Several last bug fixes

Washington-University · Oct 29, 2019 · 36c6beb · 36c6beb
1 parent 66843ba
commit 36c6beb
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/DiffusionPreprocessing/scripts/DiffusionToStructural.sh b/DiffusionPreprocessing/scripts/DiffusionToStructural.sh
@@ -109,7 +109,7 @@ if [ ${GdcorrectionFlag} -eq 1 ]; then
 
     # 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
+    ${FSLDIR}/bin/applywarp --rel -i "$DataDirectory"/warped/fov_mask_warped -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
@@ -129,7 +129,7 @@ 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
 
-# Mask out data outside the brain adn outside the fov
+# Mask out data outside the brain and 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

diff --git a/DiffusionPreprocessing/scripts/eddy_postproc.sh b/DiffusionPreprocessing/scripts/eddy_postproc.sh
@@ -100,9 +100,9 @@ if [ ! $GdCoeffs = "NONE" ] ; then
     ${FSLDIR}/bin/immv ${datadir}/data ${datadir}/data_warped
 
     # 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 ${datadir}/data pixdim1`
+	DiffRes=`${FSLDIR}/bin/fslval ${datadir}/data_warped pixdim1`
     DilateDistance=`echo "$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
+    ${CARET7DIR}/wb_command -volume-dilate ${datadir}/data_warped.nii.gz $DilateDistance NEAREST ${datadir}/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"