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plugin:inputoutput:dicom_open:start

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plugin:inputoutput:dicom_open:start [2019/11/17 22:57]
fred
plugin:inputoutput:dicom_open:start [2019/11/21 07:13] (current)
fred
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 The DICOM_open plugin provides additional functionality on top of the DICOM plugin. ​ There were three main impetuses for developing this plugin, first was to be able to search the DICOM files for a series to open, second was to open the series and get at the actual voxel data, and, third was to properly arrange the images in a hyperstack.  ​ The DICOM_open plugin provides additional functionality on top of the DICOM plugin. ​ There were three main impetuses for developing this plugin, first was to be able to search the DICOM files for a series to open, second was to open the series and get at the actual voxel data, and, third was to properly arrange the images in a hyperstack.  ​
  
-DICOM datasets, that I generally come across, are stored in a hierarchical directory structure in which the directory names do not enlighten the content. ​ The DICOM files are database entries, and the parameters within hold the clues to which datasets may be desired. ​ This plugin'​s GUI provides an interactive interface to find the series of interest to open.  For dealing with a single hodgepodge directory of DICOM files, see DICOM_explode plugin.+DICOM datasets, that I generally come across, are stored in a hierarchical directory structure in which the directory names do not enlighten the content. ​ The DICOM files are database entries, and the parameters within hold the clues to which datasets may be desired. ​ This plugin'​s GUI provides an interactive interface to find the series of interest to open.  For dealing with a single hodgepodge directory of DICOM files, see [[plugin:​utilities:​dicom_explode:​start|DICOM_explode plugin]].
  
 MRI DICOM dataset'​s voxel data tends to be stored as 16 bit unsigned integers, i.e., magnitude data, albeit, the tags within the DICOM files say they are signed. ​ ImageJ does not support signed 16 bit image data.  For some reason, they add 32768 to the dataset voxel values and store them in unsigned 16 bit integer ShortProcessor(s);​ confusing to say the least. ​ This plugin provides the means to access the voxel data as someone who deals with MRI data would expect. MRI DICOM dataset'​s voxel data tends to be stored as 16 bit unsigned integers, i.e., magnitude data, albeit, the tags within the DICOM files say they are signed. ​ ImageJ does not support signed 16 bit image data.  For some reason, they add 32768 to the dataset voxel values and store them in unsigned 16 bit integer ShortProcessor(s);​ confusing to say the least. ​ This plugin provides the means to access the voxel data as someone who deals with MRI data would expect.
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 ===== Install ===== ===== Install =====
-Place the file {{ :​plugin:​inputoutput:​dicom_open:​dicom_open.java |DICOM_open.java}} in your plugins directory, then compile&​run;​ or just place the {{ :​plugin:​inputoutput:​dicom_open:​dicom_open.class |DICOM_open.class}} file in your plugins directory and refresh the menus / restart ImageJ. ​ Note that DICOM should be in uppercase in the file names.+Place the file {{ :​plugin:​inputoutput:​dicom_open:​dicom_open.java |DICOM_open.java}} in your plugins directory, then compile&​run;​ or just place the {{ :​plugin:​inputoutput:​dicom_open:​dicom_open.class |DICOM_open.class}} file in your plugins directory and refresh the menus / restart ImageJ.  ​**Note that DICOM should be in uppercase in the file names.**
  
 ===== Licence ===== ===== Licence =====
plugin/inputoutput/dicom_open/start.1574027825.txt.gz ยท Last modified: 2019/11/17 22:57 by fred