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dicomtonifti
Convert DICOM images to NIfTI format.
dicomtonifti -o file.nii file1.dcm [file2.dcm ...]
dicomtonifti -o directory --batch file1.dcm [file2.dcm ...]
-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.
--version Print the version and exit.
--volume N Set the volume to output (starts at 0).
--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 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 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:
dicomtonifti -brz -o {SeriesDescription}-{SeriesNumber}.nii /path/to/dicom/files