ZipStudy. Utility for Packaging Study Files. A. Maudsley, 6/2015

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1 ZipStudy Utility for Packaging Study Files A. Maudsley, 6/2015 CONTENTS: 1. Introduction Starting the Program Copying and Compressing Subject Data Restoring MIDAS Data from a Zipped Study Distribution Copying Processing Files Acknowledgements Introduction This utility provides a means of copying and packaging the subject.xml file and all data files corresponding to a subject. This provides an easy method to copy projects to another location, send data to another site, or for data archival. The program can optionally include a project.xml file, and a set of processing files, which makes it easier to restore a complete project with multiple subject data in. Notes: This program uses a third party compression program, 7z, that must be obtained directly from the developer at It should be installed in the usual manner and must be located in the Program Files directory (for Windows). To reduce data sizes it is possible to copy only selected file types or image series; however, the program does not change the subject.xml file to match this selection. This means that on restoring the subject data there can be a mismatch between the subject.xml description and the data. It is up to the user to reconcile these differences if necessary, e.g. by editing the subject.xml file or using the Remove Current Node option in the MIDAS Browser. If multiple studies are present for a single subject then the program will always copy all studies. 2. Starting the Program The ZipStudy program is located in the utilities section of the MIDAS toolbar,. 1

2 3. Copying and Compressing Subject Data The first requirement is to click the Browse button and using the MIDAS Browser select the Subject(s) you want to zip. Note it is also possible to select at the project level to include all subjects. The widget will refresh to display all of the image series available for that subject. If multiple subjects are selected then only the image series included in the first subject listed will be used. An example of the widget is shown in the next figure: Then select the destination directory, which is the project-level directory where the individual subject directories will be copied to. The File Selections section of the widget is used to select which data types you want to include. There are two general options: for Raw data, if you want to copy data for reconstruction elsewhere, or Final, which allows you to save a much smaller amount of data if you only want to make a copy of the final results. Under each of these are a set of directory and file types listed. The check boxes for each of the two general selections will enable/disable all of the options under each of those categories, but the individual check boxes can also be selected. Note that the \raw directory contains the DICOM files obtained on import; however, the typical processing pipeline deletes the raw EPSI DICOM files once the initial processing step is done 2

3 (Volumizer). The raw data files for the EPSI data then become those shown in the second option, namely \mrsi\*.epsi. The following options are available: Zip all files : If this is checked then the program will first copy all selected file types to a temporary directory and then zip all of those files to create a single file with the name of the subject ID. If you don t check this option then the files will just be copied. If this option is checked you then have the additional option of selecting Delete temp directory after Zip. This is recommended to save space. Save Project XML file : Checking this option will cause a copy of the project definition file to be copies to the destination directory. This is not included in the compressed file. Note that this will be a direct copy of the file, so if data for only some of the subjects in the project are copied then the Project.xml file will need editing to list only the studies that are there. Overwrite existing Subject.xml file : This option is useful when copying data to an existing directory. For example, one type of data may have been previously copied and now the user is adding another image series. If this option is NOT checked then the program will not overwrite the subject.xml file, but if checked it will replace the existing file with a copy of the version in the source directory. Test : This option allows you to do a test run. The files that will be selected get written to the IDL log window. 4. Restoring MIDAS Data from a Zipped Study Distribution This section describes how to restore the MRI and MRSI data distributed in a zipped file into the MIDAS data management system. There are two variants of the procedure depending on whether the Project XML file for the project corresponding to the zipped data files is available or not. Example 1: This is for a case where the MIDAS project XML file is also distributed with the data: 1. Start MIDAS and click on the Utilities icon: 2. Select the option for Copy Study Data and Zip. 3. In the Read from Existing Zip File section, click Destination/Browse and select a path where the data is to be put. The Make New Folder button can be used to create a new directory, e.g. MIDASData, as shown to the right. Click OK to return to the previous widget. 4. Select the checkbox for Delete Zip file after unpacking (optional). 3

4 5. Click Select Files and Run UnZip 6. The program will bring up a file selection widget, browse to the location where the zip files are located and select the files you want to restore. After selection the program will start and display the status line, e.g. as Unzipping..zip. It will take several minutes. Exit the program when it finishes. The files will get unzipped into a separate directory for each subject, with the same name as the zip file name. 7. Copy the Project file that was distributed with the data into the same directory where the data directories were created. The file and directories should be similar to that shown in the example, where BL_Main.xml is the file that defines the project: 8. From the MIDAS toolbar, start the Importer: and select File Import Existing Project 9. Browse to the location of the data that you just unzipped and select the XML file, e.g.: Select Open and that project will become known to the MIDAS system. If you plan on processing data in this project you will need to also set the paths to the Proc Files Path and the Atlas Path. To do this select Edit Project. The widget will change to include Browse buttons that allow you to select the paths for each entry: 4

5 Select Save Changes and Exit the importer. If you want to use a local copy of the processing files then you will need to copy the files to a new subdirectory directory. 10. Now you can view the data using the Viewer or SID. For the Viewer, you need to first set the Working Project to the project that you have just imported: Notes: For SID, you may get some error messages indicating missing data when you first open a study. This can occur is options were set to not save all data types when the ZIP utility was run. This can be done to save space by not including large files that are not of interest for display, for example the *.PhaseMagn and *.ecc data, which are only needed for the data reconstruction. Example 2: This describes the procedure for the case where the Project.xml file is NOT available. This method is also easier if you have only one or two studies to import. 1. Start the Importer and create a new project using FileNew Project You will need to browse to select a new directory for the project and optionally set the paths for the Proc files and Atlas. Exit the Importer. 5

6 2. Go to the MIDAS utilities section,, and start the Zip Study tool and unzip the data to the data directory that was created in the previous step (Project Path in the example shown above), as described in the previous example. 3. Start the Importer again and add the new studies to the project using the Importer: Select FileImport Existing Subject Browse to the subject.xml file of the subject to include, e.g. Click Open and repeat this step for all studies that you want included. If you open up the tree in the Subject Browser section of the Importer you will see the imported studies: 5. Copying Processing Files This function is shown in the top right section of the widget: This will pack a batch pipeline definition file and all of the processing files used in that pipeline into a zip file. First use the Browse button to select the batch processing file. If a study has already been opened in 6

7 the Copy and Compress section then the program will default to the processing file location for the selected project. Then click the Select Destination and Save button. You will be prompted to enter the filename and path for the file to contain the zipped processing files. Only the ZIP file extension is allowed and the compression program requires that the filename have no spaces in it. The program will then copy and compress all processing files. 6. Acknowledgements Funding for this development was provided from NIH grant R01EB