dtoa - DICOM to ACR/NEMA and Analyze

Command line program to convert DICOM format to ACR/NEMA and then to Analyze v7 format.

dtoa [-ana | -nif | -nii [-delses | -nodelses] [-over] [-isfil] [-rcv] [-noge] [-notime] [-scale]
     [-diff [-fdt] [-fnomask] [-fnoeddy] [-pq] [-gfa] [-medinria]]
     [-scracr] [-acr] [-fpv] [-dv] [-quiet] [-gz]] [-add] [-noadd] [-anon] [-date] [-datefirst] [-s<num>]
     [-c] [-float] [-spos] [-itime] [-[no]spmo] [-exe <path>] [-v] [-time] [-coil] [-meta] [-mono] [-clip]
     [DICOM_source_directory_root [ACR/NEMA or Analyze_destination_directory_root]]

-ana

Converts ACR/NEMA files to Analyze format. If this flag has been specified, the following indented flags will also become active. If this flag is present with -nif or -nii flags then the last flag specified takes priority.

-nif

Converts ACR/NEMA files to NIFTI-1 format, with separate .hdr and .img files. If this flag has been specified, the following indented flags will also become active. If this flag is present with -ana or -nii flags then the last flag specified takes priority.

-nii

Converts ACR/NEMA files to NIFTI-1 format as a combined .nii file. If this flag has been specified, the following indented flags will also become active. If this flag is present with -ana or -nif flags then the last flag specified takes priority.

-delses

After conversion, delete the temporary ACR/NEMA or DICOM files created during conversion (this is now the default). The source ACR/NEMA or DICOM files will not be deleted.

-nodelses

After conversion, do not delete the temporary ACR/NEMA or DICOM. They will remain in a subdirectory named session_1.

-over

This flag is passed to acrtoana. The converted Analyze files will overwrite existing Analyze files with the same name. If this option is not specified, existing Analyze files should not be overwritten but will be named with subsequent series numbers to the previously existing files. Also see the -date option, below.

-gz

This flag is passed to acrtoana. The converted files will be compressed using gzip with resulting filename extensions .gz. This option is only available if the zlib libraries have been included during compilation with an ANSI C compiler.

-isfil

This flag is passed to acrtoana. While converting to Analyze, try to determine whether images are in Siemens mosaic format and if so, split them into individual images.

-rcv

Rotate coronal VENDIE. This flag is passed to acrtoana. If the images appear to be a coronal VENDIE acquisition (according to the sequence filename or protocol name stored in the ACR/NEMA header) then call the mirrot program to produce an additional Analyze file containing axial images.

-noge

Do not perform additional slice reordering on GE DICOM files. This flag is passed to acrtoana.

-notime

This flag is passed to acrtoana. The acquisition time ACR/NEMA message is ignored in the algorithm that determines which images belong togther in an acquisition series. This may be useful when converted Analyze files are created with one image per file while the desire is to produce a combined Analyze file. This may occur from some manufacturer's images for dynamic acquisitions or when images have been post-processed on the scanner, e.g., a cardiac cine or rotating MIP.

-scale

This flag is passed to acrtoana. If the intensity scaling factor stored in the ACR/NEMA header changes then start a new Analyze file. If this flag is not specified then changes in intensity scaling factor are ignored in the algorithm that determines which images belong together in an acquisition series.

-diff

This flag is passed to acrtoana which attempts to recognise diffusion weighted acquisitions from information in the ACR/NEMA header. If a diffusion acquisition is detected, write the diffusion gradient vectors to an associated text file _dgv.txt, write a second Analyze file in which the images are ordered correctly for FSL's diffusion toolbox and also write associated the _bvecs, _bvals files, and write a text file containing the diffusion b matrices _bmat. Appears to work for Philips (normal and overplus), Siemens, and GE product sequences although largely untested for mainly sagittal or coronal acquisitions.

-fdt

This flag is passed to acrtoana. If a diffusion acquisition is detected then after all file conversion has finished, perform basic post-processing using FSL's diffusion toolbox to perform eddy current correction, calculate the diffusion tensor, produce maps of Mean Diffusivity, Fractional Anisotropy, and an isotropic diffusion weighted image. This options requires that FSL is installed correctly and that the detected diffusion acquisition contained at least six diffusion directions. The processing is set running in the background and may take some time; no confirmation is given when processing is complete (other than appearence of the relevant image files) and this must be taken into consideration when rebooting the computer, especially if using Cygwin. Under UNIX or GNU/Linux, the background jobs are batched to run one after another which should prevent the system running too slowly, however, this feature is not available under Cygwin so be aware that converting DICOM images with more than one diffusion acquisition at any one time will slow down the computer significantly.

-fnomask

This flag is passed to acrtoana.

-fnoeddy

This flag is passed to acrtoana.

-pq

This flag is passed to acrtoana.

-gfa

This flag is passed to acrtoana.

-medinria

This flag is passed to acrtoana.

-mtr

This flag is passed to acrtoana.

-srcacr

This flag is passed to acrtoana.

-acr

This flag is passed to acrtoana.

-fpv

This flag is passed to acrtoana. Philips DICOM files contain two intensity scaling/offset values, a floating point scaling factor/offset and a display value scaling factor/offset. The floating point scaling factor/offset should best represent the MR signal. If the ACR/NEMA file contains Philips data then the floating point scale/offset will be stored in the Analyze header as funused1 and funused2 respectively, else the display value scaling factor/offset values will be stored in the Analyze header instead. This option is currently on by default.

-dv

This flag is passed to acrtoana. The intensity scaling factor/offset stored in the Analyze header as funused1 and funused2 will always be the display value scale/offset regardless of whether the ACR/NEMA file contains Philips data or not. This is the current default for non-Philips data.

-float

This flag is passed to acrtoana. Converted Analyze files are saved as scaled floats (32 bits-per-pixel) with the intensity scaling and offset applied to the intensities in the image file.

-spos

This flag is passed to acrtoana. Writes an additional text file containing slice positions for each slice in an Analyze file. If the DICOM header indicates a multistack acquisition, then examines the slice positions to determine whether the volume may contain overlapping stacks (with an integer number of overlapping slices). If so, then also write another text file containing command like options for mergestacks although mergestacks is not run automatically.
This option works for multistack anatomicals style acquisitions, however it may not work in a general case involving multivolume, multiecho, etc., acquisitions, so interpret the results carefully.

-itime

This flag is passed to acrtoana. Writes an additional text file containing image acquisition time for each slice in the Analyze file. This information may be useful when attempting to synchronise image acquisition time with other recordings, such as fMRI stimulus delivery systems or physiological signal recordings.
This option works for standard fMRI style acquisitions, however it may not work in a general case involving multiecho, etc., acquisitions, so interpret the results carefully.

-spmo or -nospmo

These flags are passed to acrtoana and specifies what information is written to the Originator field in the Analyze header.

-pl

This flag is passed to acrtoana and indicates whether a CSV file of the key acquisition parameters, extracted from the DICOM headers, should also be saved.

-quiet

This flag is passed to acrtoana and suppresses most of the output describing the conversion progress.

-add

By default the converted ACR/NEMA files will be named 0.img, 1.img, 2.img, ... as required by the old conversion software provided by Radionics. However, this results in the images being ordered incorrectly if they are sorted by filename alone which may cause problems for some other software (although not acrtoana). If this flag is specified, the ACR/NEMA filenames will be padded by zeroes to solve this problem, i.e., 000.img, 001.img, 002.img, ...

-noadd

Disable the -add option, above. Currently, this is the default. If both options are specified, the last occurence takes precedence.

-date

As well as naming the subdirectory containing the Analyze files after the patient name (from the DICOM header), the acquisition date and time are also appended to the directory name. This allows images acquired in different sessions on the same patient to be separated into different directories. If this option is not specified and the -over option, above, is specified then the images from the later scanning sessions may overwrite images from earlier acquisitions if the patient name has been entered exactly the same for both scanning sessions.

-datefirst

Same as above except that the date is prefixed to the directory name rather than appended.

-s<num>

Specifies how the ACR/NEMA files are organised in subdirectories. <num> is one of the following, entered with no space between it and the preceeding s -

0

Files from each acquisition series will be stored in separate sub-directories where the sub-directory will be named after the series number in the DICOM header. If the series number is not present or stated incorrectly in the DICOM header then converted ACR/NEMA files may get overwritten. The ACR/NEMA file are named after the image number stated in the ACR/NEMA header file and as such may not be numbered contiguously.

1

As above but all series and image names are renamed to be in ascending order.

2

All ACR/NEMA files are combined in one subdirectory named session_1 and renamed to be in ascending order, with images from later series following on from image numbers of earlier acquisitions. This replicates how ACR/NEMA files were named after being receieved on the old Radionics workstation from the Merge PC. This is the default.

-c

Before reading the DICOM header of each file, first copies the DICOM file to a temporary file on the hard disk. This should speed up conversion where the source DICOM files are on a slow medium, e.g., a CDROM with a small cache or a slow network drive.

-anon

Pseudo-anonymization of patient identification is achieved by replacing the patient's name by the numeric date and time of the first acquisition in each scanning session. The patient name is replaced by the date and time where ever it appears.

-anon2

As above, except the real patient name remains in the .txt file associated with each Analyze file pair.

-srcacr

By default, dtoa converts DICOM format to ACR/NEMA. Specifying this flag allows both DICOM and ACR/NEMA files to be considered as input. It is useful to sort ACR/NEMA images into patient-by-patient subdirectories. Currently, this option doesn't work reliably.

-destacr

This options explicitly forces conversion of DICOM images into ACR/NEMA format regardless of whether subsequent conversion to Analyze format has been requested (see below). This is the default unless the -ana flag has been specified.

-destdicom

By default, dtoa convert DICOM to ACR/NEMA format. If the -ana flag is specified then these ACR/NEMA files are subsequently converted to Analyze. If dtoa is just being using to convert DICOM to Analyze, there is no need for the intermediate conversion to ACR/NEMA as acrtoana can convert both ACR/NEMA and DICOM to Analyze. Also, the conversion to ACR/NEMA may result in the lose of some information from the header which may be useful, especially for interpreting private company messages, SQ messages, and explicit VR. If this flag is specified then no conversion to ACR/NEMA is performed; however the DICOM images are still sorted into patient subdirectories, sorted by image number and renamed. This flag is implied if the -ana flag has been supplied, unless the -destacr flag is also present, see above.

-exepath <path>

dtoa converts to Analyze format by calling acrtoana. By default it assumes that acrtoana is in the current PATH. If not, its location may be defined explicitly by including the directory containing acrtoana as part of this flag. If the path contains spaces it must be enclosed in double quotes. Note, enclosing a PATH in quotes in Windows may cause problems if the back-slash separator is taken as an escape character.

-d

Displays additional diagnostic output.

-v

Displays the date and time that dtoa was compiled, and exits.

-time

Displays additional information about the duration that the various stages of the program took to perform.

-coil

Appends the MR receive RF coil name to the patient's name when creating output subdirectories for the converted image files. Note, this may not work as expected on all configurations of RF coil selections on Siemens MR scanners.

-meta

This flag is passed to acrtoana which then saves an additional text file containing some information from the DICOM header which may be required for subsequent scripting.

-mono

This flag is passed to acrtoana to indicate that any colour DICOM files should be converted and saved as a monochrome image.

-clip

This flag is passed to acrtoana and sets any intesity values greater than 32767 to be 32767. This ensures that unsigned data spanning all 16 bits will fit within signed short intensities. ('Unsigned short' is not a valid data type in the Analyze format, only in NIFTI, and as such, acrtoana would otherwise promote full range 16 bit unsigned short DICOM data to 'signed int', which is a valid Analyze datatype although twice the size.)

DICOM_source_directory_root

The top level subdirectory containing the DICOM files to be converted. All files in this directory and all subdirectories are examined to see if they in the DICOM format and if so, included in the conversion. As such, do not specify this to be the top-level directory else the entire hard disk will be searched for DICOM files, all of which will then be converted. If no directory is specified then the current directory is used by default. If only one directory is specified on the command line then it is assumed to be the DICOM source directory.

ACR/NEMA or Analyze_destination_directory_root

The subdirectory under which the converted ACR/NEMA or Analyze files will be saved. The user must have write permission on this directory. If no directory is specified then the current directory is used.

dtoa was originally written to convert DICOM images into the previous incarnation of DICOM format, ACR/NEMA 2, in order to support old software which would only accept ACR/NEMA format. As such, the a in dtoa stands for ACR/NEMA. However, the most common use of the program is to convert DICOM to Analyze format, requiring the -ana command line flag, which in turn calls the ACR/NEMA to Analyze conversion program acrtoana, which must be in the PATH.

The conversion is performed in three stages. First, a list of all files in all subdirectories under the DICOM source directory is constructed. Then each file is opened and examined in turn to see if it is in DICOM format. Files in DICOM format are converted to ACR/NEMA and copied to the destination directory, renamed according to information read from the DICOM header (patient name, series number, image number). Finally, if the -ana flag was specified then acrtoana is called in each new subdirectory in the destination directory to convert the ACR/NEMA files to Analyze. For details of the Analyze conversion see the page for acrtoana.

dtoa and acrtoana are similar programs with considerable overlap. Use dtoa routinely to convert DICOM to ACR/NEMA or Analyze format especially from a DICOM CD or DVD containing several patients' scans which need to be sorted and separated into unique subdirectories. Use acrtoana to convert DICOM or ACR/NEMA to Analyze format in a single subdirectory without sorting the input files in any way other than their filename. If conversion using dtoa fails then trying to identify the troublesome DICOM files may be more successful using acrtoana directly.

Examples

dtoa -ana

Converts all DICOM images found under the current directory to Analyze format, also saved under the current directory.

dtoa -ana -datefirst -c -diff /cdrom /data/exp1

Converts all DICOM images found under the directory /cdrom to Analyze format. The converted Analyze images will be saved under /data/exp1. The -datefirst option prefixes each patient subdirectory with the date and time of the scan which is useful when converting DICOM files from multiple patients (or the same patient ID scanned multiple times). As the source images are on a CD, the -c flag results in each DICOM image being copied to the hard disk before interegating the header, which should speed up conversion. The -diff flag is also used while converting to Analyze which results in any diffusion weighted acquisitions being converted further into a suitable format for FSL.

References

• David Clunie's Medical Image Format Site
• DICOM Standard Homepage