diff --git a/docs/Pipeline_Branches.md b/docs/Pipeline_Branches.md
new file mode 100644
index 0000000..4e3cfa5
--- /dev/null
+++ b/docs/Pipeline_Branches.md
@@ -0,0 +1,49 @@
+There are many tasks in our Luigi pipeline defined in [different modules](../workflows):
+
+* struct_pipe.py
+* dwi_pipe.py
+* fs2dwi_pipe.py
+
+Some of them can be run standalone. Others require a task to be run beforehand. Such various routes are outlined below:
+
+---
+
+#### T1 + T2 templates
+
+    StructMask, Freesurfer
+    
+#### dwi + T2 templates
+
+    EddyEpi, Ukf, Wma800
+    
+Provided that `Freesurfer` task was run:
+
+    EddyEpi, Ukf, Fs2Dwi, Wmql, Wmqlqc, TractMeasures
+    
+---
+
+#### Only T1 template
+
+    StructMask, Freesurfer
+    
+#### dwi+T1 template
+
+    SynB0, Ukf, Wma800
+
+#### ap_pa_template
+
+    TopupEddy, Ukf, Wma800
+
+---
+    
+#### Only dwi template
+
+    DwiAlign, GibbsUn, CnnMask, PnlEddy, FslEddy, Ukf, Wma800
+    
+Provided that `Freesurfer` task was run:
+
+    DwiAlign, GibbsUn, CnnMask, PnlEddy, FslEddy, Ukf, Fs2Dwi, Wmql, Wmqlqc, TractMeasures
+
+Provided that `GibbsUn` task was run:
+
+    HcpPipe, Ukf, Wma800
diff --git a/docs/SynB0-Wma800.png b/docs/SynB0-Wma800.png
new file mode 100644
index 0000000..d445f2f
Binary files /dev/null and b/docs/SynB0-Wma800.png differ
diff --git a/docs/TUTORIAL.md b/docs/TUTORIAL.md
index 34bd5b9..47bfe51 100644
--- a/docs/TUTORIAL.md
+++ b/docs/TUTORIAL.md
@@ -23,7 +23,9 @@ Table of Contents
       * [Correct eddy and epi](#correct-eddy-and-epi)
          * [EddyEpi](#eddyepi)
             * [FslEddy and PnlEddy](#fsleddy-and-pnleddy)
+         * [SynB0](#synb0)
          * [TopupEddy](#topupeddy)
+         * [HcpPipe](#hcppipe)
       * [UKFTractography](#ukftractography)
       * [Wma800](#wma800)
    * [Fs2Dwi pipeline](#fs2dwi-pipeline)
@@ -384,7 +386,9 @@ Different methods for eddy and epi corrections are described below:
 
 * PnlEddy + PnlEpi (EddyEpi)
 * FslEddy + PnlEpi (EddyEpi)
+* SynB0
 * TopupEddy
+* HcpPipe
 
 
 ### EddyEpi
@@ -459,6 +463,47 @@ The mask and baseline image provided to `FslEddy` are approximated as eddy corre
 be fed into later task FslEddyEpi.
 
 
+### SynB0
+
+When an axial T2w image is absent and there is only AP or PA acquisition, we make use of [Synb0-DISCO](https://github.com/MASILab/Synb0-DISCO)
+program to perform EPI distortion correction. The Synb0-DISCO program is a replacement of topup. It creates a distortion corrected B0 from a single
+AP or PA acquisition. It also provides the usual topup correction parameters that are used to perform eddy correction later.
+However, Synb0-DISCO requires a T1w image.
+
+![](https://github.com/pnlbwh/luigi-pnlpipe/blob/0d2229e1f27fcc6b02825e9a147c0146924eae43/docs/SynB0-Wma800.png)
+
+
+The configuration file used for `SynB0` task is same as the above [dwi_pipe_params.cfg](../params/dwi_pipe_params.cfg). Specifically, `SynB0` requires
+the following parameters definition:
+
+```cfg
+## [SynB0] ##
+acqp: /path/to/acqp.txt
+index: /path/to/index.txt
+```
+
+Where `acqp.txt` just:
+
+```
+0 1 0 0.05
+0 1 0 0
+```
+
+Run it:
+
+```bash
+export LUIGI_CONFIG_PATH=/path/to/dwi_pipe_params.cfg
+
+exec/ExecuteTask --task SynB0 \
+--bids-data-dir /data/pnl/Collaborators/EDCRP/1110/1110_ses-002_T1_nii/rawdata/ \
+-c ne00181 -s 002 \
+--dwi-template sub-*/ses-*/dwi/*_dwi.nii.gz \
+--t1-template sub-*/ses-*/anat/*_T1w.nii.gz
+```
+
+Note that, `SynB0` task is run in coordination with [_synb0_eddy.sh](_synb0_eddy.sh) .
+
+
 ### TopupEddy
 
 When two opposing acquisitions--AP and PA are available such as in Human Connectom Project (HCP), 
@@ -506,6 +551,22 @@ for corrected data is determined as follows:
     *_dir-214_*
 
 
+### HcpPipe
+
+This task supersedes *TopupEddy* task. The *HcpPipe* way of processing opposing pair of DWIs is inherited 
+from [Washington-University/HCPpipelines](https://github.com/Washington-University/HCPpipelines).
+PNL introduced some improvements in that pipeline including:
+
+  * Use [CNN brain masking](https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation) program to generate topup mask
+  * Replace outliers (`--repol` flag) for >500 b-shells
+
+Since external processing is involved in this task, it is run via a [separate script](https://github.com/pnlbwh/luigi-pnlpipe/blob/b311000073047b40db9b7b8c1752cdbba883aa6c/workflows/hcp_pnl_topup.lsf) in three steps:
+
+  * Gibbs unringing of opposing pair of DWIs via Luigi
+  * HCP pipeline via shell scripts
+  * Creation of soft links in `sub-*/ses-*/dwi/` directory according to BIDS convention via Luigi
+
+This *HcpPipe* task has been used to process *HCP-EP* data.
 
 
 ## UKFTractography
diff --git a/workflows/ExecuteTask.py b/workflows/ExecuteTask.py
index ffc933c..cc546fe 100755
--- a/workflows/ExecuteTask.py
+++ b/workflows/ExecuteTask.py
@@ -6,7 +6,7 @@
 from _define_outputs import IO
 from struct_pipe import StructMask, Freesurfer
 from dwi_pipe import DwiAlign, GibbsUn, CnnMask, \
-    PnlEddy, FslEddy, TopupEddy, HcpPipe, EddyEpi, Ukf
+    PnlEddy, FslEddy, SynB0, TopupEddy, HcpPipe, EddyEpi, Ukf, Wma800
 from fs2dwi_pipe import Fs2Dwi, Wmql, Wmqlqc, TractMeasures
 from scripts.util import abspath, isfile, pjoin, LIBDIR
 from os import getenv, stat, remove
@@ -56,9 +56,9 @@ def _rm_tempfiles(names):
                         default= argparse.SUPPRESS,
                         choices=['StructMask', 'Freesurfer',
                                  'DwiAlign', 'GibbsUn', 'CnnMask',
-                                 'PnlEddy', 'FslEddy', 'TopupEddy', 'HcpPipe',
+                                 'PnlEddy', 'FslEddy', 'SynB0', 'TopupEddy', 'HcpPipe',
                                  'EddyEpi',
-                                 'Ukf',
+                                 'Ukf', 'Wma800',
                                  'Fs2Dwi', 'Wmql', 'Wmqlqc', 'TractMeasures'])
 
     parser.add_argument('--num-workers', type=int, default=1, help='number of Luigi workers')
@@ -93,158 +93,125 @@ def _rm_tempfiles(names):
             if args.t2_template:
 
                 if args.task=='StructMask':
-                    jobs.append(StructMask(bids_data_dir=args.bids_data_dir,
-                                           derivatives_dir=derivatives_dir,
-                                           id=id,
-                                           ses=ses,
-                                           struct_template=args.t2_template))
+                    jobs.append(StructMask(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        struct_template=args.t2_template))
 
                 elif args.task=='Freesurfer':
-                    jobs.append(Freesurfer(bids_data_dir=args.bids_data_dir,
-                                           derivatives_dir=derivatives_dir, 
-                                           id=id,
-                                           ses=ses,
-                                           t1_template=args.t1_template,
-                                           t2_template=args.t2_template))
+                    jobs.append(Freesurfer(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        t1_template=args.t1_template,
+                        t2_template=args.t2_template))
 
-                
                 elif args.task=='EddyEpi':
-                    jobs.append(eval(args.task)(bids_data_dir=args.bids_data_dir,
-                                                derivatives_dir=derivatives_dir,
-                                                id=id,
-                                                ses=ses,
-                                                dwi_template=args.dwi_template,
-                                                struct_template=args.t2_template))
-
-
-
-                # Ukf task does not have pa_ap_template because
-                # when axt2 is available, pa_ap acquisition should be unavailable
-                # in other words, PnlEpi and TopupEddy are mutually exclusive
-                elif args.task=='Ukf':
-                    jobs.append(Ukf(bids_data_dir=args.bids_data_dir,
-                                    derivatives_dir=derivatives_dir,
-                                    id=id,
-                                    ses=ses,
-                                    dwi_template=args.dwi_template,
-                                    struct_template=args.t2_template))
-
-
-                elif args.task=='Fs2Dwi':
-                    jobs.append(Fs2Dwi(bids_data_dir=args.bids_data_dir,
-                                       derivatives_dir=derivatives_dir,
-                                       id=id,
-                                       ses=ses,
-                                       dwi_template=args.dwi_template,
-                                       struct_template=args.t2_template))
-
-                elif args.task=='Wmql':
-                    jobs.append(Wmql(bids_data_dir=args.bids_data_dir,
-                                     derivatives_dir=derivatives_dir,
-                                     id=id,
-                                     ses=ses,
-                                     dwi_template=args.dwi_template,
-                                     struct_template=args.t2_template))
-                                     
-                elif args.task=='TractMeasures':
-                    jobs.append(TractMeasures(bids_data_dir=args.bids_data_dir,
-                                              derivatives_dir=derivatives_dir,
-                                              id=id,
-                                              ses=ses,
-                                              dwi_template=args.dwi_template,
-                                              struct_template=args.t2_template))
-
-
-
-                elif args.task=='Wmqlqc':
-                    jobs.append(Wmqlqc(bids_data_dir=args.bids_data_dir,
-                                       derivatives_dir=derivatives_dir,
-                                       id=id,
-                                       ses=ses,
-                                       dwi_template=args.dwi_template,
-                                       struct_template=args.t2_template))
-
+                    jobs.append(EddyEpi(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template,
+                        struct_template=args.t2_template))
+
+
+                # This Ukf task does not have pa_ap_template because
+                # when AXT2 is available, pa_ap acquisition should be unavailable.
+                # In other words, PnlEpi and TopupEddy are mutually exclusive
+                elif args.task in ['Ukf','Wma800']:
+                    jobs.append(eval(args.task)(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template,
+                        struct_template=args.t2_template))
+
+                elif args.task in ['Fs2Dwi','Wmql','TractMeasures','Wmqlqc']:
+                    jobs.append(eval(args.task)(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template,
+                        struct_template=args.t2_template))
+
+                        
 
             # just t1_template
             else:
                 if args.task=='StructMask':
-                    jobs.append(StructMask(bids_data_dir=args.bids_data_dir,
-                                           derivatives_dir=derivatives_dir,
-                                           id=id,
-                                           ses=ses,
-                                           struct_template=args.t1_template))
+                    jobs.append(StructMask(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        struct_template=args.t1_template))
 
                 elif args.task=='Freesurfer':
-                    jobs.append(Freesurfer(bids_data_dir=args.bids_data_dir,
-                                           derivatives_dir=derivatives_dir,
-                                           id=id,
-                                           ses=ses,
-                                           t1_template=args.t1_template))
-
-                
+                    jobs.append(Freesurfer(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        t1_template=args.t1_template))
                 
                 elif args.task in ['DwiAlign','GibbsUn','CnnMask','PnlEddy','FslEddy','HcpPipe']:
-                    jobs.append(eval(args.task)(bids_data_dir=args.bids_data_dir,
-                                                derivatives_dir=derivatives_dir,
-                                                id=id,
-                                                ses=ses,
-                                                dwi_template=args.dwi_template))
-
+                    jobs.append(eval(args.task)(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template))
+
+                elif args.task=='SynB0':
+                    jobs.append(SynB0(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template,
+                        struct_template=args.t1_template))
 
                 elif args.task=='TopupEddy':
-                    jobs.append(TopupEddy(bids_data_dir=args.bids_data_dir,
-                                          derivatives_dir=derivatives_dir,
-                                          id=id,
-                                          ses=ses,
-                                          pa_ap_template=args.dwi_template))
-
-                # Ukf task has both dwi_template and pa_ap_template
-                # because a user may want to run {PnlEddy,FslEddy} or TopupEddy
-                elif args.task=='Ukf':
-                    jobs.append(Ukf(bids_data_dir=args.bids_data_dir,
-                                    derivatives_dir=derivatives_dir,
-                                    id=id,
-                                    ses=ses,
-                                    dwi_template=args.dwi_template,
-                                    pa_ap_template=args.dwi_template))
-
-
-                elif args.task=='Fs2Dwi':
-                    jobs.append(Fs2Dwi(bids_data_dir=args.bids_data_dir,
-                                       derivatives_dir=derivatives_dir,
-                                       id=id,
-                                       ses=ses,
-                                       dwi_template=args.dwi_template))
-
-
-                elif args.task == 'Wmql':
-                    jobs.append(Wmql(bids_data_dir=args.bids_data_dir,
-                                     derivatives_dir=derivatives_dir,
-                                     id=id,
-                                     ses=ses,
-                                     dwi_template=args.dwi_template))
-
-
-                elif args.task=='Wmqlqc':
-                    jobs.append(Wmqlqc(bids_data_dir=args.bids_data_dir,
-                                       derivatives_dir=derivatives_dir,
-                                       id=id,
-                                       ses=ses,
-                                       dwi_template=args.dwi_template))
-                                       
-                                       
-                elif args.task=='TractMeasures':
-                    jobs.append(TractMeasures(bids_data_dir=args.bids_data_dir,
-                                              derivatives_dir=derivatives_dir,
-                                              id=id,
-                                              ses=ses,
-                                              dwi_template=args.dwi_template))
+                    jobs.append(TopupEddy(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        pa_ap_template=args.dwi_template))
+
+
+                # This Ukf task has both dwi_template and pa_ap_template
+                # because a user may want to run {PnlEddy,FslEddy,HcpPipe} or TopupEddy
+                elif args.task in ['Ukf','Wma800']:
+                    jobs.append(eval(args.task)(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template,
+                        pa_ap_template=args.dwi_template,
+                        struct_template=args.t1_template))
+
+                elif args.task in ['Fs2Dwi','Wmql','TractMeasures','Wmqlqc']:
+                    jobs.append(eval(args.task)(
+                        bids_data_dir=args.bids_data_dir,
+                        derivatives_dir=derivatives_dir,
+                        id=id,
+                        ses=ses,
+                        dwi_template=args.dwi_template))
+
 
 
     build(jobs, workers=args.num_workers)
     
     
-    print('Removing temporary provenance files')
+    # print('Removing temporary provenance files')
     _rm_tempfiles(glob(pjoin(gettempdir(), 'hashes-*.txt')))
     _rm_tempfiles(glob(pjoin(gettempdir(), 'env-*.yml')))
     
diff --git a/workflows/_synb0_eddy.sh b/workflows/_synb0_eddy.sh
new file mode 100755
index 0000000..bac2046
--- /dev/null
+++ b/workflows/_synb0_eddy.sh
@@ -0,0 +1,90 @@
+#!/bin/bash
+
+# for time profiling
+date
+
+unring_prefix=${1//.nii.gz/}
+b0=$2
+T1=$3
+eddy_prefix=${4//.nii.gz/}
+eddy_mask=$5
+eddy_bse=$6
+ACQPARAMS=$7
+INDEX=$8
+
+
+pushd .
+SES_FOLDER=$(dirname $(dirname $unring_prefix))
+cd $SES_FOLDER
+mkdir -p INPUTS OUTPUTS
+
+cp $b0 INPUTS/b0.nii.gz
+cp $T1 INPUTS/T1.nii.gz
+
+cp $ACQPARAMS INPUTS/
+cp $INDEX INPUTS/
+
+
+echo "3. run synb0 container"
+TMPDIR=$HOME/tmp/
+mkdir -p $TMPDIR
+if [ ! -f OUTPUTS/b0_all_topup.nii.gz ]
+then
+    TMPDIR=$TMPDIR \
+    singularity run -B INPUTS/:/INPUTS -B OUTPUTS/:/OUTPUTS \
+    -B ${NEW_SOFT_DIR}/fs7.1.0/license.txt:/extra/freesurfer/license.txt \
+    ${NEW_SOFT_DIR}/containers/synb0-disco_v3.0.sif --stripped
+fi
+
+echo "4. create mask of topup (synb0) corrected b0"
+# CNN method
+_caselist=$(mktemp --suffix=.txt)
+realpath OUTPUTS/b0_all_topup.nii.gz > $_caselist
+echo "0 0" > OUTPUTS/b0_all_topup.bval
+dwi_masking.py -i $_caselist -f ${NEW_SOFT_DIR}/CNN-Diffusion-MRIBrain-Segmentation/model_folder
+mask=`ls OUTPUTS/*-multi_BrainMask.nii.gz`
+rm $_caselist
+
+if [ -z $mask ]
+then
+    echo topup mask creation failed
+    exit 1
+fi
+
+
+_eddy_out=OUTPUTS/$(basename $eddy_prefix)
+echo "5. run eddy_cuda"
+eddy_cuda \
+  --imain=${unring_prefix}.nii.gz \
+  --bvecs=${unring_prefix}.bvec \
+  --bvals=${unring_prefix}.bval \
+  --mask=$mask \
+  --topup=OUTPUTS/topup \
+  --acqp=INPUTS/acqparams.txt \
+  --index=INPUTS/index.txt \
+  --repol --data_is_shelled --verbose \
+  --out=${_eddy_out} || { exit 1; }
+
+
+
+echo "6. organize outputs"
+# provide masked eddy_out for clarity, quality, and convenience
+fslmaths ${_eddy_out}.nii.gz -mul $mask ${_eddy_out}.nii.gz
+
+mv ${_eddy_out}.nii.gz ${eddy_prefix}.nii.gz
+mv ${_eddy_out}.eddy_rotated_bvecs ${eddy_prefix}.bvec
+cp ${unring_prefix}.bval ${eddy_prefix}.bval
+
+mv $mask $eddy_mask
+mv OUTPUTS/b0_all_topup_bse.nii.gz $eddy_bse
+
+
+
+echo "Luigi-SynB0-Eddy pipeline has completed"
+echo "See outputs at $PWD/dwi/"
+
+popd
+
+# for time profiling
+date
+
diff --git a/workflows/dwi_pipe.py b/workflows/dwi_pipe.py
index d4b85a6..6b5ec25 100755
--- a/workflows/dwi_pipe.py
+++ b/workflows/dwi_pipe.py
@@ -12,7 +12,7 @@
 from time import sleep
 import re
 
-from struct_pipe import StructMask
+from struct_pipe import StructMask, N4BiasCorrect
 from _task_util import _mask_name
 
 from scripts.util import N_PROC, B0_THRESHOLD, BET_THRESHOLD, QC_POLL, LIBDIR, \
@@ -87,7 +87,7 @@ def output(self):
         dwi = local.path(re.sub('_desc-Xc_', '_desc-XcUn_', self.input()['dwi']))
         bval = dwi.with_suffix('.bval', depth=2)
         bvec = dwi.with_suffix('.bvec', depth=2)
-
+        
         return dict(dwi=dwi, bval=bval, bvec=bvec)
 
 
@@ -323,6 +323,69 @@ def output(self):
 
 
 
+@requires(GibbsUn,CnnMask,N4BiasCorrect)
+class SynB0(Task):
+    
+    mask_qc= BoolParameter(default=False)
+    acqp = Parameter()
+    index = Parameter()
+    
+    
+    def run(self):
+        
+        # synb0 wrapper
+        DIR= abspath(dirname(__file__))
+        cmd = (' ').join([f'{DIR}/_synb0_eddy.sh',
+                          self.input()[0]['dwi']._path,
+                          self.input()[1]['bse']._path,
+                          self.input()[2]['n4corr']._path,
+                          self.output()['dwi']._path,
+                          self.output()['mask'],
+                          self.output()['bse'],
+                          self.acqp,
+                          self.index])
+        p = Popen(cmd, shell=True)
+        p.wait()
+        
+        version_file= self.output()['dwi'].dirname.join('fsl_version.txt')
+        check_call(f'eddy_openmp 2>&1 | grep Part > {version_file}', shell= True)
+
+
+        write_provenance(self, self.output()['dwi'])
+
+        # self.dwi= self.output()['dwi']
+        # yield self.clone(BseExtract)
+
+
+
+    def output(self):
+    
+        eddy_epi_prefix= self.input()[0]['dwi'].rsplit('_dwi.nii.gz')[0]
+        eddy_epi_prefix= eddy_epi_prefix.replace('_acq-PA','')
+        eddy_epi_prefix= eddy_epi_prefix.replace('_acq-AP','')
+        eddy_epi_prefix+= 'EdEp'
+        
+        dwi = local.path(eddy_epi_prefix+ '_dwi.nii.gz')
+        bval = dwi.with_suffix('.bval', depth= 2)
+        bvec = dwi.with_suffix('.bvec', depth= 2)
+
+
+        mask_prefix = dwi.rsplit('_desc-')[0]
+        desc= re.search('_desc-(.+?)_dwi.nii.gz', basename(dwi)).group(1)
+        desc= 'dwi'+ desc
+        mask_prefix= mask_prefix+ '_desc-'+ desc
+        mask = local.path(mask_prefix+ '_mask.nii.gz')
+
+        bse_prefix= dwi._path
+        desc= re.search('_desc-(.+?)_dwi.nii.gz', bse_prefix).group(1)
+        desc= 'dwi'+ desc
+        bse= local.path(bse_prefix.split('_desc-')[0]+ '_desc-'+ desc+ '_bse.nii.gz')
+
+
+        return dict(dwi=dwi, bval=bval, bvec=bvec, bse=bse, mask=mask)
+
+
+
 @inherits(FslEddy, PnlEddy, StructMask, BseExtract)
 class EddyEpi(Task):
     debug = BoolParameter(default=False)
@@ -405,9 +468,9 @@ class TopupEddy(Task):
     config = Parameter(default=pjoin(LIBDIR, 'scripts', 'eddy_config.txt'))
 
     useGpu = BoolParameter(default=False)
-    numb0 = Parameter(default=1)
+    numb0 = Parameter(default='1')
     whichVol = Parameter(default='1')
-    scale = Parameter(default=2)
+    scale = Parameter(default='2')
     
     TopupOutDir= Parameter(default='fsl_eddy')
 
@@ -595,7 +658,7 @@ def output(self):
 
 
 
-@inherits(PnlEddy, FslEddy, EddyEpi, TopupEddy, HcpPipe)
+@inherits(PnlEddy, FslEddy, SynB0, EddyEpi, TopupEddy, HcpPipe)
 class Ukf(Task):
 
     ukf_params = Parameter(default='')
@@ -609,6 +672,8 @@ def requires(self):
             return self.clone(PnlEddy)
         elif self.eddy_epi_task=='fsleddy':
             return self.clone(FslEddy)
+        elif self.eddy_epi_task=='synb0':
+            return self.clone(SynB0)
         elif self.eddy_epi_task=='eddyepi':
             return self.clone(EddyEpi)
         elif self.eddy_epi_task=='topupeddy':
@@ -654,7 +719,7 @@ class Wma800(Task):
     wma_cleanup= IntParameter(default=0)
 
     def run(self):
-
+        outDir = self.input().dirname.join('wma800')
         cmd = (' ').join(['wm_apply_ORG_atlas_to_subject.sh',
                           '-i', self.input(),
                           '-a', self.atlas,
@@ -664,12 +729,19 @@ def run(self):
                           f'-n {self.wma_nproc}',
                           f'-c {self.wma_cleanup}',
                           '-d 1',
-                          '-o', self.output()])
+                          '-o', outDir])
         p = Popen(cmd, shell=True)
         p.wait()
-
-        write_provenance(self)
+        
+        write_provenance(self, outDir)
 
     def output(self):
-        return self.input().dirname.join('wma800')
+        prefix= self.input().dirname.join('wma800',self.input().basename.split('.vtk')[0],
+            'FiberClustering/SeparatedClusters')
+        
+        clusters=[]
+        for region in 'commissural left_hemisphere right_hemisphere'.split():
+            clusters.append( local.path(f'{prefix}/diffusion_measurements_{region}.csv') )
 
+        
+        return clusters
diff --git a/workflows/synb0_eddy.sh b/workflows/synb0_eddy.sh
index 386096a..a4bf611 100755
--- a/workflows/synb0_eddy.sh
+++ b/workflows/synb0_eddy.sh
@@ -2,6 +2,7 @@
 
 # for time profiling
 date
+START_TIME=$(date +%s)
 
 # User will edit only this block =========================================================
 caselist=$1
@@ -35,7 +36,6 @@ fi
 
 echo "1. run Luigi pipeline and prepare DWI for synb0 container"
 export LUIGI_CONFIG_PATH
-# source /rfanfs/pnl-zorro/software/pnlpipe3/bashrc3-gpu \
 /rfanfs/pnl-zorro/software/pnlpipe3/luigi-pnlpipe/exec/ExecuteTask --task CnnMask \
 --bids-data-dir $BIDS_DATA_DIR \
 --dwi-template "$DWI_TEMPLATE" \
@@ -64,7 +64,6 @@ unring_prefix=${_unring_prefix//.nii.gz}
 unring_mask=`ls dwi/sub-${c}_ses-${s}_*desc-dwiXcUnCNN_mask.nii.gz`
 if [ ! -f INPUTS/b0.nii.gz ]
 then
-    # source /rfanfs/pnl-zorro/software/pnlpipe3/bashrc3-gpu && \
     fslmaths ${unring_prefix}.nii.gz -mul $unring_mask ${unring_prefix}.nii.gz && \
     bse.py -i ${unring_prefix}.nii.gz -o INPUTS/b0.nii.gz
 fi
@@ -98,16 +97,9 @@ echo "4. create mask of topup (synb0) corrected b0"
 _caselist=$(mktemp --suffix=.txt)
 realpath OUTPUTS/b0_all_topup.nii.gz > $_caselist
 echo "0 0" > OUTPUTS/b0_all_topup.bval
-# source /rfanfs/pnl-zorro/software/pnlpipe3/bashrc3-gpu && \
 dwi_masking.py -i $_caselist -f ${NEW_SOFT_DIR}/CNN-Diffusion-MRIBrain-Segmentation/model_folder
 mask=`ls OUTPUTS/*-multi_BrainMask.nii.gz`
 rm $_caselist
-# BET method
-# cd OUTPUTS/
-# fslroi b0_all_topup.nii.gz _b0.nii.gz 0 1
-# bet _b0.nii.gz b0_all_topup -m -n
-# mask=`realpath b0_all_topup_mask.nii.gz`
-# cd ..
 
 if [ -z $mask ]
 then
@@ -123,7 +115,6 @@ eddy_out=OUTPUTS/sub-${c}_ses-${s}_dir-${dir}_desc-XcUnEdEp_dwi
 # so omit masking at this step
 # fslmaths ${unring_prefix}.nii.gz -mul $mask ${unring_prefix}.nii.gz
 echo "5. run eddy_cuda"
-# source /rfanfs/pnl-zorro/software/pnlpipe3/bashrc3-gpu-cuda-10.2 && \
 eddy_cuda \
   --imain=${unring_prefix}.nii.gz \
   --bvecs=${unring_prefix}.bvec \
@@ -145,7 +136,11 @@ bids_prefix=dwi/sub-${c}_ses-${s}_dir-${dir}_desc-XcUnEdEp_dwi
 mv ${eddy_out}.nii.gz ${bids_prefix}.nii.gz
 mv ${eddy_out}.eddy_rotated_bvecs ${bids_prefix}.bvec
 cp ${unring_prefix}.bval ${bids_prefix}.bval
-mv $mask dwi/sub-${c}_ses-${s}_dir-${dir}_desc-dwiXcUnEdEp_mask.nii.gz
+
+mask_prefix=${bids_prefix//_dwi/}
+mask_prefix=${mask_prefix//XcUn/dwiXcUn}
+mv $mask ${mask_prefix}_mask.nii.gz
+mv OUTPUTS/b0_all_topup_bse.nii.gz ${mask_prefix}_bse.nii.gz
 
 
 
@@ -156,4 +151,5 @@ popd
 
 # for time profiling
 date
-
+ELAPSED_TIME=$(($(date +%s) - $START_TIME))
+echo "Elapsed time: $(($ELAPSED_TIME/60)) min $(($ELAPSED_TIME%60)) sec"