fMRIbox_docker

This fork is not intended to be merged back into the original. The idea is to be free to diverge to add more functionality for my use cases. For now on, keeping the original description.

About

The preprocessing script pd_dockerParallelized.sh takes the functional and anatomical MRI files and produces a smoothed, registered NIfTI file in MNI 152 space. If the appropriate field maps and acquisition parameters are provided as input from the user, TOPUP and bias correction take place. Otherwise, they are skipped.

Using on the HPC Cluster

Overview: The script processes one run at a time, meaning it processes one fMRI/sMRI pair at once. An entire set of fMRI/sMRI pairs can be submitted to the SLURM scheduler on the high performance computing (HPC) cluster. The set of fMRI/sMRI file pairs, along with the desired output directory, should be provided to the script such that the entire set is processed as individual, parallel instances of SLURM jobs. Each SLURM job is an instance of the script being executed inside a container instance. The resulting processed file is written to the output directory specified for that particular sMRI/fMRI pair.

First Time Setup

1. Clone this Repository

Connect to the cluster and clone this repository into your data directory by issuing the following command.

git clone https://github.com/neuroneural/nshor_docker/

2. Prepare the Docker Container

The Dockerfile is already specified for this script in the root directory of this project, named Dockerfile. This copies pd_dockerParallelized.sh into a file inside the container that can later be called through the Singularity commands.

Enter a cluster node that has docker. Currently this includes arctrdcn017 and arctrdgndev101
If you get permissions errors using the following commands, submit a ticket at hydra.gsu.edu (with assignee arctic_developers) asking to be added to the docker group.
Enter your cloned nshor_docker directory.
Build the Docker container using the premade Dockerfile:

docker build . -t fmriproc:latest

Note that fmriproc is an arbitrary name and may be overwritten if someone else creates a Docker image with the same name on the same cluster node. It's recommended to use a unique name, such as fmriproc_YOUR-USERNAME. Be sure to future instances of fmriproc with your chosen name.

The tag name ("latest" here) is also arbitrary, but does not need to be unique. If you set no tag, it will be set to "latest", so that's what's used in the following demo commands. (Some future commands may throw errors if no tag is specified when referencing your image, which is why it matters.)

You may use docker image ls to confirm your Docker image exists.
(OPTIONAL/SITUATIONAL) There may be a scenario in which archiving the docker image to a tar file would be beneficial. In a case where singularity and docker are not available on the same server, then exporting to a tar file would make it possible to build the singularity file without the docker daemon running. To archive an existing docker image, use: docker save -o fmriproc.tar fmriproc:latest

3. Prepare the Singularity Container

Singularity is a container software used in HPC settings to work with Docker. You can create Singularity images and containers without needing administrative rights on the server. This script should be executed inside a Singularity container build off of a Docker image. With the Docker image built, load the Singularity module and build the .sif image.

Load the singularity module:

module load singularity

Build the singularity container:

singularity build --writable-tmpfs output.sif docker-daemon://fmriproc:latest

If your docker image has been archived as a .tar file, then you can use Singularity's docker-archive option without needing the docker daemon to be awake: singularity build --writable-tmpfs output.sif docker-archive://fmriproc.tar

The --writable-tmpfs flag creates a temporary file system in the sif container that you can write intermediate files to. This script writes all intermediate files to the sif container's temporary file system's shm directory, or shared memory.

Usage

Process A Single File

singularity exec --writable-tmpfs --bind $func_bind:/func,$anat_bind:/anat,$out_bind:/out $SIF_FILE /app/main.sh -f $func_file -a $anat_file -o $out_bind

Mandatory:

$SIF_FILE is a path to your Singularity container file, as specified by the --writable-tmpfs argument when running singularity build earlier. Our example named it output.sif.
$func_file is an fMRI file inside the $func_bind absolute directory
$anat_file is an sMRI file inside the $anat_bind absolute directory
$out_bind is an existing output directory to which subject's processed file is written out

Optional extra arguments:

-j : name of json sidecar file containing metadata
-c : bias channel field map file
-b : bias body coil field map file
-s : single band reference (SBREF) image file
-l : left-right spin echo field map file
-r : right-left spin echo field map file

You must use module load singularity before running singularity commands in a given session. Otherwise, you will get a "command 'singularity' not found" error.

Set Up for Slurm Job Submissions

The script can be run on the cluster using an interactive SLURM job, or using sbatch (recommended). It is recommended to submit the job via sbatch when processing more than one subject. This is because each subject can take anywhere from 13 to 20 minutes each.

You can view more examples in the examples section of this repository. Look at About the Examples for more info on the purpose of each file, and additional helper files that show up in the examples section.

Here's a simple example setup for submitting a large number of files to the cluster for processing.

`paths.txt`

The script expects an input text file of the follwing format, where order matters and lines with (OPTIONAL) at the end should only be included when their associated flags are utilized with the singularity exec call. Given output directories should be unique & should already exist on the cluster. See the Preparing Output Directories section for more info.

full file path on the cluster to functional MRI file for 1st run
full file path on the cluster to anatomical MRI file for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the left right spin echo field map file for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the right left spin echo field map file for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the bias channel field map file for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the bias body coil field map file for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the single band reference (SBREF) image for 1st run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the acquisition parameters file for 1st run
full file path on the cluster to the subject's output directory to which processed files are to be written for 1st run
.
.
.
full file path on the cluster to functional MRI file for nth run
full file path on the cluster to anatomical MRI file for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the left right spin echo field map file for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the right left spin echo field map file for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the bias channel field map file for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the bias body coil field map file for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the single band reference (SBREF) image for nth run
(OPTIONAL/DEPENDS ON FLAGS) full file path on the cluster to the acquisition parameters file for nth run
full file path on the cluster to the subject's output directory to which processed files are to be written for nth run

Where n is the number of runs that you wish to process. The user is responsible for generating such a file, which can be done using bash. There are some example scripts in each example project directory as part of this repository. For more information, see the About the Examples informational section above.

The simplest version of this file (with no optional flags provided) looks like:

PATH_TO_FMRI_FILE_1
PATH_TO_ANAT_FILE_1
PATH_TO_OUT_DIRECTORY_1
PATH_TO_FMRI_FILE_2
PATH_TO_ANAT_FILE_2
PATH_TO_OUT_DIRECTORY_2
...

`procruns.job`

The file that sets up each slurm submission.

#!/bin/bash
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=64g
#SBATCH -p qTRD
#SBATCH --time=20:00:00
#SBATCH -J NAME_OF_JOB
#SBATCH -e FULL/PATH/TO/LOGS/OUTPUT/DIRECTORY/%A_%a.err
#SBATCH -o FULL/PATH/TO/LOGS/OUTPUT/DIRECTORY/%A_%a.out
#SBATCH -A psy53c17
#SBATCH --mail-type=ALL
#SBATCH --mail-user=YOUR_EMAIL
#SBATCH --oversubscribe

sleep 5s

module load singularity/3.10.2

SUB_PATHS_FILE=FULL/PATH/TO/paths.txt

SIF_FILE=FULL/PATH/TO/SINGULARITY/CONTAINER.sif

IFS=$'\n'
paths_array=($(cat ${SUB_PATHS_FILE}))

anat_ix=$(( 3*SLURM_ARRAY_TASK_ID ))
func_ix=$(( 3*SLURM_ARRAY_TASK_ID + 1 ))
out_ix=$(( 3*SLURM_ARRAY_TASK_ID + 2 ))

anat_filepath=${paths_array[${anat_ix}]}
func_filepath=${paths_array[${func_ix}]}

out_bind=${paths_array[${out_ix}]}
anat_bind=`dirname $anat_filepath`
func_bind=`dirname $func_filepath`

anat_file=`basename $anat_filepath`
func_file=`basename $func_filepath`

singularity exec --writable-tmpfs --bind $func_bind:/func,$anat_bind:/anat,$out_bind:/out $SIF_FILE /app/main.sh -f $func_file -a $anat_file -o $out_bind &

wait

sleep 10s

`submit.sh`

The file to run on the login node to submit the above in an array:

#!/bin/bash

project_dir=FULL/PATH/TO/nshor_docker
paths_file=${project_dir}/paths.txt

num_lines=`wc -l <  $paths_file`
num_total_runs=$(( num_lines / 3 ))

runix=$(( num_total_runs ))

cd $project_dir

sbatch --array=0-${runix} ${project_dir}/procruns.job

After creating these files and filling out the paths, you would then run bash submit.sh on the login node.

Misc. Troubleshooting

If having trouble submitting ry manually processing a single file from your PATHS file (on a dev node), to make sure your paths are correct.

Errors like "Can't open dataset" showing up in your logs usually means there's a problem with your file paths. Double check that all paths are correct and listed in the right places across your submission and paths files.

Additional Information

Running using an Interactive Session

For more information, see the setvarstest.sh script section and associated outer section, About the Examples. For running this script in an interactive session on the cluster, it is not required to use GPU partitions. You can use an interactive session for processing one or more subjects in the following way:

allocate an interactive session on the cluster using srun
move into the project directory and source the setvarstest.sh file
- or your own bash file which sets the required environment variables for the singularity exec call
run the pd_dockerParallelized.sh script inside the sif container using singularity exec
note, you need to adjust the SLURM_ARRAY_TASK_ID to control which run to process from your paths input file
- setting SLURM_ARRAY_TASK_ID=0 processes the first run from your paths input file
- this only applies to interactive runs that use the setvarstest.sh scripts to set environment variables

For more information about running SLURM interactive jobs, see the resource allocation guide in the cluster documentation.

About the Examples

The repository contains example project directories in the examples directory. Each example is named <DATASET>-project where <DATASET> is replaced by the dataset name. Inside each of these project directories are some helper scripts for each dataset to perform various tasks related to this script.

The `mkpths.sh` Script

looks at the raw data on the cluster
counts the number of subjects from the input subjects.txt file
iterates over all subjects' runs
writes the desired files (func/anat/fieldmaps/params) to the paths file
creates output directories in the user's data directory for the processed results

The `procruns.job` Script

sets the SBATCH settings for SLURM
loads the singularity module
tells the script where the paths file is located (see "Preparing the Paths File")
parses the data filepaths and bindpoints from the paths file
mounts the location on the cluster of the input data for the sif container to access
executes the script in the sif container providing filepaths as input

The `submit.sh` Script

sets the project directory and paths file
counts the number of lines in the paths file
divides num lines by the number of files per subject to determine number of total runs included in file
sets the SLURM array to the number calculated in the previous step
submits the procruns.job script to SLURM as an sbatch submission

The `setvarstest.sh` Script

sets the environment variables necessary to run this script in the container
source this setvarstest.sh script for testing in an interactive SLURM session
you can then execute a singularity exec call to test the script (in SLURM interactive mode)

Preparing Output Directories

The script expects an output directory for each run to exist on the cluster which is provided by the user in the paths input file. It is the user's responsibility to prepare the output directory on the cluster. There are some example scripts on how to do this in each example project directory as part of this repository. For more information, see the About the Examples section above.

For example, if you are trying to process a number of runs from the BSNIP dataset, you might create an output directory BSNIP which will hold the processed information for each subject. You can create a subdirectory for each subject and within that, a directory for each session or run that you wish to process. See the file structure below for an illustration of this example.

/data/users2/<GSU_ID>/nshor_docker/
├── bsnip-project
│   ├── BSNIP
│   │   └── Boston
│   │       ├── mkpths.sh
│   │       ├── paths
│   │       ├── S0153WRT1
│   │       │   └── ses_01
│   │       │       └── processed
│   │       │           └── S0153WRT1_rsfMRI_processed_rest.nii.gz
│   │       ├── S0914NVL1
│   │       │   └── ses_01
│   │       │       └── processed
│   │       │           └── S0914NVL1_rsfMRI_processed_rest.nii.gz
│   │       ├── S1424WOT1
│   │       │   └── ses_01
│   │       │       └── processed
│   │       │           └── S1424WOT1_rsfMRI_processed_rest.nii.gz
.
.
.
│   │       ├── S9670AKK1
│   │       │   └── ses_01
│   │       │       └── processed
│   │       │           └── S9670AKK1_rsfMRI_processed_rest.nii.gz
│   │       ├── S9875KAK1
│   │       │   └── ses_01
│   │       │       └── processed
│   │       │           └── S9875KAK1_rsfMRI_processed_rest.nii.gz
│   │       └── subjects.txt

The <SUBJECT_ID>_rsfMRI_processed_rest.nii.gz files are the result of running the preprocessing script, where SUBJECT_ID is the subject ID for the subject and GSU_ID is your GSU ID.

Hierakonpolis/fMRIbox_docker

fMRIbox_docker

About

Using on the HPC Cluster

First Time Setup:

Usage:

Additional Information: