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.

       --time-tag
              Set the tag to use for time coordinate.

       --time-delta-tag
              Set the tag to use for time spacing.

       --time-delta
              Force the time spacing to be the given value.

       --volume N
              Set which 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.

       The  --time-tag,  --time-delta-tag, and --time-delta options can be used to tweak the time
       information.   By  default,  tags  such  as  TriggerTime,  TemporalPositionIdentifier,  or
       TriggerTime are used to perform temporal sorting, but --time-tag can be used to explicitly
       name a tag.  The --time-delta-tag option can be used  to  set  which  tag  gives  temporal
       spacing,  if  there is no tag that gives the temporal coordinate.  The --time-delta option
       will force the temporal spacing to be a specific value, e.g. 500ms, 2s, or 2600us.

       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 hierarchical 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.