DMRIharmonization-Sapelo2

Category

Engineering

Program On

Sapelo2

Version

20240227

Author / Distributor

See https://github.com/pnlbwh/dMRIharmonization

Description

"dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)." More details are at https://github.com/pnlbwh/dMRIharmonization.

Running Program

• Version 20240227 is installed as a Python virtual environment on Sapelo2 at /apps/gb/dMRIharmonization/20240227

To use it, please load the module and activate its env with:

ml dMRIharmonization/20240227
source ${EBROOTDMRIHARMONIZATION}/harmonization/bin/activate
source ${EBROOTDMRIHARMONIZATION}/../env.sh

To deactivate its env, please do:

deactivate

Below is an example of a job submission script (sub.sh) to run harmonization.py with 24 parallel processes on a single compute node on the batch parttition:

#!/bin/bash
#SBATCH --job-name=test_dMRIharmonization           
#SBATCH --partition=batch          
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --cpus-per-task=1
#SBATCH --mem=100G
#SBATCH --time=7-00:00:00
#SBATCH --constraint="Genoa|Milan"

#SBATCH --mail-type=ALL     
#SBATCH --mail-user=<yourMyID>@uga.edu

cd $SLURM_SUBMIT_DIR

ml purge
ml dMRIharmonization/20240227
source ${EBROOTDMRIHARMONIZATION}/harmonization/bin/activate
source ${EBROOTDMRIHARMONIZATION}/../env.sh

export OMP_NUM_THREADS=1

harmonization.py --nproc 24 <your other options and arguments>

In your actual submission script, please ensure that you request the appropriate computing resources for your job. For example, you can request CPU cores for running parallel processes using the Slurm headers, such as --ntasks=24 and --cpus-per-task=1.

Please note:

• Use the header --constraint="Genoa|Milan" in your job submission script for optimal job performance.
• The value for the header --ntasks, e.g., --ntasks=24, should match the number specified for the --nproc option on your command line, i.e., --nproc=24.
• We highly recommend setting --cpus-per-task=1 and exporting OMP_NUM_THREADS=1 by including export OMP_NUM_THREADS=1in your job submission script.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml dMRIharmonization/20240227 
source ${EBROOTDMRIHARMONIZATION}/harmonization/bin/activate
source ${EBROOTDMRIHARMONIZATION}/../env.sh
harmonization.py -h

===============================================================================
dMRIharmonization (2018) pipeline is written by-

TASHRIF BILLAH
Brigham and Women's Hospital/Harvard Medical School
tbillah@bwh.harvard.edu, tashrifbillah@gmail.com

===============================================================================
See details at https://github.com/pnlbwh/dMRIharmonization
Submit issues at https://github.com/pnlbwh/dMRIharmonization/issues
View LICENSE at https://github.com/pnlbwh/dMRIharmonization/blob/master/LICENSE
===============================================================================

Template creation, harmonization, and debugging

Usage:
    harmonization.py [SWITCHES] 

Meta-switches:
    -h, --help                          Prints this help message and quits
    --help-all                          Prints help messages of all sub-commands and quits
    -v, --version                       Prints the program's version and quits

Switches:
    --bvalMap VALUE:str                 specify a bmax to scale bvalues into
    --create                            turn on this flag to create template
    --debug                             turn on this flag to debug harmonized data (valid only with --process)
    --denoise                           turn on this flag to denoise voxel data
    --force                             turn on this flag to overwrite existing data
    --harm_list VALUE:ExistingFile      harmonized csv/txt file with first column for dwi and 2nd column for mask: dwi1,mask1\n dwi2,mask2\n...
    --nproc VALUE:str                   number of processes/threads to use (-1 for all available, may slow down your system); the default is 4
    --nshm VALUE:str                    spherical harmonic order; the default is -1
    --nzero VALUE:str                   number of zero padding for denoising skull region during signal reconstruction; the default is 10
    --process                           turn on this flag to harmonize
    --ref_list VALUE:ExistingFile       reference csv/txt file with first column for dwi and 2nd column for mask: dwi1,mask1\n dwi2,mask2\n...
    --ref_name VALUE:str                reference site name
    --resample VALUE:str                voxel size MxNxO to resample into
    --stats                             print statistics of all sites, useful for recomputing --debug statistics separately
    --tar_list VALUE:ExistingFile       target csv/txt file with first column for dwi and 2nd column for mask: dwi1,mask1\n dwi2,mask2\n...; required
    --tar_name VALUE:str                target site name; required
    --template VALUE:str                template directory; required
    --travelHeads                       travelling heads

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Installation

Source code is download from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

System

64-bit Linux