Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix diffusion mask in voxels outside the FOV #129

Merged
merged 19 commits into from
Oct 29, 2019
Merged

Fix diffusion mask in voxels outside the FOV #129

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
220fc20
BUG: only include voxels fully within the FOV in every volume
Sep 2, 2019
afcc633
BUG: only zero-values are outside FOV, not negative values
Sep 9, 2019
0b9f133
Change threshold for floating point rounding error
MichielCottaar Sep 10, 2019
d84edef
OPT: use first volume to extract FOV mask
Sep 24, 2019
da6baaf
BUG: dilate the diffusion data before spline interpolation
Sep 24, 2019
05f42c2
Typo: -volume_dilate -> -volume-dilate
Sep 25, 2019
b161b1d
BUG: added extensions to filenames for wb_command
Sep 25, 2019
26108f6
ENH: added text file with percentage of brain mask in final mask
Oct 6, 2019
33afc22
BUG: reduce number of voxels to dilate
Oct 6, 2019
76578ca
BUG: fixed several typos preventing code to run
Oct 11, 2019
cfe5076
BUG: use fslmaths data -abs -Tmax -bin to only mask out data where al…
Oct 11, 2019
6c3d360
REF: rename DILATE_DISTANCE to DilateDistance
Oct 11, 2019
7684b3c
Merge branch 'master' into mask_diff
Oct 12, 2019
ddcad3b
Back to using Tmin, but now filling holes
Oct 12, 2019
588eb5e
Fixed comments as suggested by @mharms
Oct 12, 2019
b40903b
Do not remove the field of view mask
Oct 12, 2019
39c59ce
REF: compute fov_mask in eddy_postproc rather than Diffusion2Structural
Oct 17, 2019
1b5ca79
Updated comments and other minor changes suggested by @mharms
Oct 18, 2019
56972db
Several last bug fixes
Oct 26, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 7 additions & 8 deletions DiffusionPreprocessing/scripts/DiffusionToStructural.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ cp "$DataDirectory"/bvals "$T1wOutputDirectory"/bvals

DilateDistance=`echo "$DiffRes * 4" | bc` # Extrapolates the diffusion data up to 4 voxels outside of the FOV

#Register diffusion data to T1w space. Account for gradient nonlinearities if requested
# Register diffusion data to T1w space. Account for gradient nonlinearities (using one-step resampling) if requested
if [ ${GdcorrectionFlag} -eq 1 ]; then
echo "Correcting Diffusion data for gradient nonlinearities and registering to structural space"
# We combine the GDC warp with the diff2str affine, and apply to warped/data_warped (i.e., the post-eddy, pre-GDC data)
Expand All @@ -108,11 +108,13 @@ if [ ${GdcorrectionFlag} -eq 1 ]; then
${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/data_warped_dilated -r "$T1wRestoreImage"_${DiffRes} -w "$WorkingDirectory"/grad_unwarp_diff2str --interp=spline -o "$T1wOutputDirectory"/data

# Transforms field of view mask to T1-weighted space
# (Be sure to use the fov_mask derived prior to application of GDC)
${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/fov_mask -r "$T1wRestoreImage"_${DiffRes} -w "$WorkingDirectory"/grad_unwarp_diff2str --interp=trilinear -o "$T1wOutputDirectory"/fov_mask
mharms marked this conversation as resolved.
Show resolved Hide resolved
MichielCottaar marked this conversation as resolved.
Show resolved Hide resolved

# Now register the grad_dev tensor
${FSLDIR}/bin/vecreg -i "$DataDirectory"/grad_dev -o "$T1wOutputDirectory"/grad_dev -r "$T1wRestoreImage"_${DiffRes} -t "$WorkingDirectory"/diff2str.mat --interp=spline
${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/grad_dev -mas "$T1wOutputDirectory"/nodif_brain_mask_temp "$T1wOutputDirectory"/grad_dev #Mask-out values outside the brain
${FSLDIR}/bin/imrm $DataDirectory/warped/data_warped_dilated
else
# Dilation outside of the field of view to minimise the effect of the hard field of view edge on the interpolation
${CARET7DIR}/wb_command -volume-dilate $DataDirectory/data.nii.gz $DilateDistance NEAREST $DataDirectory/data_dilated.nii.gz
Expand All @@ -121,13 +123,15 @@ else

# Transforms field of view mask to T1-weighted space
${FSLDIR}/bin/flirt -in "$DataDirectory"/fov_mask -ref "$T1wRestoreImage"_${DiffRes} -applyxfm -init "$WorkingDirectory"/diff2str.mat -interp trilinear -out "$T1wOutputDirectory"/fov_mask
${FSLDIR}/bin/imrm $DataDirectory/data_dilated
fi

# only include voxels fully(!) within the field of view for every volume
${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/fov_mask -thr 0.999 -bin "$T1wOutputDirectory"/fov_mask

${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/data -mas "$T1wOutputDirectory"/nodif_brain_mask_temp -mas "$T1wOutputDirectory"/fov_mask "$T1wOutputDirectory"/data #Mask-out data outside the brain
${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/data -thr 0 "$T1wOutputDirectory"/data #Remove negative intensity values (caused by spline interpolation) from final data
# Mask out data outside the brain adn outside the fov
MichielCottaar marked this conversation as resolved.
Show resolved Hide resolved
${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/data -mas "$T1wOutputDirectory"/nodif_brain_mask_temp -mas "$T1wOutputDirectory"/fov_mask "$T1wOutputDirectory"/data
${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/data -thr 0 "$T1wOutputDirectory"/data #Remove negative intensity values (from eddy) from final data
${FSLDIR}/bin/imrm "$T1wOutputDirectory"/nodif_brain_mask_temp

# Identify any voxels that are zeros across all frames and remove those from the final nodif_brain_mask
Expand All @@ -144,10 +148,5 @@ echo "${PctCoverage}, ${NvoxFinalMask}, ${NvoxBrainMask}" >> "$T1wOutputDirector

${FSLDIR}/bin/imrm "$T1wOutputDirectory"/temp
${FSLDIR}/bin/imrm "$T1wOutputDirectory"/nodif_brain_mask_old
if [ ${GdcorrectionFlag} -eq 1 ]; then
${FSLDIR}/bin/imrm $DataDirectory/warped/data_warped_dilated
else
${FSLDIR}/bin/imrm $DataDirectory/data_dilated
fi

echo " END: DiffusionToStructural"
12 changes: 7 additions & 5 deletions DiffusionPreprocessing/scripts/eddy_postproc.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,8 @@ fi
#fi


#Create a mask representing voxels within the field of view for all volumes prior to dilation
# Create a mask representing voxels within the field of view for all volumes prior to dilation
# 'eddy' can return negative values in some low signal locations, so use -abs for determining the fov mask
${FSLDIR}/bin/fslmaths ${datadir}/data -abs -Tmin -bin -fillh ${datadir}/fov_mask
MichielCottaar marked this conversation as resolved.
Show resolved Hide resolved


Expand All @@ -106,12 +107,10 @@ if [ ! $GdCoeffs = "NONE" ] ; then
# apply gradient distortion correction
${globalscriptsdir}/GradientDistortionUnwarp.sh --workingdir="${datadir}" --coeffs="${GdCoeffs}" --in="${datadir}/data_warped_dilated" --out="${datadir}/data" --owarp="${datadir}/fullWarp"

# Transform field of view mask (using conservative trilinear interolation with high threshold)
# Transform field of view mask (using conservative trilinear interpolation with high threshold)
${FSLDIR}/bin/immv ${datadir}/fov_mask ${datadir}/fov_mask_warped
${FSLDIR}/bin/applywarp --rel --interp=trilinear -i ${datadir}/fov_mask_warped -r ${datadir}/fov_mask_warped -w ${datadir}/fullWarp -o ${datadir}/fov_mask
${FSLDIR}/bin/fslmaths ${datadir}/fov_mask -thr 0.999 -bin ${datadir}/fov_mask
# mask out any data outside the field of view
${FSLDIR}/bin/fslmaths ${datadir}/data -mas ${datadir}/fov_mask ${datadir}/data

echo "Computing gradient coil tensor to correct for gradient nonlinearities"
${FSLDIR}/bin/calc_grad_perc_dev --fullwarp=${datadir}/fullWarp -o ${datadir}/grad_dev
Expand All @@ -130,7 +129,10 @@ if [ ! $GdCoeffs = "NONE" ] ; then
${FSLDIR}/bin/immv ${datadir}/fullWarp_abs ${datadir}/warped
fi
MichielCottaar marked this conversation as resolved.
Show resolved Hide resolved

#Remove negative intensity values (caused by spline interpolation) from final data
# mask out any data outside the field of view
${FSLDIR}/bin/fslmaths ${datadir}/data -mas ${datadir}/fov_mask ${datadir}/data

# Remove negative intensity values (from eddy) from final data
${FSLDIR}/bin/fslmaths ${datadir}/data -thr 0 ${datadir}/data
${FSLDIR}/bin/fslroi ${datadir}/data ${datadir}/nodif 0 1
${FSLDIR}/bin/bet ${datadir}/nodif ${datadir}/nodif_brain -m -f 0.1
Expand Down