The XML template file is used by the LocalHumanUpload.sh and AddVisit2HID.sh scripts to configure the subject, visit, study, and series information for both image uploads to the SRB and general HID database GUI operations such as adding assessments.
2. A valid upload XML template consists of the following tags
2.1. <FileSystem> - Exactly 1 of these tag groups
2.1.1. The scripts are designed to operate in 3 modes, Local, Local-SRB, and SRB. The Local mode does some image wrapping and conversion to NIfTI 1.0 and Analyze 7.5 image formats and reorganizes the directory structure storing the output data in the <TARGET_DIR>. Local mode does not copy the data to the SRB nor link it into your local HID database. Local-SRB mode operates in the same was as the Local upload but does the transfer of the data to the SRB and updates your local HID database. The SRB is the same as Local-SRB mode except the local copy that was put into <TARGET_DIR> is deleted after the upload.
2.1.2. Valid entries: Local, Local-SRB, or SRB
2.2. <BIRNID> - Exactly 1 of these tag groups
2.2.1. ID of the subject being uploaded
2.3. <acquisitionSiteID> - Exactly 1 of these tags
2.3.1. Site ID of the acquisition site
2.4. <subjectGroup> - Exactly 1 of these tags
2.4.1.1. Name of this group of subjects (ie. control adults, AD patients, etc).
2.4.1.2. This needs to match the name in the experiment configuration XML file <subjectGroup> if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.5. <project> - Exactly 1 of these tag groups
2.5.1.
<name>
2.5.1.1. Name of project, same as the name used to register the project with BIRN: https://portal.nbirn.net/BIRN/cgi-bin/Login/rd.cgi?location=https://portal.nbirn.net/BIRN/cgi-bin/Projects
2.5.1.2. This needs to match the name in the experiment configuration XML file <project><name> if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.5.2.
<ID>
2.5.2.1. Project ID from the BIRN project registration page
2.5.2.2. This needs to match the ID in the experiment configuration XML file <project><ID> if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.6. <visit> - Exactly 1 of these tag groups
2.6.1.
<name>
2.6.1.1. Name of the visit, common names are scan, clinical, screening, etc.
2.6.2.
<ID>
2.6.2.1. The order number of this visit for this particular subject
2.6.3.
<visitDate>
2.6.3.1. Date of the visit – format: 2005-08-31
2.6.4.
<visitType>
2.6.4.1. Visit type needs to match the <visitType><name> in the experiment configuration XML file if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.6.5.
<description>
2.6.5.1. Description of the visit
2.7. <study> - Exactly 1 of these tag groups
2.7.1.
<name>
2.7.1.1. Name of the study (ie. MRI, EEG, NeuroCog, etc)
2.7.2.
<ID>
2.7.2.1. Study order for a particular visit. If a subject did an MRI then an EEG on the same physical visit then the study ID for the MRI = 1 and the EEG = 2.
2.7.3.
<studyTime>
2.7.3.1. Time of the study – format: 13:45:30
2.7.4.
<description>
2.7.4.1. Description of the study
2.8. <series> - There can be N number of these tag groups
2.8.1. For series that represent collected data:
2.8.1.1.
<nameLocal>
2.8.1.1.1. Local directory name of the data under the ROOT_IMAGE_DIRECTORY (See README)
2.8.1.2.
<nameStandard>
2.8.1.2.1. Standard name of the directory you’d like to store the data in the local target or SRB (if using Local-SRB or SRB mode). Usually these are agreed upon names by the members of an experiment to help in locating and understanding the enclosed data files
2.8.1.3.
<ID>
2.8.1.3.1. This is the order number for this series. If a subject did 3 series during an MRI scanning session these IDs would be 1,2, and 3.
2.8.1.4.
<seriesTime>
2.8.1.4.1. Time of the series data collection: 13:45:30
2.8.1.5.
<description>
2.8.1.5.1. Description of the series
2.8.1.6.
<type>
2.8.1.6.1. The type can be:
2.8.1.6.1.1. functional = EPI data
2.8.1.6.1.2. structural = standard structural MRI data
2.8.1.6.1.3. structural-anon = Anonymized structural data (see below 2.8.2 for derived data)
2.8.1.6.1.4. behavioral = EPrime or other behavioral data formats, no imaging data collected
2.8.1.6.1.5. segmentation = segmentation or label data
2.8.1.6.1.6. exclude = want to exclude this data from upload
2.8.1.6.1.7. extra = extra miscellaneous data, nothing done except uploading
2.8.1.7.
<paradigm>
2.8.1.7.1. This is the paradigm name and needs to match the <seriesParadigm><paradigm> tag in the experiment configuration XML file if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.8.1.8.
<paradigmVersion>
2.8.1.8.1. Version of the paradigm and needs to match the <seriesParadigm><paradigmVersion> tag in the experiment configuration XML file if using HID database support, else call it whatever you like (See README_AddExperiment2HID)
2.8.1.9. <number> - Optional for FIPS Image Processing Pipeline Use
2.8.1.9.1. The repetition number of a particular run. For example if you collected 3 runs of the SIRP task your series blocks would get <number> tags equal to 1, 2, and 3.
2.8.1.10.
<sliceorder>
2.8.1.10.1. The slice order the scanner acquires
2.8.1.11.
<discardAcq>
2.8.1.11.1. The number of volumes to discard from the dataset when running an analysis (for fMRI datasets)
2.8.1.12. <analysislevel> - Optional for FIPS Image Processing Pipeline Use
2.8.1.12.1.
<level>
2.8.1.12.1.1. should be set = “none”
2.8.1.12.2.
<name>
2.8.1.12.2.1. should be set = “none”
2.8.2. For series that are derived from other series (ie. defaced T1’s, brain segmentations)
2.8.2.1.
<nameLocal>
2.8.2.1.1. Local directory name of the data under the ROOT_IMAGE_DIRECTORY (See README)
2.8.2.2.
<nameStandard>
2.8.2.2.1. Standard name of the directory you’d like to store the data in the SRB. Usually these are agreed upon names by the members of an experiment to help in locating and understanding the enclosed data files
2.8.2.3.
<type>
2.8.2.3.1.1. functional = EPI data
2.8.2.3.1.2. structural = standard structural MRI data
2.8.2.3.1.3. structural-anon = Anonymized structural data (see below 2.8.2 for derived data)
2.8.2.3.1.4. behavioral = EPrime or other behavioral data formats, no imaging data collected
2.8.2.3.1.5. segmentation = segmentation or label data
2.8.2.3.1.6. exclude = want to exclude this data from upload
2.8.2.3.1.7. extra = extra miscellaneous data, nothing done except uploading
2.8.2.4. There can be N many of the following <source> and <ID> tags. These basically link this derived data to <series> blocks defined previously in this XML file
2.8.2.4.1.
<source>
2.8.2.4.1.1. The <paradigm> tag from the <series> block that this derived data is based on (see 2.8.1.7 above)
2.8.2.4.2.
<ID>
2.8.2.4.2.1. The <ID> tag number from the <series> block that this derived data is based on (see 2.8.1.3 above)
Example Files: Ped_SubjectVisit.xml, PhaseI_Template_SIRP.xml, PhaseII_Template.xml
*****NOTE: IF A
SERIES BLOCK DOES NOT EXIST IN THE XML FILE FOR A PARTICULAR SUB-DIRECTORY OF
THE ROOT_IMAGE_DIR IT WON'T BE "UPLOADED" AND WILL BE IGNORED DURING
THE UPLOAD PROCESS!
*****Note: The study
date and series date must be the same as the visit date.
*****Note: Please
note that segment order in HID will follow the <ID> tags in each
<series> block in the xml configuration file.
Dingying Wei -
UCI (dywei@uci.edu)
David Keator - UCI (dbkeator@uci.edu)
Karen Pease - UIowa (karen-pease@uiowa.edu)