LIDC-IDRI MITK Plugin Manual
作者 Xinglong Liu | 发布于 2017-08-08
Tools

LIDC XML Simple Manual

  • NEW, CODE added, compatible with MITK_Version >= 2016.05

  • Firstly, compile and build the MITK according to manuals on mitk.org, make sure the lib.org.lidcxml is compiled.

  • Start the startMitkWorkbench_release.bat in buid/mitk_build/bin

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  • Load the original LIDC datasets

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select one of the .dcm file to open them in mitk

  • You can get this page (right click-open in new tab to see the original image)

    • the 1st arrow, open the data set

    • after opened the data, select it in data manager, and click 2nd arrow, load annotations

    • then, the annotation (.xml in corresponding lidc data sets) will be loaded

    • since original data sets are not isotrophic, we need resample them first. use Resample Tex&G then Resample Non-nondule or just click on Resample All which actually consists these two steps.

    • wait one minute and you get three new data in data manager, normalized_texture, normalized_groundtruth and normalized_nonnodule

    • then, click on step2 on the right tab.

    • here you go

      • make the original data set (here is the 1.5.1.4.xxxxxxx) selected and press the Select Working Dir and select the corresponding image in the dropboxes (texture--->texture, ground--->ground, nonnodule--->nonnodule), (right click-open in new tab to see the original image)

  • finally, click on the List Groundtruth and Non-nodules, the corresponding nodules will be shown.

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    • in the list, the color of corresponding nodule is shown and followed by the nodule type. the infor shown the position and size of the nodule.
    • for my use, i have written the output ANN training and output BOW training two functions corresponding to the two buttons on the page, for more uses please change the code.

  • I suggest to resample all original images as a united .mitk file including the texture-groundtruth-nonnodule.