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
- Reformat the 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.
- --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 enabled, then the filenames will automatically be generated
from the series description in the DICOM meta data:
"PatientName/StudyDescription-ID/SeriesDescription_N.nii.gz".
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 .
/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.