Biowulf High Performance Computing at the NIH
dcm2niix on Biowulf

dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[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 dcm2niix/1.0.20171017
[user@cn3144 ~]$ dcm2niix -h

Chris Rorden's dcm2niiX version v1.0.20171017 (OpenJPEG build) GCC7.2.0 (64-bit Linux)
usage: dcm2niix [options] 
 Options :
  -1..-9 : gz compression level (1=fastest..9=smallest, default 6)
  -b : BIDS sidecar (y/n/o(o=only: no NIfTI), default y)
   -ba : anonymize BIDS (y/n, default y)
  -c : comment stored as NIfTI aux_file (up to 24 characters)
  -d : diffusion volumes sorted by b-value (y/n, default n)
  -f : filename (%a=antenna  (coil) number, %c=comments, %d=description, %e echo number, %f=folder name, %i ID of patient, %j seriesInstanceUID, %k studyInstanceUID, %m=manufacturer, %n=name of patient, %p=protocol, %s=series number, %t=time, %u=acquisition number, %v=vendor, %x=study ID; %z sequence name; default '%f_%p_%t_%s')
  -h : show help
  -i : ignore derived, localizer and 2D images (y/n, default n)
  -m : merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)
  -o : output directory (omit to save to input folder)
  -p : Philips precise float (not display) scaling (y/n, default y)
  -s : single file mode, do not convert other images in folder (y/n, default n)
  -t : text notes includes private patient details (y/n, default n)
  -v : verbose (n/y or 0/1/2 [no, yes, logorrheic], default 0)
  -x : crop (y/n, default n)
  -z : gz compress images (y/i/n/3, default n) [y=pigz, i=internal, n=no, 3=no,3D]
 Defaults file : /home/wresch/.dcm2nii.ini
 Examples :
  dcm2niix /Users/chris/dir
  dcm2niix -c "my comment" /Users/chris/dir
  dcm2niix -o /users/cr/outdir/ -z y ~/dicomdir
  dcm2niix -f %p_%s -b y -ba n ~/dicomdir
  dcm2niix -f mystudy%s ~/dicomdir
  dcm2niix -o "~/dir with spaces/dir" ~/dicomdir
Example output filename: '/myFolder_MPRAGE_19770703150928_1.nii'

[user@cn3144 ~]$ cp $DCM2NIIX_TEST_DATA/CR-MONO1-10-chest.gz .
[user@cn3144 ~]$ gunzip CR-MONO1-10-chest.gz
[user@cn3144 ~]$ dcm2niix /CR-MONO1-10-chest
Chris Rorden's dcm2niiX version v1.0.20171017 (OpenJPEG build) GCC7.2.0 (64-bit Linux)
Found 1 DICOM image(s)
Convert 1 DICOM as /home/wresch/notes/software/dcm2niix/dcm2niix__0_1a (440x440x1x1)
Warning: Check that 2D images are not mirrored.
Conversion required 0.047990 seconds (0.020000 for core code).

# or for a whole folder
[user@cn3144 ~]$ dcm2niix -o ./my_nifty -z y ./my_dicom

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

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. dcm2niix.sh), which uses the input file 'dcm2niix.in'. For example:

#!/bin/bash
module load dcm2niix/1.0.20171017
dcm2niix  -o ./my_nifty -z y ./my_dicom

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] dcm2niix.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. dcm2niix.swarm). For example:

dcm2niix  -o ./my_nifty1 -z y ./my_dicom1
dcm2niix  -o ./my_nifty2 -z y ./my_dicom2
dcm2niix  -o ./my_nifty3 -z y ./my_dicom3

Submit this job using the swarm command.

swarm -f dcm2niix.swarm [-g #] [-t #] --module dcm2niix
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module dcm2niix Loads the dcm2niix module for each subjob in the swarm