dcm2niix_afni

Contents

• dcm2niix_afni

Compression will be faster with /usr/local/bin/pigz
Chris Rorden's dcm2niiX version v1.0.20170411 GCC5.4.0 (64-bit Linux)
usage: dcm2niix_afni [options] <in_folder>
 Options :
  -1..-9 : gz compression level (1=fastest, 9=smallest)
  -b : BIDS sidecar (y/n, default y)
  -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, %z sequence name; default '%f_%p_%t_%s')
  -h : show help
  -i : ignore derived, localizer and 2D images (y/n, default n)
  -t : text notes includes private patient details (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, default n) [y=pigz, i=internal, n=no]
 Defaults file : /home/afniHQ/.dcm2nii.ini
 Examples :
  dcm2niix_afni /Users/chris/dir
  dcm2niix_afni -o /users/cr/outdir/ -z y ~/dicomdir
  dcm2niix_afni -f mystudy%s ~/dicomdir
  dcm2niix_afni -o "~/dir with spaces/dir" ~/dicomdir