DCMULTI(1)

NAME
dcmulti - ACR/NEMA DICOM PS3 ... DICOM PS3 - Make multiframe image from single frames

SYNOPSIS

dcmulti " inputfile1 [ inputfile2 ... ]" [ -v|verbose|vv|veryverbose|vvv|veryveryverbose ] [ -l ] [ -noicons ] [ -position ] [ -sortby elementname [ -descending ] ] [ -nomrmf ] [ -makestack [ -stackdescending ] ] [ -temporalposition ] [ -dimension elementname functionalgroupname ] [ -multidimension elementname functionalgroupname organizationlabel organizationuid ] [ -addreferenced class instance frames purposescheme code mng vers [ -perframereference ] ] [ -addderivation class instance frames derivationcheme code mng vers purposecheme code mng vers [ -perframederivation ] ] [ -addsatslab thickness orientX orientY orientZ midpointX midpointY midpointZ ] [ -addcolorlut numberofentries firstvaluemapped firstred incrred firstgreen incrgreen firstblue incrblue ] [ -accumulateduration ] [ -derivedurationfromtiming ] [ -addnonderivedstuffanyway ] [ -addpositionstuffanyway ] [ -addtimingstuffanyway ] [ -phasecontrast ] [ -minimalattributes ] [ -nowindow ] [ -enhancedcontrast ] [ -sync ] [ -copyall ] [ -input-nometa ] [ -input-ts uid ] [ -input-default ] [ -input-byteorder|-input-endian big|little ] [ -input-vr implicit|explicit ]

DESCRIPTION

dcmulti reads the named dicom single frame input files, checks to ensure that patient, study, series and image information, are consistent and concatenates all the images into a multiframe image as output.

Moderately extensive checking is performed to ensure that patient, study and series level identifiers and UIDs are consistent. Image level attributes related to pixel representation (i.e. the Image Pixel Module) are also checked, since inconsistency in these will render the output meaningless. For specific modalities, such as CT and MR, other image level attributes are checked for consistency, such as rescale parameters, pulse sequence parameters and slice thickness.

It is recommended that before building a multiframe object, the source images be manually checked for consistency of important attributes, for example by using the dctable(1) utility on the same set of images.

The images will be concatenated in the order specified on the command line, unless the -sortby option is specified, in which case they will first be sorted in ascending order (unless -descending is specified) by the values of the attribute. Any numeric attribute that is expected to be present in the images can be specified.

In addition, either ImagePositionPatient or ImageOrientationPatient may be specified as sort keys. These multi-valued attributes are handled specially for sorting.

For ImagePositionPatient, the images will be sorted by relative position along a vector normal to the plane of the first image (which ideally be the same plane and normal for all images though this is not required). For example, for axial images that are oriented as if viewed from below, images closer to the feet will sort before images closer to the head, since the normal is directed from the image plane toward the viewer, and the DICOM coordinate system along the Z axis values toward the head are more positive. Note that the first image supplied on the command line does not have to be the first in the volume for this to work.

Note that a similar effect can be achieved by sorting on SliceLocation, but this is an optional attribute, may not be present or completed, does not have a defined sign with respect to orientation of the patient, and may not correctly reflect complicated oblique slices in MR.

For ImageOrientationPatient, the images will be sorted by relative angle between vectors normal to the planes of the current image and the first image. Ideally, all these normals should be coplanar for the sort to be meaningful. Note that the first image supplied on the command line does not have to be the first rotation in the volume for this to work.

The output file will contain a Number Of Frames attribute with the number of frames generated (equal to the number of input files), but there is no provision to automatically generate a Frame Increment Pointer. If necessary this can be added on the command line together with the appropriate vectors of values, using the -r option, or built using ancreate(1) and merged into the output of this utility with dcmerge(1).

The output file will contain attributes for the general and SOP Class specific modules copied from the first image, unless -copyall is specified in which case it will contain all the same attributes as the the first sorted input file. This includes patient, study and series level identifiers and UIDs, except that Instance Number will be set to 1 and a new SOP Instance UID will be generated. Any Data Set Trailing Padding in the input images will also be removed.

Note especially that the SOPClassUID will not be changed, that is it will be the same as the (first sorted) input file, with the exception of the SC and MR SOP Classes, in which case an appropriate new SC multi-frame oir MR SOP Class will be chosen. In the case of CT images, where multiframe images are not allowed, this will generate an illegal DICOM dataset. The SOPClassUID can be replaced on the command line by using the -r option, but since there is no standard SOP Class for multiframe CT, it is not obvious what the output SOP Class should be. Until the standard is extended, the use of a private SOP class is recommended. In the case where the multiframe output of this utility is only being used as an intermediate step to another multiframe file format or for import into a viewing application that can't sort slices but can read volumes, then the issue of SOP Class can probably safely be ignored.

The input encoding of the file will be automatically determined, or can be explicitly specified in pathological cases using the input options described in dcintro(1).

The output encoding of the file needs to have the same byte order (little or big endian) as the input files.

OPTIONS
The verbose output goes to standard error.

The basic input switches are described in dcintro(1). Options specific to this program are:

-v|verbose
    List sort order and which file contributres to which frame as it is written.

-vv|veryverbose
-vvv|veryveryverbose
    Dump contents of files and data structures with increasing verbosity.

-sortby elementname [-descending]
    Sort by the specified DICOM element name in ascending (default) or descending numeric order.

-nomrmf
    Do not make MR multi-frame, and leave the single frame MR SOP Class UID alone.

-makestack [-stackdescending]
    Build MR multi-frame object stacks from position and orientation information and assign each frame a Stack ID and In-stack Position Number. The order in which the frames in a stack are sorted by position along the normal to the plane orientation is ascending unless descending is specified. Note that the frames are not physically re-organized by stack ... only the identifiers are created. The sort direction (ascending or descending) of the stack may be different from the direction of the encoded frames themselves.

-temporalposition
    For MR multi-frame, find temporal positions based on Trigger Time, or Acquisition Time if Trigger Time is absent, and insert Temporal Position Index into Frame Content Macro. Note that the frames are not physically re-organized by temporal position ... only the identifiers are created.

-dimension elementname functionalgroupname
-multidimension elementname functionalgroupname organizationlabel organizationuid
    Zero or more dimensions may be specified, those encountered earlier on the command line being the major dimensions (varying slowest). It is necessary to specify both the name of the element that is used as the index of the dimension (e.g. TriggerDelayTime, InStackPositionNumber) as well as the name of the sequence of the functional group in which it is contained (e.g. CardiacTriggerSequence, FrameContentSequence). The specified element should be of a numeric VR, except for selected exceptions that include FrameType and ContrastBolusAgentPhase, for which pre-determined sort orders are defined. If the -dimension argument is used, there is only a single dimension organization. If the -multidimension argument is used, then more than one dimension organization (set of dimensions) can be specified, and these are distinguished from each other if either the specified label or the specified uid are distinct. Either the label or the uid or both may be blank. If they are both blank, then a default dimension organization will be used (this is then the same as using -dimension). If the uid is blank then a uid will be generated by the application for each dimension organization (including the default and those with distinct labels).

-addreferenced class instance frames purposescheme code mng vers
    Add Referenced Image Sequence using the supplied parameters (frame may be zero length if whole image).

-perframereference
    Add the Referenced Image Sequence to the Per-frame rather than Shared functional groups sequence (even though all identical).

-addderivation class instance frames derivationcheme code mng vers purposecheme code mng vers
    Add Derivation Image Sequence using the supplied parameters (frame may be zero length if whole image).
-perframederivation
    Add the Derivation Image Sequence to the Per-frame rather than Shared functional groups sequence (even though all identical).

-addsatslab thickness orientX orientY orientZ midpointX midpointY midpointZ
    Add Saturation Slab using the supplied parameters.

-addcolorlut numberofentries firstvaluemapped firstred incrred firstgreen incrgreen firstblue incrblue
    Add a Supplemental Color LUT using the supplied parameters.

-accumulateduration
    Summate frame acquisition durations to compute acquisition duration for whole object (e.g. for a cine MR acquisition). Default is to expect that frame and image acquisition durations are the same

-derivedurationfromtiming
    Derive a value for frame acquisition duration and acquisition duration from MR timing parameters like number of averages, number of frequency encoding steps, repetition time and echo train length.

-addnonderivedstuffanyway
    Normally at the image and frame level if the first value of Image Type is DERIVED, acquisition specific stuff is not added ... this option forces it to be added anyway.

-addpositionstuffanyway
    Normally at the image and frame level if the first value of Image Type is DERIVED, position and orientation stuff is not added ... this option forces it to be added anyway.

-addtimingstuffanyway
    Normally at the image and frame level if the first value of Image Type is DERIVED, acquisition and reference timing stuff is not added ... this option forces it to be added anyway.

-phasecontrast
    Add MR Velocity Encoding Sequence.

-minimalattributes
    Only add minimal required standard attributes for the Enhanced CT or MR SOP Class and nothing more.

-nowindow
    Do not add.

-enhancedcontrast
    Add Enhanced Contrast/Bolus Module and Contrast/Bolus Usage Sequence. Requires non-standard multivalued string attributes in source.

-sync
    Add the Synchronization Module. Replaces any Synchronization Frame of Reference UID already present in source, any adds default values for minimal attributes if not already present in source.

-copyall
    Copy all attributes from first file rather than only those in modules thought to be relevant to the multi-frame IOD being created.

ENVIRONMENT

EXAMPLES

% dcmulti IMAGES/[0-9]* -verbose >MFIMAGE
wrote frame 0 from filename <IMAGES/0>
wrote frame 1 from filename <IMAGES/1>
 ...
% dcmulti IMAGES/[0-9]* -verbose -sortby InstanceNumber -descending >MFIMAGE
After sorting
InstanceNumber[0] = 10 in IMAGES/9
InstanceNumber[1] = 9 in IMAGES/8
 ...
wrote frame 0 from filename <IMAGES/9>
wrote frame 1 from filename <IMAGES/8>
 ...
% dcmulti IMAGES/[0-9]* -verbose -sortby ImageOrientationPatient >MFIMAGE
After sorting
ImageOrientationPatient[0] = 0 in IMAGES/0
ImageOrientationPatient[1] = 45 in IMAGES/1
 ...
wrote frame 0 from filename <IMAGES/0>
wrote frame 1 from filename <IMAGES/1>
 ...
% dcmulti IMAGES/[0-9]* -verbose -sortby ImagePositionPatient >MFIMAGE
After sorting
ImageOrientationPatient[0] = -124.262 in IMAGES/0
ImageOrientationPatient[1] = -120.872 in IMAGES/1
 ...
wrote frame 0 from filename <IMAGES/0>
wrote frame 1 from filename <IMAGES/1>
 ...

FILES

SEE ALSO
dcintro(1), ancreate(1), dcmerge(1), dctable(1)

AUTHOR
Copyright (c) 1993-2015, David A. Clunie DBA PixelMed Publishing. All rights reserved.

BUGS

Data Set Trailing Padding is explicitly removed from the input images, but if there is anything else after the Pixel Data tag, the output file will be invalid (tags out of order) since the multiframe Pixel Data tag is added after everything else in the first input file is copied. If there are private things after the Pixel Data the use of the -removeprivate option may help. This is only a problem when using the -copyall flag.

Byte order of input and output must be the same, due to the crude raw copying that is used to build the multiframe pixel data.

There is no support for bulding encapsulated transfer syntax representations of the multiframe image pixel data (i.e. with delimiters, JPEG, RLE, etc.)

If any of the Image Pixel Module attributes are inconsistent, such as different matrix sizes, an error will be flagged but the output file will still be built (though it will be meaningless).

Should check some multi valued attributes like PixelSpacing are consistent but doesn't yet.