bionic (1) dicomtonifti.1.gz

NAME

       dicomtonifti - vtk-dicom CLI

DESCRIPTION

   usage:
              dicomtonifti -o file.nii file1.dcm [file2.dcm ...]

              dicomtonifti -o directory --batch file1.dcm [file2.dcm ...]

   options:
       -o <output.nii[.gz]>
              The output file (or directory, if --batch).

       -z --compress
              Compress output files.

       -r --recurse
              Recurse into subdirectories.

       -b --batch
              Do multiple series at once.

       -s --silent
              Do not echo output filenames.

       -v --verbose
              Verbose error reporting.

       -L --follow-symlinks
              Follow symbolic links when recursing.

       --fsl  Format axial image for use in FSL.

       --reformat-to-axial
              Reformat the image into axial orientation.

       --no-slice-reordering
              Never reorder the slices.

       --no-row-reordering
              Never reorder the rows.

       --no-column-reordering
              Never reorder the columns.

       --no-reordering
              Never reorder slices, rows, or columns.

       --no-qform
              Don't include a qform in the NIFTI file.

       --no-sform
              Don't include an sform in the NIFTI file.

       --volume N
              Set the volume to output (starts at 0).

       --version
              Print the version and exit.

       --build-version
              Print source and build version.

       --help Documentation for dicomtonifti.

       This program will convert a DICOM series into a NIfTI file.

       It  reads  the  DICOM  Position and Orientation metadata, and uses this information to generate qform and
       sform entries for the NIfTI header, after doing a conversion from the  DICOM  coordinate  system  to  the
       NIfTI coordinate system.

       By default, it will also reorder the columns of the image so that columns with higher indices are further
       to the patient's right (or in the case of sagittal images, further anterior).   Likewise,  rows  will  be
       rearranged  so  that  rows  with higher indices are superior (or anterior for axial images).  Finally, it
       will reorder the slices so that the column direction, row  direction,  and  slice  direction  follow  the
       right-hand rule.

       It  is also possible to reformat the images into the axial orientation via the --reformat-to-axial option
       This option is mutually exclusive with the no-reordering options.  The resulting orientation matrix  will
       be the identity matrix.

       If  the  output  NIFTI  files  are  to  be  used with the FMRIB FSL package, then use the --fsl option to
       reformat the images to match the standard FSL orientation: axial images with  the  slices  arranged  from
       inferior  to  superior,  column  number  increasing  from  right  to left, and row number increasing from
       posterior to anterior.  This will also convert the data type from unsigned 16-bit  to  signed  16-bit  if
       necessary.

       If  batch  mode is selected, the output file given with "-o" can be constructed from DICOM attributes, by
       providing  the  attribute  names  within  curly   braces.    For   example,   consider   the   following:
       "{PatientID}-{StudyDate}/{SeriesDescription}-{SeriesNumber}.nii"   or  something  similar  to  produce  a
       hierarchichal directory structure.  The attributes used in the path should be from the following list:

              PatientID,  PatientName,  PatientBirthDate,  PatientSex,  StudyID,  StudyDescription,   StudyDate,
              StudyTime,   StudyInstanceUID,   SeriesNumber,   SeriesDescription,  SeriesInstanceUID,  Modality,
              AccessionNumber.

       Here is an example of batch mode that recurses into  subdirectories  and  compresses  the  output  files,
       putting the results in the current directory:

       ./obj-x86_64-linux-gnu/bin/dicomtonifti        -brz       -o       {SeriesDescription}-{SeriesNumber}.nii
       /path/to/dicom/files

AUTHOR

       This  manual  page was written by Mathieu Malaterre <malat@debian.org> for the Debian  GNU/Linux  system,
       but may be used by others.