REF: compute fov_mask in eddy_postproc rather than Diffusion2Structural

DiffusionPreprocessing/scripts/DiffusionToStructural.sh

@@ -107,21 +107,19 @@ if [ ${GdcorrectionFlag} -eq 1 ]; then
     ${CARET7DIR}/wb_command -volume-dilate $DataDirectory/warped/data_warped.nii.gz $DilateDistance NEAREST $DataDirectory/warped/data_warped_dilated.nii.gz
     ${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/data_warped_dilated -r "$T1wRestoreImage"_${DiffRes} -w "$WorkingDirectory"/grad_unwarp_diff2str --interp=spline -o "$T1wOutputDirectory"/data
 
-    #Create a mask representing voxels within the field of view for all volumes prior to dilation
-    ${FSLDIR}/bin/fslmaths "$DataDirectory"/warped/data_warped -abs -Tmin -bin -fillh "$DataDirectory"/warped/fov_mask
+    # Transforms field of view mask to T1-weighted space
     ${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/fov_mask -r "$T1wRestoreImage"_${DiffRes} -w "$WorkingDirectory"/grad_unwarp_diff2str --interp=trilinear -o "$T1wOutputDirectory"/fov_mask
 
-    #Now register the grad_dev tensor 
+    # 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 
 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
-    #Register diffusion data to T1w space without considering gradient nonlinearities
+    # Register diffusion data to T1w space without considering gradient nonlinearities
     ${FSLDIR}/bin/flirt -in "$DataDirectory"/data_dilated -ref "$T1wRestoreImage"_${DiffRes} -applyxfm -init "$WorkingDirectory"/diff2str.mat -interp spline -out "$T1wOutputDirectory"/data
 
-    #Create a mask representing voxels within the field of view for all volumes prior to dilation
-    ${FSLDIR}/bin/fslmaths "$DataDirectory"/data -abs -Tmin -bin -fillh "$DataDirectory"/fov_mask
+    # 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
 fi
 

DiffusionPreprocessing/scripts/eddy_postproc.sh

@@ -87,13 +87,31 @@ else
 fi
 #fi
 
+
+#Create a mask representing voxels within the field of view for all volumes prior to dilation
+${FSLDIR}/bin/fslmaths ${datadir}/data -abs -Tmin -bin -fillh ${datadir}/fov_mask
+
 
 if [ ! $GdCoeffs = "NONE" ] ; then
     echo "Correcting for gradient nonlinearities"
 	# Note: "data_warped" is eddy-current and suspectibility distortion corrected (via 'eddy'), but prior to gradient distortion correction
 	# i.e., "data_posteddy_preGDC" would be another way to think of it
     ${FSLDIR}/bin/immv ${datadir}/data ${datadir}/data_warped
-    ${globalscriptsdir}/GradientDistortionUnwarp.sh --workingdir="${datadir}" --coeffs="${GdCoeffs}" --in="${datadir}/data_warped" --out="${datadir}/data" --owarp="${datadir}/fullWarp"
+
+    # Dilation outside of the field of view to minimise the effect of the hard field of view edge on the interpolation
+	  DiffRes=`${FSLDIR}/bin/fslval ${datadir}/data pixdim1`
+    DilateDistance=`echo "$DiffRes * 4" | bc`  # Extrapolates the diffusion data up to 4 voxels outside of the FOV
+    ${CARET7DIR}/wb_command -volume-dilate ${datadir}/warped/data_warped.nii.gz $DilateDistance NEAREST ${datadir}/warped/data_warped_dilated.nii.gz
+
+    # 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)
+    ${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
@@ -102,10 +120,12 @@ if [ ! $GdCoeffs = "NONE" ] ; then
     ${FSLDIR}/bin/imrm ${datadir}/grad_dev_?
     ${FSLDIR}/bin/imrm ${datadir}/trilinear
     ${FSLDIR}/bin/imrm ${datadir}/data_warped_vol1
-
+    ${FSLDIR}/bin/imrm ${datadir}/data_warped_dilated
+
     #Keep the original warped data and warp fields
     mkdir -p ${datadir}/warped
     ${FSLDIR}/bin/immv ${datadir}/data_warped ${datadir}/warped
+    ${FSLDIR}/bin/immv ${datadir}/fov_mask_warped ${datadir}/warped
     ${FSLDIR}/bin/immv ${datadir}/fullWarp ${datadir}/warped
     ${FSLDIR}/bin/immv ${datadir}/fullWarp_abs ${datadir}/warped
 fi