|
|
| (11 intermediate revisions by one other user not shown) |
| Line 7: |
Line 7: |
| | ** Key Investigators: | | ** Key Investigators: |
| | ** Brief Description: | | ** Brief Description: |
| | + | ** Use: What kinds of queries will be important? |
| | * NCIGT_Tumor_Resection (HK/AG) | | * NCIGT_Tumor_Resection (HK/AG) |
| | ** Key Investigators: | | ** Key Investigators: |
| | ** Brief Description: | | ** Brief Description: |
| | + | ** Use: What kinds of queries will be important? |
| | + | * NCIGT_Glioma_Resection (HK) |
| | + | ** Key Investigators: |
| | + | ** Brief Description: Intraoperative MRT brain only |
| | + | ** Use: What kinds of queries will be important? sex,age,tumor size, tumor grade, tumor location (lobe) |
| | * NCIGT_Prostate (HE/CT) | | * NCIGT_Prostate (HE/CT) |
| | ** Key Investigators: | | ** Key Investigators: |
| | ** Brief Description: | | ** Brief Description: |
| | + | ** Use: What kinds of queries will be important? |
| | * NCIGT_Prostate_Fully_Segmented (HE/CT) | | * NCIGT_Prostate_Fully_Segmented (HE/CT) |
| | ** Key Investigators: | | ** Key Investigators: |
| | ** Brief Description: | | ** Brief Description: |
| | + | ** Use: What kinds of queries will be important? |
| | * NCIGT_Brain_Biopsy (FT) | | * NCIGT_Brain_Biopsy (FT) |
| | ** Key Investigators: | | ** Key Investigators: |
| | ** Brief Description: | | ** Brief Description: |
| | + | ** Use: What kinds of queries will be important? |
| | | | |
| | =Use-Case Goals= | | =Use-Case Goals= |
| Line 38: |
Line 47: |
| | '''Step 3. Disseminating & Sharing''' | | '''Step 3. Disseminating & Sharing''' |
| | * In addition to NCIGT mandate to share data, each effort listed above will have different requirements for being able to make data available to collaborating and other interested groups. | | * In addition to NCIGT mandate to share data, each effort listed above will have different requirements for being able to make data available to collaborating and other interested groups. |
| | + | |
| | + | '''Step 4. Moving data from central.xnat.org to BWH instance of XNAT''' |
| | | | |
| | =Outcome Metrics= | | =Outcome Metrics= |
| Line 59: |
Line 70: |
| | | | |
| | ==Current Data Management Process== | | ==Current Data Management Process== |
| | + | Data on local disk. |
| | | | |
| − | ==Target Data Management Process (Step 1.) Option A.== | + | ==Target Data Management Process (Step 1.) Option A. interactive upload using various tools and web gui == |
| − | * Create new project using web GUI
| + | See [[ CTSC_DataManagementWorkflow | here ]] |
| − | * Manage project using web GUI: Configure settings to automatically place data into the archive (no pre-archive)
| |
| − | * Create a subject template (download from web GUI)
| |
| − | * Create a spreadsheet conforming to subject template
| |
| − | * Upload spreadsheet using web GUI to create subjects
| |
| − | * Run CLI Tool for batch anonymization (See here for HowTo: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html)
| |
| − | * Need pointer for script to do batch upload & apply DICOM metadata.
| |
| − | * Confirm data is uploaded & represented properly with web GUI
| |
| − | | |
| − | ==Target Data Management Process (Step 1.) Option B. (web services API) '''CURRENTLY BEING TESTED!'''==
| |
| − | | |
| − | '''1. Create new project on XNAT instance using web GUI'''
| |
| − | | |
| − | * Create a new project by selecting the New button at the GUI top
| |
| − | * Select the project from the project list.
| |
| − | * From within the Project view, Click "Access" tab and set permissions to be appropriate
| |
| − | * From within the Project view, Select the "Manage" tab and configure settings to automatically place data into the archive (no pre-archive)
| |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''2. Batch Anonymize'''
| |
| − | * The approach to writing anonymization scripts is here: http://nrg.wustl.edu/projects/DICOM/AnonScript.jsp
| |
| − | * See description for batch anonymization here: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html
| |
| − | * Download and install commandline tools: http://nrg.wustl.edu/projects/DICOM/DicomBrowser-cli.html
| |
| − | | |
| − | '''2.a''' Create a remapping config xml file to describe the spreadsheet to be built from the DICOM data. Root element is "Columns" and each subelement describes a column in the spreadsheet:
| |
| − | | |
| − | * tag = DICOM tag
| |
| − | * level = (global, patient, study, series) describes the level at which the remapping is applied
| |
| − | | |
| − | An example is:
| |
| − | | |
| − | <Columns>
| |
| − | <Global remap="Fixed Institution Name">(0008,0080)</Global>
| |
| − | <Global remap="Anon Requesting Physician" (0032,1032)</Global>
| |
| − | <Patient remap="Anon Patient Name">(0010,0010)</Patient>
| |
| − | <Patient remap="Anon PatientID">(0010,0020)</Patient>
| |
| − | <Patient remap="Anon Patient Address" (0010,1040)</Patient>
| |
| − | <Study>(0020,0010)</Study>
| |
| − | <Study>(0008,0020)</Study>
| |
| − | <Series>(0020,0011)</Series>
| |
| − | <Series>(0008,0031)</Series>
| |
| − | </Columns>
| |
| − | | |
| − | '''2.b''' Generate a spreadsheed from the data that includes the remapped dicom tags:
| |
| − | DicomSummarize -c remap-config-file.xml -v remap.csv [directory-1 ...]
| |
| − | | |
| − | The arguments in brackets are a '''list''' of directories containing the source DICOM data (separated by spaces?)
| |
| − | | |
| − | '''2.c''' Write an anonymization script for any simple changes, such as deleting an attribute, or setting an attribute value to either a fixed value or a simple function of other attribute values in the same file. Here, make sure to remove patient address and requesting physician as noted, plus whatever else you'd like (recommendations?)
| |
| − | | |
| − | See http://nrg.wustl.edu/projects/DICOM/AnonScript.jsp for detailed information about writing anonymization scripts. Here's a script written by Mark during his testing.
| |
| − | // removes all attributes specified in the
| |
| − | // DICOM Basic Application Level Confidentiality Profile
| |
| − | // mark@bwh.harvard.edu added the following tags:
| |
| − | // (0010,1040) PatientsAddress
| |
| − | // (0032,1032) RequestingPhysician
| |
| − | // is seems the study and series InstanceUID tags are needed (0020,000D) (0020,000E)
| |
| − | //- (0020,000D)
| |
| − | //- (0020,000E)
| |
| − | // - (0010,1010) preserve pt age
| |
| − | // - (0010,1040) preserve pt sex
| |
| − | - (0008,0014)
| |
| − | - (0008,0050)
| |
| − | - (0008,0080)
| |
| − | - (0008,0081)
| |
| − | - (0008,0090)
| |
| − | - (0008,0092)
| |
| − | - (0008,0094)
| |
| − | - (0008,1010)
| |
| − | (0008,1030) := "SPL_IGT"
| |
| − | - (0008,1040)
| |
| − | - (0008,1048)
| |
| − | - (0008,1050)
| |
| − | - (0008,1060)
| |
| − | - (0008,1070)
| |
| − | - (0008,1080)
| |
| − | - (0008,2111)
| |
| − | (0010,0010) := "case143"
| |
| − | (0010,0020) := "case143"
| |
| − | - (0010,0030)
| |
| − | - (0010,0032)
| |
| − | - (0010,1040)
| |
| − | - (0010,0040)
| |
| − | - (0010,1000)
| |
| − | - (0010,1001)
| |
| − | - (0010,1020)
| |
| − | - (0010,1030)
| |
| − | - (0010,1090)
| |
| − | - (0010,2160)
| |
| − | - (0010,2180)
| |
| − | - (0010,21B0)
| |
| − | - (0010,4000)
| |
| − | - (0018,1000)
| |
| − | - (0018,1030)
| |
| − | (0020,0010) := "MR1"
| |
| − | - (0020,0052)
| |
| − | - (0020,0200)
| |
| − | - (0020,4000)
| |
| − | - (0032,1032)
| |
| − | - (0040,0275)
| |
| − | - (0040,A124)
| |
| − | - (0040,A730)
| |
| − | - (0088,0140)
| |
| − | - (3006,0024)
| |
| − | - (3006,00C2)
| |
| − | | |
| − | '''2.d''' Edit the spreadsheet (remap.csv file) that is generated as output.
| |
| − | | |
| − | This spreadsheet will contain all the columns you defined, plus some additional columns needed to uniquely identify each patient, study, and series.
| |
| − | | |
| − | Each new (remap) column should be filled with values. In some cases, some cells in the spreadsheet can be left blank: for a Patient-level remap, one value must be specified for each patient; if the spreadsheet contains multiple rows for each patient, the column needs only be filled in one row for each patient. Similarly, for a Study-level remap, the value need only be filled once. If you don't fill in a required cell, the remapper will complain. If you give, for example, a Patient-level remap column multiple values for a single patient, the remapper will complain.
| |
| − | | |
| − | '''2.e''' Run the remapper:
| |
| − | | |
| − | DicomRemapper -c remap-config-file.xml -o <path-to-output-directory> -v remap.csv [directory-1 ...]
| |
| − | | |
| − | *the remap config XML should be the same file used in 2.a,
| |
| − | * remap.csv is the spreadsheet generated in 2.c and edited in 2.d, and
| |
| − | * list of directories is the same list of source directories from 2.e.
| |
| − | * add an anonymization script to be applied at this stage by using the -d option.
| |
| − | * first time you use a script to generate new UIDs, you'll need a new UID root;
| |
| − | ** do this by adding -s http://nrg.wustl.edu/UIDGen to the DicomRemapper command line.
| |
| − | | |
| − | | |
| − | '''NOTE''' DicomBrowser doesn't write directly into the database -- it can send to a DICOM server. Below we use webservices to write directly to the database. Does this violate best practices?
| |
| − | | |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | For next steps using web services, use curl or XNATRestClient (See here to '''download XNATRestClient''' in xnat_tools.zip from here: http://nrg.wikispaces.com/XNAT+REST+API+Usage)
| |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''3. Authenticate''' with server and create new session; use the response as a sessionID ($JSessionID) to use in subsequent queries
| |
| − | curl -d POST $XNE_Svr/REST/JSESSION -u $XNE_UserName:$XNE_Password
| |
| − | or, use the XNATRestClient
| |
| − | XNATRestClient -host $XNE_Svr -u $XNE_UserName -p $XNE_Password -m POST -remote /REST/JSESSION
| |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''4. Create subject'''
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT /REST/projects/$ProjectID/subjects/s0001
| |
| − | (This will create a subject called 'S0001' within the project $ProjectID)
| |
| − | | |
| − | A script can be written to automatically create all subjects for the project.
| |
| − | | |
| − | '''4a. specify the demographics of a subject already created, or create with demographic specification'''
| |
| − | | |
| − | '''4.a.1''' No demographics are applied to each subject by default. To edit the demographics (like gender or handedness) of a subject '''already created''' using XML Path shortcuts.
| |
| − | | |
| − | xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/gender = male
| |
| − | xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/handedness = left
| |
| − | | |
| − | The entire command looks like this (Append XML path shortcuts and separate each by an ''&''. Note that querystring parameters must be separated from the actual URI by a ?):
| |
| − | | |
| − | XNATRestClient -host $XNE_svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/s0001?xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/gender=male&xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/handedness=left"
| |
| − | | |
| − | All XML Path shortcuts that can be specified on commandline for projects, subject, experiments are listed here: http://nrg.wikispaces.com/XNAT+REST+XML+Path+Shortcuts
| |
| − | | |
| − | '''4.a.2''' Alternatively, specify the demographics '''during subject creation''' by generating and uploading an xml file with the subject:
| |
| − |
| |
| − | XNATRestClient -host $XNE_srv -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/s0002" - local ./$ProjectID_s0002.xml
| |
| − | | |
| − | The XML file you create and post looks like this:
| |
| − | | |
| − | <xnat:Subject ID="s0002" project="$ProjectID" group="control" label="1" src="12" xmlns:xnat="http://nrg.wustl.edu/xnat" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
| |
| − | <xnat:demographics xsi:type="xnat:demographicData">
| |
| − | <xnat:dob>1990-09-08</xnat:dob>
| |
| − | <xnat:gender>female</xnat:gender>
| |
| − | <xnat:handedness>right</xnat:handedness>
| |
| − | <xnat:education>12</xnat:education>
| |
| − | <xnat:race>12</xnat:race>
| |
| − | <xnat:ethnicity>12</xnat:ethnicity>
| |
| − | <xnat:weight>12.0</xnat:weight>
| |
| − | <xnat:height>12.0</xnat:height>
| |
| − | </xnat:demographics>
| |
| − | </xnat:Subject>
| |
| − | | |
| − | '''4.b (optional check) Query the server to see what subjects have been created:'''
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m GET -remote /REST/projects/$ProjectID/subjects
| |
| − | | |
| − | '''4.c Create experiments (collections of image data) you'd like to have for each subject'''
| |
| − | | |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/MRExperiment?xnat:mrSessionData/date=01/02/09"
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/CTExperiment1?xnat:ctSessionData/date=01/02/09"
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/PETExperiment1?xnat:petSessionData/date=01/02/09"
| |
| − | | |
| − | '''4.d (optional check) Query the server to see what experiments have been created:'''
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m GET -remote /REST/projects/$ProjectID/subjects/s0001/experiments?format=xml
| |
| − | | |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''5. Batch Anonymize ''' scan data
| |
| − | | |
| − | * Run CLI Tool for batch anonymization (See here for info: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html)
| |
| − | | |
| − | * Also See here for new (please report bugs as noted) command line options: http://nrg.wustl.edu/projects/DICOM/DicomBrowser-cli.html
| |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''6. Create metadata from DICOM headers'''
| |
| − | | |
| − | <br>
| |
| − | <br>
| |
| − | '''7. Create uris for scans, reconstructions and upload them.'''
| |
| | | | |
| − | Note: when uploading images, it is good form to define the format of the images (DICOM, ANALYZE, etc) and the content type of the
| + | ==Target Data Management Process (Step 1.) Option B. batch scripted upload via DICOM Server == |
| − | data. '''This will not translate any information in the DICOM header into metadata on the scan.'''
| + | See [[ CTSC_DataManagementWorkflow | here ]] |
| | | | |
| − | //create SCAN1
| + | ==Target Data Management Process (Step 1.) Option C. batch scripted upload via web services== |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN1?xnat:mrScanData/type=T1"
| + | See [[ CTSC_DataManagementWorkflow | here ]] |
| − |
| |
| − | /upload SCAN1 files...
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN1/files/1232132.dcm?format=DICOM&content=T1_RAW" -local /data/subject1/session1/RAW/SCAN1/1232132.dcm
| |
| − |
| |
| − |
| |
| − | //create SCAN2
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN2?xnat:mrScanData/type=T2"
| |
| − |
| |
| − | //upload SCAN2 files...
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN2/files/1232133.dcm?format=DICOM&content=T2_RAW" -local /data/subject1/session1/RAW/SCAN2/1232133.dcm
| |
| − |
| |
| − |
| |
| − | //create reconstruction 1
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0343?xnat:reconstructedImageData/type=T1_RECON"
| |
| − |
| |
| − | //upload reconstruction 1 files...
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0343/files/0343.nfti?format=NIFTI" -local /data/subject1/session1/RECON/T1_0343/0343.nfti
| |
| − |
| |
| − |
| |
| − | //create reconstruction 2
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0344?xnat:reconstructedImageData/type=T2_RECON"
| |
| − |
| |
| − | //upload reconstruction 2 files...
| |
| − | XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0344/files/0344.nfti?format=NIFTI" -local /data/subject1/session1/RECON/T1_0344/0344.nfti
| |
| − |
| |
| | | | |
| − | <br>
| |
| − | <br>
| |
| − | '''8. Confirm''' data is uploaded & represented properly with web GUI
| |
| | | | |
| | ==Target Query Formulation (Step 2.)== | | ==Target Query Formulation (Step 2.)== |
