Updated comments and other minor changes suggested by @mharms

DiffusionPreprocessing/scripts/DiffusionToStructural.sh

@@ -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)
@@ -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
 
     # 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
@@ -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
+${FSLDIR}/bin/fslmaths "$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
@@ -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"

DiffusionPreprocessing/scripts/eddy_postproc.sh

@@ -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
 
 
@@ -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
@@ -130,7 +129,10 @@ if [ ! $GdCoeffs = "NONE" ] ; then
     ${FSLDIR}/bin/immv ${datadir}/fullWarp_abs ${datadir}/warped
 fi
 
-#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