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

• dcm2niix Manual
• dcm2niix GitHub

• Module Name: dcm2niix (see the modules page for more information)
• The developer of dcm2niix, Chris Rorden, has provided the Biowulf group with the following comments to help HPC users of dmc2nix:
  • If you want nii.gz compressed output, note that you have two options:
    • "-z y" will write the raw data to disk and then compress with the parallel pigz (assuming pigz is found)
    • "-z i" will use the internal zip compressor: this writes uses a single thread to write compressed data directly to disk.
    In general, "-z y" is faster for single user computers that have fast SSD drives. However, clusters often have slow disk IO and the user may only want to allocate a single thread so that other tasks can run concurrently. For this reason, it may be faster to use "-z i" in a cluster situation.

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/user/.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/user/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 ~]$

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

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