文件列表:

correct_path.m (1416, 2014-09-02)
find_files.m (2680, 2014-09-02)
LICENSE.txt (35146, 2014-09-02)
LIDC_mat_2_gt_image.m (8509, 2014-09-02)
LIDC_mat_2_mask.m (10018, 2014-09-02)
LIDC_pmap_2_mat.m (5499, 2014-09-02)
LIDC_process_annotations.m (8683, 2014-09-02)
LIDC_split_annotations.m (5476, 2014-09-02)
LIDC_xml_2_pmap.m (5113, 2014-09-02)
support_software\max-V107b\CopyrightAndLicense.txt (1623, 2014-09-02)
support_software\max-V107b\filelist (199, 2014-09-02)
support_software\max-V107b\get_image_geom.pl (22, 2014-09-02)
support_software\max-V107b\get_image_geom-V201.pl (7765, 2014-09-02)
support_software\max-V107b\getfiles.sh (2572, 2014-09-02)
support_software\max-V107b\getpix.sh (14, 2014-09-02)
support_software\max-V107b\getpix-V100.sh (4867, 2014-09-02)
support_software\max-V107b\max.pl (12, 2014-09-02)
support_software\max-V107b\max-faq.txt (3390, 2014-09-02)
support_software\max-V107b\max-V107b.pl (463219, 2014-09-02)
support_software\max-V107b\ReleaseNotes.txt (18663, 2014-09-02)
support_software\max-V107b\Site_Max (15290, 2014-09-02)
support_software\max-V107b\Site_Max.pm (15290, 2014-09-02)

LIDC Matlab Toolbox ------------------- Author ------ Thomas A. Lampert ICube University of Strasbourg tomalampert@hotmail.com This work was carried out as part of the FOSTER project, which is funded by the French Research Agency (Contract ANR Cosinus, 2011–2013): http://foster.univ-nc.nc/ License ------- Copyright 2013 This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this software. If not, see . README Introduction ------------ This toolbox accompanies the following paper: T. Lampert, A. Stumpf, and P. Gancarski, 'An Empirical Study of Expert Agreement and Ground Truth Estimation', (submitted). I kindly request you to cite the paper if you use this toolbox for research purposes. The toolbox contains functions for converting the LIDC database XML annotation files into images. The main function is LIDC_process_annotations, this function extracts the readings for each individual marker in the database, and then creates a TIFF image related to each slice of the scan. Overview -------- The function works whether the images are present or not, the only caveat is that it uses the images to order the slices and therefore if this information is not present the output's order is not in 'anatomical' order. There are two paths to set in the LIDC_process_annotations.m file, the first to the LIDC dataset, this will be searched recursively for all XML files and the processing will be performed on each. The second path is the output path, if the images are present in the dataset then three folders will be created: gts, images, masks. Please note that neither of these paths can contain a space. Each of these folders will contain folders that are named after the StudyInstanceID of the relevant scan (minus the first '1.3.6.1.4.1.14519.5.2.1.6279.6001.', which seems to be constant throughout the dataset), and within the gts folder several folders named slice1 ... sliceX, where X is the number of slices for which reader annotations were found. Each of these folders contains the files GT_id1.tif ... GT_isY.tif where Y is the number of readers found for that particular scan (each file is a binary image where ones denote the markers GT). The gts folder will also contain a text file that details the correspondence between the folder's name (slice number), the SOPInstanceUID (unique for each slice of the scan) and the DICOM filename that contains that slice (if the images are present). The masks folder contains binary images slice1.tif ... sliceY.tif, where one indicates that the area is out-of-bounds of the scan. The images folder contains images slice1.tif ... sliceY.tif, which contain the slice images. The masks and images folder are only created if the images are present in the folder in which the XML annotations exist (as is the structure when the LIDC dataset is downloaded). The toolbox will only extract the slices for which annotations are found, the remaining slices can be obtained from the DICOM images quite easily. Installation ------------ To use the toolbox's functions, simply add the toolbox directory to Matlab's path. Within the header of each function may be found a short description of its purpose. The function LIDC_xml_2_pmap uses the external Perl script max.pl (https://wiki.cancerimagingarchive.net/display/Public/Lung+Image+Database+Consortium) and therefore requires that Perl is installed, furthermore the following packages should be installed: XML::Twig XML::Parser Math::Polygon::Calc Tie::IxHash More information can be found in the header of LIDC_process_annotations.m and the max.pl script located in ./support_software/max.pl. If you are using OSX (and perhaps Linux) you may also need to update the perl_library_path variable in LIDC_xml_2_pmap.m to point to the correct location of these libraries (particularly if you receive the error "Can't locate XML/Twig.pm" or it complains that XML::Twig is not installed, when it is). To install these packages the following command can be executed (use sudo if on OSX): perl -MCPAN -e "install XML::Twig" NOTE: This toolbox was created under Matlab 2013a and OSX, I have also tested it under Windows 7 x*** using Matlab 2012b. NOTE: Many functions include assignments such as [~, var1] = someFunction(input), which is only supported in versions of Matlab newer than 2009b. You can replace these assignments to [ignore, var1] = someFunction(input) for versions earlier than 2010a, although I've not tested that no other incompatibilities exist. Quick Start - Windows --------------------- 1. Download and Install Activestate (http://www.activestate.com/activeperl/downloads) 2. Install the following perl packages XML::Twig XML::Parser Math::Polygon::Calc Tie::IxHash >> To do that, start the Windows command prompt and execute the following commands: perl -MCPAN -e "install XML::Twig" perl -MCPAN -e "install XML::Parser" perl -MCPAN -e "install Math::Polygon::Calc" perl -MCPAN -e "install Tie::IxHash" 4.Restart your PC Your computer is now ready to use the toolbox. To begin using the toolbox 1. Open the file "LIDC_process_annotations.m" 2. Set the Paths for the LIDC-IDRI folder and to the Output folder Note: Make sure your path does not include a space, For example: ->> "c:\LIDCtoolbox v1.3" is an invalid path due to the space between "toolbox" and "v1.3" ->> "c:\LIDCtoolbox_v1.3" is a valid path 3. Open the file 3. Run "LIDC_process_annotations.m" Quick Start - OS X/Linux ------------------ 1. Install the following perl packages XML::Twig XML::Parser Math::Polygon::Calc Tie::IxHash >> To do that, start the terminal and execute the following commands: sudo perl -MCPAN -e "install XML::Twig" sudo perl -MCPAN -e "install XML::Parser" sudo perl -MCPAN -e "install Math::Polygon::Calc" sudo perl -MCPAN -e "install Tie::IxHash" Your computer is now ready to use the toolbox. To begin using the toolbox 1. Open the file "LIDC_process_annotations.m" 2. Set the Paths for the LIDC-IDRI folder and to the Output folder Note: Make sure your path does not include a space, For example: ->> "/users/LIDCtoolbox v1.3" is an invalid path due to the space between "toolbox" and "v1.3" ->> "/users/LIDCtoolbox_v1.3" is a valid path 3. Open the file "LIDC_xml_2_pmap.m" 4. Set the path stored in the variable "perl_library_path" to that which contains the above installed perl packages. 5. Run "LIDC_process_annotations.m" If you find any problems or would like to contribute some code to the toolbox then please contact me. Acknowledgements ---------------- Peyton Bland gave considerable advice with regards to the Max software upon which this toolbox is based. Hamada Rasheed Hassan also contributed through extensive testing of the toolbox under Windows and in helping write this readme file.

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