Merge pull request #96 from Washington-University/feature/freesurfer_…

…v6_latest

Feature/freesurfer v6 latest

DiffusionPreprocessing/DiffPreprocPipeline_Eddy.sh

@@ -156,6 +156,12 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
                           --extra-eddy-arg=--verbose --extra-eddy-arg=T 
                           will ultimately be translated to --verbose T when
                           passed to the eddy binary.
+  [--no-gpu]              If specified, use the non-GPU-enabled version of eddy.
+                          Defaults to using the GPU-enabled version of eddy.
+  [--cuda-version=X.Y]    If using the GPU-enabled version of eddy, then this
+                          option can be used to specify which eddy_cuda binary
+                          version to use. If specified, FSLDIR/bin/eddy_cudaX.Y 
+                          will be used.
 
 Return Status Value:
 
@@ -205,6 +211,11 @@ EOF
 #  ${ol_nstd_value}        Value of user specified --ol_nstd= parameter
 #  ${extra_eddy_args}      Value of user specified --extra-eddy-arg parameters, space 
 #                          separated tokens
+#  ${no_gpu}               TRUE if we should use the non-GPU-enabled version of eddy
+#                          Anything else or unset means use the GPU-enabled version of eddy
+#  ${cuda_version}         If using the GPU-enabled version, this value _may_ be
+#                          given to specify the version of the CUDA libraries in use.
+#                        
 #
 get_options()
 {
@@ -226,6 +237,8 @@ get_options()
 	resamp_value=""
 	unset ol_nstd_value
 	extra_eddy_args=""
+    no_gpu=""
+	cuda_version=""
 
 	# parse arguments
 	local index=0
@@ -325,6 +338,14 @@ get_options()
 				extra_eddy_args+=" ${extra_eddy_arg} "
 				index=$(( index + 1 ))
 				;;
+			--no-gpu)
+				no_gpu="TRUE"
+				index=$(( index + 1 ))
+				;;
+			--cuda-version=*)
+				cuda_version=${argument#*=}
+				index=$(( index + 1 ))
+				;;
 			*)
 				usage
 				echo "ERROR: Unrecognized Option: ${argument}"
@@ -372,6 +393,8 @@ get_options()
 	echo "   resamp_value: ${resamp_value}"
 	echo "   ol_nstd_value: ${ol_nstd_value}"
 	echo "   extra_eddy_args: ${extra_eddy_args}"
+	echo "   no_gpu: ${no_gpu}"
+	echo "   cuda-version: ${cuda_version}"
 	echo "-- ${SCRIPT_NAME}: Specified Command-Line Parameters - End --"
 }
 
@@ -484,7 +507,15 @@ main()
 	run_eddy_cmd+=" ${rms_option} "
 	run_eddy_cmd+=" ${ff_option} "
 	run_eddy_cmd+=" ${ol_nstd_value_option} "
-	run_eddy_cmd+=" -g "
+
+	if [ "${no_gpu}" != "TRUE" ]; then
+		# default is to use the GPU-enabled version
+		run_eddy_cmd+=" -g "
+		if [ ! -z "${cuda_version}" ]; then
+			run_eddy_cmd+=" --cuda-version=${cuda_version}"
+		fi
+	fi
+
 	run_eddy_cmd+=" -w ${outdir}/eddy "
 
 	if [ ! -z "${dont_peas}" ] ; then

DiffusionPreprocessing/scripts/DiffusionToStructural.sh

@@ -119,5 +119,6 @@ ${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/data -Tmean "$T1wOutputDirectory"/t
 ${FSLDIR}/bin/immv "$T1wOutputDirectory"/nodif_brain_mask.nii.gz "$T1wOutputDirectory"/nodif_brain_mask_old.nii.gz
 ${FSLDIR}/bin/fslmaths "$T1wOutputDirectory"/nodif_brain_mask_old.nii.gz -mas "$T1wOutputDirectory"/temp "$T1wOutputDirectory"/nodif_brain_mask
 ${FSLDIR}/bin/imrm "$T1wOutputDirectory"/temp
+${FSLDIR}/bin/imrm "$T1wOutputDirectory"/nodif_brain_mask_old
 
 echo " END: DiffusionToStructural"

DiffusionPreprocessing/scripts/eddy_postproc.sh

@@ -24,24 +24,24 @@ datadir=${workingdir}/data
 #    cp ${eddydir}/Pos.bvec ${datadir}/bvecs
 #    $FSLDIR/bin/imcp ${eddydir}/eddy_unwarped_images ${datadir}/data
 #else
-    if [ ${CombineDataFlag} -eq 2 ]; then
+if [ ${CombineDataFlag} -eq 2 ]; then
 	${FSLDIR}/bin/imcp  ${eddydir}/eddy_unwarped_images ${datadir}/data
 	cp ${eddydir}/Pos_Neg.bvals ${datadir}/bvals
 	cp ${eddydir}/Pos_Neg.bvecs ${datadir}/bvecs
-    else
+else
 	echo "JAC resampling has been used. Eddy Output is now combined."
 	PosVols=`wc ${eddydir}/Pos.bval | awk {'print $2'}`
 	NegVols=`wc ${eddydir}/Neg.bval | awk {'print $2'}`    #Split Pos and Neg Volumes
 	${FSLDIR}/bin/fslroi ${eddydir}/eddy_unwarped_images ${eddydir}/eddy_unwarped_Pos 0 ${PosVols}
 	${FSLDIR}/bin/fslroi ${eddydir}/eddy_unwarped_images ${eddydir}/eddy_unwarped_Neg ${PosVols} ${NegVols}
 	${FSLDIR}/bin/eddy_combine ${eddydir}/eddy_unwarped_Pos ${eddydir}/Pos.bval ${eddydir}/Pos.bvec ${eddydir}/Pos_SeriesVolNum.txt \
-                    ${eddydir}/eddy_unwarped_Neg ${eddydir}/Neg.bval ${eddydir}/Neg.bvec ${eddydir}/Neg_SeriesVolNum.txt ${datadir} ${CombineDataFlag}
+             ${eddydir}/eddy_unwarped_Neg ${eddydir}/Neg.bval ${eddydir}/Neg.bvec ${eddydir}/Neg_SeriesVolNum.txt ${datadir} ${CombineDataFlag}
 
 	${FSLDIR}/bin/imrm ${eddydir}/eddy_unwarped_Pos
 	${FSLDIR}/bin/imrm ${eddydir}/eddy_unwarped_Neg
 	cp ${datadir}/bvals ${datadir}/bvals_noRot
 	cp ${datadir}/bvecs ${datadir}/bvecs_noRot
-     
+
 	#rm ${eddydir}/Pos.bv*
 	#rm ${eddydir}/Neg.bv*
 
@@ -61,7 +61,7 @@ datadir=${workingdir}/data
 	echo $Posline1 > ${eddydir}/Pos_rotated.bvec
 	echo $Posline2 >> ${eddydir}/Pos_rotated.bvec
 	echo $Posline3 >> ${eddydir}/Pos_rotated.bvec
-
+	
 	Negline1=""
 	Negline2=""
 	Negline3=""
@@ -79,11 +79,11 @@ datadir=${workingdir}/data
 	# Average Eddy-Rotated bvecs. Get for each direction the two b matrices, average those and then eigendecompose the average b-matrix to get the new bvec and bval.
 	# Also outputs an index file (1-based) with the indices of the input (Pos/Neg) volumes that have been retained in the output
 	${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval ${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec ${datadir}/avg_data ${eddydir}/Pos_SeriesVolNum.txt ${eddydir}/Neg_SeriesVolNum.txt
-
+	
 	mv ${datadir}/avg_data.bval ${datadir}/bvals
 	mv ${datadir}/avg_data.bvec ${datadir}/bvecs
 	rm -f ${datadir}/avg_data.bv??
-    fi
+fi
 #fi
 
 
@@ -109,8 +109,7 @@ fi
 
 #Remove negative intensity values (caused by spline interpolation) from final data
 ${FSLDIR}/bin/fslmaths ${datadir}/data -thr 0 ${datadir}/data
-${FSLDIR}/bin/bet ${datadir}/data ${datadir}/nodif_brain -m -f 0.1
-$FSLDIR/bin/fslroi ${datadir}/data ${datadir}/nodif 0 1
+${FSLDIR}/bin/fslroi ${datadir}/data ${datadir}/nodif 0 1
+${FSLDIR}/bin/bet ${datadir}/nodif ${datadir}/nodif_brain -m -f 0.1
 
 echo -e "\n END: eddy_postproc"
-