraig-ibme
mcraig-ibme committed Nov 19, 2018
1 parent 382d138 commit 6a1864b
Showing 1 changed file with 21 additions and 12 deletions.
33 changes: 21 additions & 12 deletions oxford_asl.in
View file
Original file line number Diff line number Diff line change
Expand Up @@ -646,7 +646,7 @@ ApplyWarps() {
Log " - Moco: $moco_xfm"
appremat="--premat=$moco_xfm"
fi
applywarp -i $tempdir/asldata_orig -r $tempdir/meanasl -o $tempdir/asldata $appremat -w $corrwarp --rel $APPLYWARP_OPTS
applywarp -i $tempdir/asldata_orig -r $tempdir/nativeref -o $tempdir/asldata $appremat -w $corrwarp --rel $APPLYWARP_OPTS

# Correct for quantitative signal magnitude as volume has been locally scaled by the Jacobian
fslmaths $tempdir/asldata -mul $jacobian $tempdir/asldata
Expand All @@ -663,14 +663,15 @@ ApplyWarps() {
Log " - Calib->ASL: $calib_xfm"
appremat="--premat=$calib_xfm"
fi
applywarp -i $tempdir/calib_orig -r $tempdir/meanasl -o $tempdir/calib $appremat -w $corrwarp --rel $APPLYWARP_OPTS

applywarp -i $tempdir/calib_orig -r $tempdir/nativeref -o $tempdir/calib $appremat -w $corrwarp --rel $APPLYWARP_OPTS
fslmaths $tempdir/calib -mul $jacobian $tempdir/calib
if [ ! -z $cref ]; then
applywarp -i $tempdir/cref_orig -r $tempdir/meanasl -o $tempdir/cref $appremat -w $corrwarp --rel $APPLYWARP_OPTS
applywarp -i $tempdir/cref_orig -r $tempdir/nativeref -o $tempdir/cref $appremat -w $corrwarp --rel $APPLYWARP_OPTS
fslmaths $tempdir/cref -mul $jacobian $tempdir/cref
fi
if [ ! -z $cblip ]; then
applywarp -i $tempdir/cblip_orig -r $tempdir/meanasl -o $tempdir/cblip $appremat -w $corrwarp --rel $APPLYWARP_OPTS
applywarp -i $tempdir/cblip_orig -r $tempdir/nativeref -o $tempdir/cblip $appremat -w $corrwarp --rel $APPLYWARP_OPTS
fslmaths $tempdir/cblip -mul $jacobian $tempdir/cblip
fi
fi
Expand Down Expand Up @@ -1194,6 +1195,14 @@ imcp $infile $tempdir/asldata # this is the MAIN data that we will reflect any c
# take a copy that will not be subject to any subsequent corrections
imcp $tempdir/asldata $tempdir/asldata_orig

# Take the mean of the ASL data to use as a reference image in applywarp.
# This is required because in FSL6, applywarp duplicates the output for every
# volume of the reference image, so it is imperative that it is a 3D image!
# Note that in applywarp the only function of the reference image is to define
# the output space, so this never needs to be changed as our 'native' space is
# always the same space as the input ASL data
fslmaths $tempdir/asldata -Tmean $tempdir/nativeref

### Motion Correction (main)
# note motion correction within calibration data is done above
if [ ! -z $moco ]; then
Expand All @@ -1214,7 +1223,7 @@ if [ ! -z $moco ]; then
done
# Concatenate the motion matrices for use with applywarp
cat $tempdir/asldata.mat/MAT* > $tempdir/asldata.cat
applywarp --ref=$tempdir/asldata --in=$tempdir/asldata_orig --out=$tempdir/asldata --premat=$tempdir/asldata.cat $APPLYWARP_OPTS
applywarp --ref=$tempdir/nativeref --in=$tempdir/asldata_orig --out=$tempdir/asldata --premat=$tempdir/asldata.cat $APPLYWARP_OPTS
# Convert all calibration images to align with asldata
flirt -in $tempdir/calib -out $tempdir/calib -ref $tempdir/asldata -init $tempdir/calib2asl.mat -applyxfm $APPLYXFM_OPTS
if [ ! -z $cref ]; then
Expand Down Expand Up @@ -1244,7 +1253,7 @@ if [ ! -z $gdcwarp ]; then

# Convert the supplied warp image to extract the jacbbian (as parts)
# (meanasl here is just a reference). Using relative warp convention
convertwarp -r $tempdir/meanasl -o $tempdir/asldist_userwarp -w $gdcwarp --rel -j $tempdir/distcorr/jacobian_parts
convertwarp -r $tempdir/nativeref -o $tempdir/asldist_userwarp -w $gdcwarp --rel -j $tempdir/distcorr/jacobian_parts

# Calculation of the jacobian for the warp - method suggested in:
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;d3fee1e5.0908
Expand Down Expand Up @@ -1475,7 +1484,7 @@ if [ ! -z $fasthasrun ]; then

if [ ! -z $tempdir/biasfield_struct ]; then
# transform the bias field and invert to use for sensitivity correction in calibration
applywarp --ref=$tempdir/asldata --in=$tempdir/biasfield_struct --out=$tempdir/biasfield --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
applywarp --ref=$tempdir/nativeref --in=$tempdir/biasfield_struct --out=$tempdir/biasfield --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
fi

if [ ! -z $senscorr ]; then
Expand Down Expand Up @@ -1618,15 +1627,15 @@ if [ -e $tempdir/fmap.* ]; then
Registration $distbase "-m $tempdir/mask --tissseg $tempdir/tissseg --imat $tempdir/asl2struct.mat --finalonly" distcorr

# Generate the correction warp in ASL space
convertwarp -r $tempdir/meanasl -o $tempdir/asldist_warp -w $tempdir/distcorr/asl2struct_warp.nii.gz --postmat=$tempdir/distcorr/struct2asl.mat --rel -j $tempdir/distcorr/jacobian_parts
convertwarp -r $tempdir/nativeref -o $tempdir/asldist_warp -w $tempdir/distcorr/asl2struct_warp.nii.gz --postmat=$tempdir/distcorr/struct2asl.mat --rel -j $tempdir/distcorr/jacobian_parts

# If we ALSO have a user supplied GDC warp then we need to merge that with the one we have found here
# use convert warp to combine the warps. Note that we cannot do this in a single step becase we need
# to use --postmat above to transform into ASL space but this needs to happen before we apply
# the user warp
if [ ! -z $gdcwarp ]; then
Log "Adding user-supplied GDC warp to distortion correction warp"
convertwarp -r $tempdir/meanasl -o $tempdir/asldist_warp -w $tempdir/asldist_warp --warp2=$tempdir/asldist_userwarp --rel -j $tempdir/distcorr/jacobian_parts
convertwarp -r $tempdir/nativeref -o $tempdir/asldist_warp -w $tempdir/asldist_warp --warp2=$tempdir/asldist_userwarp --rel -j $tempdir/distcorr/jacobian_parts
fi

# Calculation of the jacobian for the warp - method suggested in:
Expand Down Expand Up @@ -1982,9 +1991,9 @@ if [ ! -z $fasthasrun ] && [ -z $pvgm ]; then
convert_xfm -omat $tempdir/struct2asl.mat -inverse $tempdir/asl2struct.mat

# Gray matter - assume this will be PVE 1
applywarp --ref=$tempdir/asldata --in=$tempdir/pvgm_struct --out=$tempdir/pvgm_inasl --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
applywarp --ref=$tempdir/nativeref --in=$tempdir/pvgm_struct --out=$tempdir/pvgm_inasl --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
# white matter - assume this will be PVE 2
applywarp --ref=$tempdir/asldata --in=$tempdir/pvwm_struct --out=$tempdir/pvwm_inasl --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
applywarp --ref=$tempdir/nativeref --in=$tempdir/pvwm_struct --out=$tempdir/pvwm_inasl --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
# threshold (upper and lower) the PVE to avoid artefacts of spline interpolation and also ignore very low PVE that could cause numerical issues.
fslmaths $tempdir/pvgm_inasl -thr 0.1 -min 1 $tempdir/pvgm_inasl
fslmaths $tempdir/pvwm_inasl -thr 0.1 -min 1 $tempdir/pvwm_inasl
Expand Down Expand Up @@ -2138,7 +2147,7 @@ if [ ! -z $pvcorr ]; then
if [ ! -z $senscorr ]; then
# Struct->ASL registration may have changed, so re-transform the bias field and invert to use for sensitivity correction
Log "Re-registering bias field and calculating sensitivity map"
applywarp --ref=$tempdir/asldata --in=$tempdir/biasfield_struct --out=$outdir/native_space/biasfield --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
applywarp --ref=$tempdir/nativeref --in=$tempdir/biasfield_struct --out=$outdir/native_space/biasfield --premat=$tempdir/struct2asl.mat $APPLYWARP_OPTS
fslmaths $outdir/native_space/biasfield -recip $outdir/native_space/sensitivity
fi
fi
Expand Down

0 comments on commit 6a1864b

Please sign in to comment.