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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)

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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)
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