User`s Guide
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1. landmark information can be used to verify that the transformations are allowed 1 e the same subject examination without a change in patient position in the magnet ah1 landmark ah2 landmark The modified analyze header structure is defined in make analyze _header pro The modified header structure is compatible with conventional ANALYZE format as it uses non essential portions of the header for embedding the matrix transform information Floating Point Images The DICOM conversion doesn t work for images of type float or long These image types will be converted to integer Windows Issues The directory and filename structure for images in Windows should not have any spaces in it For example the following image filename will result in an error C My Documents and Settings Images imagel img Program information This program will take any images and create dicom files syntax convert2dicom analyze analyze images images yanalyze the analyze img filename to convert to DICOM a widget will pop open allowing you to make some limited header mods If you don t have an analyze file you can just send an image stack using the images option convert2dicom images imagestack ie a 64x64x30 image array send dicom hostname hostname files files detitle aetitle calltitle GCalltitle port port WFU Dicom Toolkit v1 0 maldjian wfubmc edu This program will send dicom images into a PACS or DICOM databas2. WEFU Dicom Toolkit v 1 0 maldjian wfubmc edu WEU DICOM Conversion Tools v1 0 The Functional MRI Laboratory Wake Forest University School of Medicine WAKE FOREST i SCHOOL of MEDICINE THE BOWMAN GRAY CAMPUS WFU Dicom Toolkit v1 0 maldjian wfubmc edu WFU DICOM IDL Toolkit 1 0 User Manual Joseph Maldjian MD 1 Software Description Installation and Setup 1 1 Description The DICOM 1 conversion toolkit provide a method for dealing with DICOM format images The programs were written using Interactive Data Language IDL Research Systems Inc Boulder Co The toolkit includes programs for converting Analyze image format to DICOM sending DICOM images into PACS and converting DICOM format to analyze The toolkit was developed in the Functional MRI Laboratory at the Wake Forest University School of Medicine Questions can be referred to maldjian wfubmce edu 1 2 Downloading the Software The WFU_ Dicom toolkit can be obtained from www rad wfubmc edu fmri 1 3 Program Installation Untar the tar file tar xvf WFU_dicom tar This will create a subdirectory called WFU dicom toolkit Start IDL from this directory To compile the code enter run from the IDL command line prompt 1 4 Compatibility The WFU Dicom toolkit requires at least IDL 5 0 The toolbox has been evaluated on both Sun Solaris and Linux platforms It has not been extensively tested for Windows 1 5 Referencing the software When using this to
3. e psyntax send dicom hostname hostname files files aetitle aetitle calltitle calltitle port port YOU Can Call this program simply using j send dicom It will prompt you for the directory of file names and it will read the entries in the dic om host tablett file This is a tab delimitted file with the format described in the file Command line options when not using the dicom host table txt file hostname the hostname of the PACS or DICOM Recipient files string array of dicom filenames to send jaetitle application entity title calltitle application call title port port on DICOM recipient to send images For the GE AW workstations all you need to send is the hostname The defaults should work KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK Pro Cycle dicon dir dir keep keepydiscard discard Program will cycle through a directory with DICOM subdirectories generating analyze files from any DICOM file types encountered poycle dicon dir dit diocard dLoCard set discard to the number of volumes to discard for any fMRI acquistions J Maldjian KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKHK pro dicom2analyze dir dir keep keep outpath outpath discard dascardjdh dh lease dh l st dh This program will convert dicom files to analyze It will work on anatomics functionals and mosaics GE Philips Siemens tested It reads th
4. e dicom headers directly and correctly fills magnet transform information ji haven t found the dicom field tor the landmark rh series se iImhor yet Ihe landmark is generated from the dicom frame of reference field syntax dicom2Zanalyze dir dir rset discard to the number of volumes to discard for any fMRI acquistions KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKEK function read dicomheaderz filename filename image image coords coords error error numimages numimages This program will read a dicom file and return some useful descriptors yd read dicomheaderz2 falename dicomfile image imags coord coords numimages numimages image image in dicom file For mosaics it gets converted to a 3D volume dh an analyze header WFU Dicom Toolkit v1 0 maldjian wfubmc edu Coords is the coords which should go into csmemp loc files Only send numimages for Philips fMRI files These files don t have the number of slices in the dicom header so we compute it from the number of temporal positions and numimages For Philips fMRI files send numimages of files in the directory so that the program doesn t have to recompute it with each read KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKHK yEUNCULON geL acm yvalue tilename filename description Cescriptu1on print print group group element element This program will return the values of individual elements in a dic
5. ol for a paper please reference 2 Maldjian JA Listerud J Khalsa S Integrating post porcessed functional MR images with PACS AJNR 2002 23 1393 7 The manuscript provides a complete description of the DICOM fields used in the conversion process WFU Dicom Toolkit v1 0 maldjian wfubmc edu 2 Analyze to DICOM Conversion The program to convert ANALYZE format to DICOM is called convert2dicom It can be called with either an ANALYZE filename or an image volume in memory convert2dicom analyze analyze img filename or convert2dicom image image array 1e 256x256x30 image array The conversion process utilizes the Central Test Node CTN software routine dcm modify elements http wuerlim wustl edu DICOM ctn html to create the DICOM header fields During the conversion process a widget will pop up allowing the user to modify some of the DICOM header entries figure 1 The GE header conversion capability described in the manuscript 2 is not provided in this suite because it contains proprietary information Patient Name Research Patient Patient ID 00000 Patient History FUSION Study Description FMRI Series Description FMRI Study Date Month 105 Day 42 Year 2003 Accession Number E 00000 Institution IDLSPM Series Number 11 x size 192 y size 192 z size 36 2 Integration with PACS The program to send DICOM images to PACS 1s send dicom WFU Dic
6. om Toolkit v1 0 maldjian wfubmc edu It can be used to send any DICOM files from a UNIX workstation to a DICOM database or PACS system The program utilizes the CTN software routine send_ image During the process a widget will pop up allowing the user to choose from a list of potential PACS or DICOM remote hosts listed in the Destination column figure 2 The Generate Dicom and Display Fusion buttons have no effect for this toolbox The list of destinations is generated based on entries in the dicom_hosts_table txt hosts file in the WFU_ dicom directory This is a tab delimitted file listing host names Application Entity titles Calling Titles port numbers and ip addresses You may have to check with your PACS system administrator to find out what these entries should be for your system and to get a calling title for your application W Generate Dicom Destination W Send Dicom w mraw Display Fusion W 1612 bng9p01 3 DICOM to ANALYZE Conversion The program to convert DICOM to ANALYZE is called dicom2analyze dir dir discard discard where dir directory of DICOM images discard of functional volumes to discard optional or cycle dicom discard discard The programs are designed to convert GE Siemens including Mosaic and Philips formats The cycle _dicom routine will prompt the user for a parent directory containing subdirectories of DICOM images as for an entire examination It will cycle thro
7. om header description should text description of the field you want from rthe dicom dictionary example pol Chick get dcm value tilename dicom Tile description silace Thickness you can also provide string values for group and element kkxkxkxkxkxkxkxkxkxkxkxkxkxkxk xkxkxkxkxkxkxkxkxkxkxkxk xkxkxkxkxkxk xkxkxk xkxkxk xkxkxk xkxkxkxkxkxkxkxkxkxkkxkxkkkxxkxk kx k function parse dicom filename filename This program will create a callable dicom header function make dicom pheader pro based on the input dicom file compile the function and return the elements of the dicom header as a structure syntax dh parse dicom filename dicom_ filename dh will contain all the dicom header fields for that dicom file as a structure The structure elements can be viewed using he lostruc an References l NEMA National Electrical Manufacturers Association Digital Imaging and Communications in Medicine DICOM In Rosslyn Va 1996 PS 3 1 1996 1993 1913 1996 PA Maldjian JA Listerud J Khalsa S Integrating postprocessed functional MR images with picture archiving and communication systems AJNR Am J Neuroradiol 2002 23 1393 1397
8. ugh the subdirectories converting any DICOM image files it encounters It 1s designed to work with either anatomic images or functional images including Siemens Mosaic format When a functional series is encountered a 4D analyze file is created Note that our site WFU is a GE site The Philips and Siemens conversion routines were based on several sample data sets provided by collaborators The mosaic conversion routine makes assumptions about resampling which were true for the sample data provided The discard keyword can be used to throw away any number of images from any fMRI or Mosaic DICOM images encountered It is ignored for anatomic DICOM images WFU Dicom Toolkit v1 0 maldjian wfubmc edu 3 Technical Notes Modified Analyze header Structure The dicom2analyze routine maintains DICOM acquisition coordinate transformation information and embeds this into a modified ANALYZE header format along with a software generated landmark field if one is not found in the DICOM header This information can be used for display gt magnet coordinate transformations and inter series transformations ahl read_analyze_header filename sagittal series ah2 read_analyze_header filename coronal series mt ahl magnet_transform invert ah2 magnet_transform Where mt 4x4 affine transformation matrix defining series gt series2 transformation in this example sagital gt coronal where transpose xl y1l z1 1 mt x2 y2 z2 1 The
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