dcm2nii(1) [debian man page]

DCM2NII(1)							   User Commands							DCM2NII(1)

NAME

       dcm2nii - convert DICOM or PAR/REC image into the NIfTI format

SYNOPSIS

       dcm2nii <options> <sourcenames>

OPTIONS

       -a Anonymize [remove identifying information]: Y,N = Y

       -b load settings from specified inifile, e.g. '-b /etc/mricron.ini'

       -c Collapse input folders: Y,N = N

       -d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y

       -e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y

       -f Source filename [e.g. filename.par -> filename.nii]: Y,N = Y

       -g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y

       -i ID  in filename [filename.dcm -> johndoe.nii]: Y,N = Y

       -n output .nii file [if no, create .hdr/.img pair]: Y,N = Y

       -o Output Directory, e.g. '/tmp' (if unspecified, source directory is used)

       -p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y

       -r Reorient image to nearest orthogonal: Y,N

       -s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N

       -v Convert every image in the directory: Y,N = Y

       -x Reorient and crop 3D NIfTI images: Y,N = N

       You can also set defaults by editing /home/michael/.dcm2nii/dcm2nii.ini

EXAMPLES

       dcm2nii -a y /home/joe/Documents/dcm/IM_0116

AUTHOR

       dcm2nii was written by Chris Rorden.

       This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).

SEE ALSO

       mricron(1)

       MRIcron Homepage: http://www.cabiatl.com/mricro/mricron/

Michael Hanke							    April 2010								DCM2NII(1)

WARPIMAGEMULTITRANSFORM(1)					   User Commands					WARPIMAGEMULTITRANSFORM(1)

NAME

       WarpImageMultiTransform - part of ANTS registration suite

DESCRIPTION

       Usage:

       ./WarpImageMultiTransform ImageDimension moving_image output_image  -R reference_image --use-NN	 SeriesOfTransformations--(See Below)

	      SeriesOfTransformations  ---  ./WarpImageMultiTransform can apply, via concatenation, an unlimited number of transformations to your
	      data .  Thus, SeriesOfTransformations may be  an Affine transform followed by a warp  another affine and then another warp.

       Inverse affine transformations are invoked by calling
	      -i MyAffine.txt

       InverseWarps are invoked by passing the InverseWarp.nii.gz
	      filename (see below for a note about this).

	      Example 1: Mapping a  warped  image  into  the  reference_image  domain  by  applying  abcdWarpxvec.nii.gz/abcdWarpyvec.nii.gz/abcd-
	      Warpzvec.nii.gz and then abcdAffine.txt

       ./WarpImageMultiTransform 3 moving_image output_image -R reference_image abcdWarp.nii.gz abcdAffine.txt

	      Example 2: To map the fixed/reference_image warped into the moving_image domain by applying the inversion of abcdAffine.txt and then
	      abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.nii.gz .

       ./WarpImageMultiTransform 3 reference_image output_image -R moving_image -i  abcdAffine.txt abcdInverseWarp.nii.gz

	      Note that the inverse maps (Ex. 2) are passed to this program in the reverse order of the forward maps (Ex. 1).

	      This makes sense, geometrically ... see ANTS.pdf for visualization of this syntax.

	      Compulsory arguments:

	      ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration)

	      moving_image: the image to apply the transformation to

	      output_image: the resulting image

	      Optional arguments:

       -R: reference_image space that you wish to warp INTO.

	      --tightest-bounding-box: Computes the tightest bounding box using all the affine transformations. It will be overrided by -R  refer-
	      ence_image  if  given.   --reslice-by-header: equivalient to -i -mh, or -fh -i -mh if used together with -R. It uses the orientation
	      matrix and origin encoded in the image file header.  It can be used together with -R. This is typically not used together  with  any
	      other transforms.

       --use-NN: Use Nearest Neighbor Interpolation.

       --use-BSpline: Use 3rd order B-Spline Interpolation.

       -i: will use the inversion of the following affine transform.

	      Other   Example	Usages:   Reslice   the   image:   WarpImageMultiTransform   3	 Imov.nii.gz  Iout.nii.gz  --tightest-bounding-box
	      --reslice-by-header Reslice the image to a  reference  image:  WarpImageMultiTransform  3  Imov.nii.gz  Iout.nii.gz  -R  Iref.nii.gz
	      --tightest-bounding-box --reslice-by-header

	      Important  Notes:  Prefixname  "abcd"  without  any  extension will use ".nii.gz" by default The abcdWarp and abcdInverseWarp do not
	      exist. They are formed on the basis of abcd(Inverse)Warpxvec/yvec/zvec.nii.gz when calling ./WarpImageMultiTransform, yet  you  have
	      to use them as if they exist.

WarpImageMultiTransform 1.9					     May 2012						WARPIMAGEMULTITRANSFORM(1)