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.

dicomtonifti 0.8.14                                April 2024                                    DICOMTONIFTI(1)