Mango (Multi-image Analysis GUI) is a viewer for medical research images. Mango contains analysis tools and a GUI to navigate image volumes. Mango also comes with the following command-line utilities: mango (loads image), mango-applytransform (applies transform to image), mango-convert2avw (converts to AVW format), mango-convert2des (converts to DES format), mango-convert2nii (converts to NIFTI format), mango-imageinfo (prints image metadata summary), mango-makeroi (makes ROI based on image threshold), mango-resizer (resizes image), mango-script (runs mango script), mango-vols2series (concatenates volumes into series).

Web site

• Home page

• Mango User Guide

• Module Name: mango (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mango

[user@cn3144 ~]$ mango-imageinfo sub-01_T1w.nii.gz

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mango_job.sh). For example:

#!/bin/bash

export TMPDIR=/lscratch/$SLURM_JOB_ID

module load mango
mango-convert2avw sub-01_T1w.nii.gz

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mango_job.sh

Create a swarmfile (e.g. mango_jobs.swarm). For example:

mango-convert2avw sub-01_T1w.nii.gz
mango-convert2avw sub-02_T1w.nii.gz
mango-convert2avw sub-03_T1w.nii.gz
mango-convert2avw sub-04_T1w.nii.gz
mango-convert2avw sub-05_T1w.nii.gz

Submit this job using the swarm command.

swarm -f mango_jobs.swarm [-g #] [-t #] --module mango