Together with some prequisite software, these bash and python scripts implement the PNL's diffusion and structural MRI processing pipelines. Given a DWI, T1w, and optionally a T2w image, the scripts generate a motion corrected DWI, T1w mask, freesurfer segmentation and freesurfer stats csv, freesurfer segmentation registered to DWI, whole brain tractography, extracted fiber bundles, and extracted fiber bundle measures. And because they are modular, you can run them individually or as a complete pipeline.

Table of Contents

1. Install
2. Quick Walkthrough
3. Pipeline Scripts Overview
4. Redo Overview
5. PNL Pipeline Implementation
6. Repo Organization
7. Issues

Install

The pipeline requires that you have the following software packages pre-installed:

1. Freesurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
2. FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
3. Python with VTK and numpy (easily obtained via anaconda: https://www.continuum.io/downloads)

To install the rest of the dependencies, run the following.

git clone https://github.com/pnlbwh/pnlutil
cd pnlutil/install-software
./all.sh
source ./addpaths.sh

That will install each of the following under the subdirectory install-software:

1. BRAINSTools
2. redo
3. measureTracts
4. UKFTractography

Quick Walkthrough

Setup and run

cd your/project/
mkpipeline.sh .  # copies files in pipeline/ to your project folder
# edit SetUpData_config.sh and make file called 'caselist.txt' with your case id's, one per line 
redo  # begins pipeline by running the default do script 'all.do'

If you only want part of the pipeline:

cd your/project/
addukf.sh .  # or addfs.sh, addmabs.sh, addepi.sh, addfsindwi.sh, etc. (these scripts are at `pnlutil/add*.sh`)
# edit SetUpData.sh to set your input variables for 'ukf'
missing ukf | xargs redo -k

Query progress

The query scripts in scripts-query query the file paths of the variables defined in your data schema, SetUpData.sh. At the PNL we use a set of standard variable names and file paths for the pipeline's output, as defined in SetUpData_pipeline.sh:

t1mabs=$case/strct/$case.t1mabs.nrrd  # generated t1 MABS mask
fs=$case/strct/$case.freesurfer # freesurfer subject directory
dwied=$case/diff/$case.dwi-Ed.nrrd  # eddy current corrected DWI
ukf=$case/diff/$case.ukf_2T.vtk.gz  # whole brain tractography
fsindwi=$case/diff/$case.fsindwi.nrrd  # freesurfer segmentation registered to DWI space
wmqltracts=$case/diff/$case.wmqltracts  # directory of fiber bundles extracted using tract_querier
tractmeasures=$case/diff/$case.tractmeasures.csv  # fiber bundle measures
tractvols=$case/diff/$case.tractvols.csv  # fiber bundle volumes

The data is queried thus:

vars  # convenient way of listing variables in the data schema SetUpData.sh
completed dwied # lists eddy current corrected DWI's generated so far
missing t1mabs  # lists missing t1 masks
all ukf # lists paths of all tractography files that are to be generated; this will be same size as your case list file
casestatus 01009  # shows what files are and are not generated for case 01009
logstatus  # shows progress of each variable in 'status_vars' (and saves the result to statuslog.csv)

logstatus is one you'll use frequently to track the pipeline's progress.

Pipeline Scripts Overview

This table summarizes the scripts in scripts-pipeline.

Category	Script	Function	Software Dependencies
General	axis_align_nrrd.py	removes oblique coordinate tranform	teem
General	center.py	changes origin to be at the center of the volume	teem
General	mask	skullstrips by applying a labelmap mask	teem ConvertBetweenFileFormats
DWI	dwiPipeline-nofilt.py	eddy and motion correction via registration	teem FSL ConvertBetweenFileFormats numpy
DWI	bse.sh	extracts a baseline b0 image	teem
DWI	dwibetmask	computes a bet mask	FSL ConvertBetweenFileFormats
DWI	maskbse	extracts a baseline b0 image and masks it	teem
DWI	epi.sh	corrects EPI distortion via registration	teem ANTs
Structural	mabs.sh	computes a brain mask from training data	teem ANTs
Structural	fs.sh	runs freesurfer but takes care of some common preprocessing steps	Freesurfer ConvertBetweenFileFormats teem
Structural	fsstats.sh	creates a csv file of select freesurfer measures	-
Structural	make_rigid_mask.sh	rigidly transforms a labelmap to align with another structural image	ANTs teem
Freesurfer to DWI	fs2dwi.sh	registers a freesurfer segmentation to a DWI	Freesurfer ANTs ConvertBewteenFileFormats teem
Freesurfer to DWI	fs2dwi_T2.sh	registers a freesurfer segmentation to a DWI using a T2 (better)	Freesurfer ANTs ConvertBewteenFileFormats teem
Tractography	wmql.sh	simple wrapper for tract_querier	tract_querier gunzip ConvertBewteenFileFormats

Redo Overview

Data pipelines are built by connecting components that read inputs and emit an output. The overall result is a workflow that reads a set of input data and outputs a set of processed data.

This makes build systems a good candiate for implementing pipelines. They have the same requirements as a data pipeline: an output file depends on the existence of other files, and if those files are missing then they must be generated first. So although they are typically used by programmers to compile code, they are also used by researchers to process data.

There are many build systems to choose from, but typically all come with their own "pipeline writing" language, and many also have the limitation of only accepting static dependencies, meaning all the dependencies have to be known up front (for example, they won't be able to find non-deterministic dependencies like files with time stamps). Fortunately, redo is a simple build system that avoids these issues, and so we use it to implement the PNL pipeline.

Redo works by executing a script for each output file or directory. In other words, the scripts are pipeline components that accept inputs and compute an output. These scripts are named in two specials ways. First, they must end with the extension '.do', so that redo can find them. Second, their names determine the name of their output. For example, if you wanted to generate a csv file called data.csv, you would name your csv making script data.csv.do

To call redo you run redo <filename>, which makes redo find and execute the matching .do script, thus creating the output <filename>.

Dependencies are declared inside each .do script. If those dependencies are found missing during execution, then redo will look for the matching .do scripts and run them before continuing with the current script. For example, if your data.csv.do relies on a text file data.txt and it doesn't exist, then redo will look for and execute data.txt.do before continuing with its execution of data.csv.do.

.do files can also be named with a leading default. to match many files you wish to build using the same script. Using the previous example, instead of having a data.csv.do, you could have a default.csv.do that takes the string matched by 'default' and uses it to find its text file dependency. So redo data.csv would invoke default.csv.do with 'data' as an argument and thus it knows to use data.txt as its input for building data.csv.

PNL Pipeline Implementation

Each .do script in the pipeline/ is a bash script that generates either an image, directory, or csv file. The scripts interpret the 'default' part of their names as case id's, which they use to find their inputs. For example, redo 0001.dwi-Ed.nrrd.do invokes default.dwi-Ed.nrrd.do which uses the case id 0001 to find its input DWI. This requires that it be able to generate the file path from a case id, but since projects have different file paths, we need a way to specify them without hardcoding them in the scripts.

This is accomplished by writing a bash config file called SetUpData.sh. Whenever a .do script is called, it sources this file and uses the file paths of specifically named variables as its input (if these variables don't exist it will complain and exit). For example, default.dwi-Ed.nrrd.do expects the path of its input to be in a variable called dwied_dwi, so in SetUpData.sh you would have a line such as dwied_dwi=path/to/${case}-dwi.nrrd. Running redo 0001.dwi-Ed.nrrd would invoke default.dwi-Ed.nrrd.do with '0001' as an argument, which sets the variable case to be '0001' and sources SetUpData.sh, and thus the variable dwied_dwi resolves to path/to/0001-dwi.nrrd which is used as the input DWI.

Because the output of one .do script will be the input of another, SetUpData.sh can define a pipeline. Here's a two step example:

## Source data ##################################
dwiraw=$case/$case-dwi.nrrd

## Derived data #################################
# Eddy current correction
# Input
dwied_dwi=$dwiraw
# Output
dwied=$case/$case.dwi-Ed.nrrd  # filename must match 'default.dwi-Ed.nrrd.do'

# BET mask
# Input
dwibetmask_dwi=$dwied
# Output
dwibetmask=$case/$case.dwibetmask.nrrd  # filename must match 'default.dwibetmask.nrrd.do'

Running redo 0001/0001.dwibetmask.nrrd would first generate the eddy current corrected dwi 0001/0001.dwi-Ed.nrrd followed by the bet mask 00001/00001.dwibetmask.nrrd.

The extra output variables dwied and dwibetmask aren't strictly necessary but they make the config file clearer and querying your data easier (see below).

The full PNL pipeline is defined in pipeline/SetUpData_pipeline.sh. There you can see how each of the components are connected together. Since the pipeline is already specified all that it needs to be run is your input data: a DWI file path, a T1 file path, and a list of your case id's in a file caselist.

Repo Organization

The main scripts are organized into directories as follows.

1. scripts-pipeline

The pipeline is built from these scripts. The are the pipeline's 'functions', and they can be run independently.

2. scripts-query

These scripts query your project's data schema and print lists of files that match certain conditions. For example, you can list all the freesurfer's that have yet to be generated, or all the T1w masks that have already been generated.

3. scripts-qc

Contains scripts to help with quality control. The main one is qc, and like the query scripts relies on you having defined a data schema for your project. You can then use it to loop through your case list and load Slicer for some subset of a subject's data, saving a csv file with your notes and whether or not they passed QC.

4. pipeline

This folder contains the scripts that are plugged together to build pipelines, and depend on and use the scripts in scripts-pipeline. These scripts are never called directly -- they are used by the build system that implements the pipeline. Instead, you are only required to define the location of your data in your data schema, and the scripts will read that information and execute the pipeline.

5. scripts-all

Contains symlinks to all other scripts so that you can access them by simply referencing this folder (for example by putting it on your PATH).

Issues

Running redo hangs

This will happen when a redo process is interrupted unexpectedly and leaves behind a lock file. To fix this, first make sure no-one else is running redo in your project, then run

find . -name "*.lock" -exec rm {} \;

or

cleanlocks.sh

This will clean up the stale lock files which lets redo know it can safely build their associated outputs.