loni image & data archive · pdf filethe loni image & data archive (ida) is a...
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Laboratory of Neuro Imaging
Dr. Arthur W. Toga, Director
April, 2017
LONI IMAGE & DATA ARCHIVE USER MANUAL
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LONI Image & Data Archive
INTRODUCTION TheLONIImage&DataArchive(IDA)isauser-friendlyenvironmenttoarchive,search,share,track,anddisseminateneuro-imagingdata.ItaccommodatesMRI,fMRI,PET,MRA,DTIandotherimagingmodalities.A flexible data de-identification engine and encrypted file transmission help ensure compliance withpatient-privacyregulations.Alldataarestoredonredundantserverswithdailyandweeklyon-andoff-sitebackups.ArchivingdataintheIDAissimple,secureandrequiresnospecializedhardwareorsoftware.TheIDAautomaticallyextractsrelevantmetadatafromde-identifiedimagefiles,andallowsdatatobesearchedwithin moments of archival. Once archived, data can be downloaded and/or streamed into the LONIPipelineworkflowenvironmentforprocessingandanalysis.IntegrationoftheLONIDebabelerfileformattranslationengineallowsuserstodownloadimagedatainanumberofcommonfileformats.
ForquestionsorproblemswiththeIDA,[email protected]
IMAGE&DATAARCHIVE(IDA)
InstituteforNeuroimagingandInformatics
KeckSchoolofMedicine
UniversityofSouthernCalifornia2001NorthSotoStreet,SSB!-102,
LosAngeles,CA90033
Phone:323-442-7246
Fax:323-442-0137https://ida.loni.usc.edu
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Contents
A. IMAGE&DATAARCHIVEOVERVIEW _______________________________________________3
SystemRequirements:_______________________________________________________________3
IDAMenuOverview_________________________________________________________________3
UserRegistration ___________________________________________________________________4
II. EnterthesecuritycodesenttoyouremailandpressCONITNUE_________________________4
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B. SEARCHIMAGES________________________________________________________________5
TheSearchMenu _________________________________________________________________5
SimpleSearch____________________________________________________________________5
AdvancedSearch__________________________________________________________________6
AddingResultstoCollectionsWheretheyMaybeDownloaded ____________________________7
ImageDataDetails________________________________________________________________7
SearchandDownloadWorkflow:_____________________________________________________8
C. IMAGECOLLECTIONS____________________________________________________________8
CreatingImageCollections__________________________________________________________9
The‘Collections’Listing ___________________________________________________________10
EditandShareImageCollections____________________________________________________10
D. DOWNLOADDATA_____________________________________________________________11
TheDownloadMenu _____________________________________________________________11
DownloadImages________________________________________________________________11
E. ARCHIVEIMAGES______________________________________________________________13
SelectingArchiveMethod(SingleorBatchArchive?) ____________________________________14
TheArchiveMenu________________________________________________________________14
ArchiveRawImages(Type1)_______________________________________________________14
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A. IMAGE&DATAARCHIVEOVERVIEWTheLONIImage&DataArchive(IDA)providesanintegratedandsafeenvironmenttoarchiveneuro-imagingdata.Thearchiveprotectsdatafromunauthorizedaccessandallowsinvestigatorstosharedata.ForquestionsorproblemswiththeIDA,[email protected]
SystemRequirements:TheIDAsystemrequiresacomputerwithinternetaccess,newerwebbrowsersoftware(IE,Netscape,Mozilla,Safari,Chrome),Javaplug-in(version1.5higherorhigher),andavaliduseraccount.
IDAMenuOverview Projects:All:Viewparticipantgenderandresearchgroupdistributiononpublicprojectsandotherprivateprojectsyouarepermittedtoaccess.PublicprojectssuchasPADareavailabletoallusers.IndividualProjects:Viewprojectinformationandparticipantgenderdistributionfromyourproject.Search:SimpleImageSearch:Databasequeriesbasedonalimitedsetofsubjectandimageparameters.AdvancedImageSearch:Databasequeriesusingamoreextensivelistofparameters.Limitedtoauthorizedusersonaproject-by-projectbasis.Archive:ArchiveFiles:De-identifyimagestoremovepotentiallyidentifyingsubjectinformation,andsecurelytransmitfilestobestoredintheLONIImage&DataArchive.Download:ImageCollections:Downloadindividualimagesorentirecollections.1-CLICKDOWNLOADandADVANCEDDOWNLOADoptions.StudyData:Downloadstudydataforselectedprojects.ProjectSummary:Viewprojectuploadanddownloadsummaryinformation.Availabletouserswithhigheraccesslevels.Manageuseraccess:Grantormodifyuser’sprivileges.Availabletoprojectleaders.Note:Availablesubmenusvarydependingonprojectanduseraccesslevel.
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UserRegistration
1. Toregisterforauseraccount,ontheImage&DataArchiveLog-InpageclickInstantfreesignupinthetoprightcorner
2. CompleteNewaccountregistration(3steps).
I. EnteryouremailaddressandpressCONTINUE.Asecuritycodewillbesenttoyouremail
II. EnterthesecuritycodesenttoyouremailandpressCONITNUE
III. CompletetheNewaccountregistrationformandpressREGISTERAlinktosetyourpasswordwillbesenttoyouremail.
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3. CreateapasswordandclickCONTINUE
B. SEARCHIMAGES
Userscansearchforimagesbasedonsubjectandimage-relatedcriteria,viewimages,formcollectionsanddownloadimages.Therearetwotypesofimagesearches:SimplesearchandAdvancedsearch.TheSimpleSearchperformsabasicdatabasequeryonsubjectsandrawimages,providinginformationsuchassubjectage,sexandimagemodalityorseriesdescription.TheAdvancedSearchsupportsamoreextensiveexplorationofthedatabase,includingprocessedimages,andprovidesadditionalinformationaboutsubjectsandimages.Todownloadimages,performaSimpleorAdvancedSearch,addtheimagestoadatacollectionthendownload.Toaccessprocessedimages,usetheAdvancedSearch.
TheSearchMenu
SimpleSearch1. SelectSimpleImageSearchontheSEARCHmenu.
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2. EnterthesearchcriteriaandclickSEARCH.Note,SimpleSearchcanonlyproviderawDICOMresults.ProcessedimagescanonlybesearchedwithAdvancedImageSearchorAdvancedImageSearch(beta).
3. IntheSearchResultsselectVIEWtoopeninimageintheIDAImageViewer4. Selectthecorrespondingcheck-box,andthetoaddanimagetoadatacollection,whereitcan
bedownloaded
AdvancedSearchTherearetwoadvancedsearchfunctions:AdvancedImageSearchandAdvancedImageSearch(beta).TheBetaversionhasmorecapabilities,butasofnowtheoriginalversionisstillavailablebecauseitallowsuserstoSAVEsearchparameters,unlikeitssuccessor.
ThismanualwillonlyoverviewAdvancedImageSearchBETA.UseittoquerythedatabaseusingamoreextensivelistofelementsthantheSimpleSearch.Chooseadditionalelementsorimagetypes,originalorprocesseddata,andsetthesortorderoftheresults.Theavailabilityofelementsvariesaccordingtoprojectanduseraccesslevel.(YoumayexploretheoriginalAdvancedImageSearchtolearnhowtosavequeries)
1. SelectADVANCEDIMAGESEARCH(beta)ontheSEARCHmenu.2. UsetheSearchOptionsboxonthelefttoexpandSearchCriteriacategoriesontheright.3. Specifyimagetypes.OriginalimagesarerawDICOMS.Preprocessedmaybeinavarietyof
formats.
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4. Selectimagecriterionusingthecheck-boxesanddrop-downmenus.Toselectmorethanoneiteminadropdown,clickeachitemwhileholdingdowntheControlkeyonPCorCommandkeyonMac.
5. SelectdatayouwantlistedintheresultsusingtheDisplayinresultcheck-boxes.Datawithcorrespondinggrayedoutboxesaredisplayedbydefault.
6. SelectSearch.
AddingResultstoCollectionsWheretheyMaybeDownloadedTheresultingSearchResultstabdisplaysinformationaboutimagesetsmatchingthesearchcriteria.Userscanviewandaddtheseresultstocollectionswheretheycanbedownloaded.Toaddanimagetoacollectionselectthecorrespondingcheck-box(1)andthentheAddtoCollectionbutton(2).UserscanVIEW(3)imagesusingtheIDAImageViewer. TheSeriesDescription(4)ofeachimageisalinktotheImageDataDetailspage.TogeneratealistofallthemetadataintheSearResultslist,selecttheCSVDownload(5)button.Youcaneditthedisplayedmetadata,orcolumns,byreturningtoAdvancedImageSearch(beta)andselectingtheDisplayinResultcheckboxfordesireddata.
ImageDataDetailsTheSeriesDescription(1)links,above,leadtotheImageDataDetailspage,whichprovidesadditionalprotocolinformationabouttheimagesuchasweighting,pulsesequence,acquisitiontype,etc.UserscanalsoVIEW(2)(below)imagesfromthispage.
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Processedimagesdisplayanadditionalsectiondescribinginformationsuchaspackagename,processname,programname,etc.
SearchandDownloadWorkflow:
C. IMAGECOLLECTIONS
TheCollectionsInterfaceprovidesaccesstoexistingcollectionsandtheirindividualcomponents.Userscanview,remove,regroupordownloadsingleimagesandentirecollections.Thislevelofinteractionappliesbothtopersonalcollectionsandsharedcollections,thosecreatedbyotheruserstowhichtheuserhasaccess.
Userscancreatecollectionswithanunlimitednumberofimages.Itisnotnecessarytoperformasearchtoaccesspreviouslycreatedcollections.Collectionscanberestructuredbyaddingorremovingimages.
Features:
• Accesspersonaldatacollections.• Downloadanynumberofimageswithasinglerequest(1-CLICKDOWNLOAD)orsplitthe
downloadintomultiplefilesusingADVANCEDDOWNLOAD.• Downloadimagesinanumberoffileformats,includingtheoriginallyarchivedformat,oran
alternateformatoftheuser’schoice(Analyze,NIfTI,NiFTI4D,MINC).• Trackdownloaded/notdownloadedimages.• Accesssharedcollections(createdbyotherusers).
Search•Performsimpleoradvancedsearches
•Viewimages
•Selectitemsfromresultslist
Collections
•Addselecteditemstoneworexistingcollections.
Download•Downloadfrompersonalorsharedcollections.
•Downloadmultipleimageandfileformats
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CreatingImageCollectionsTodownloadimagestheymustfirstbeaddedtoanImageCollection.
1. PerformaSIMPLEorADVANCEDImageSearch.2. OntheSearchResultspage,chooseimagesbyselectingtheircorrespondingcheck-boxes(2.1)
andclicktheAddtoCollectionbutton(2.2).
3. Enteranameforthecollectionorselectanexistingcollectionname(3)andclickOK
Anewwindowdisplaysthecollectioncontents.SimilartoontheSearchResultspage,theimageDescriptionslinktotheImageDataDetailspage.
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The‘Collections’ListingThereisanestedlistingofcollectionsontheleftsideofImageCollections.Usethislistingtonavigatebetweenyourpersonalandsharedcollections.
‘MyCollections’Whenexpanded,thisdirectorywilldisplayallcollectionsyouhavemade.Selectanycollectionnametonavigatetoit.
‘MySharedCollections'Thisdirectoryisnestedwithin‘MyCollections’anditwillcontainanycollectionthathasbeensharedwithyoubyaCo-Investigator.SeetheShareImageCollectionschapterformoreTheremustbeatleastoneotherinvestigatorlistedonaprojectinordertoshareanimagecollection.NavigatetotheAddCo-Investigatorschapterformoreinformation.
‘OtherSharedCollections’Thisdirectorycontainsstandardizedcollectionsthatareavailabletoallusersofaproject.OnlyspecificprojectsmakeSharedCollectionsavailable,includingADNI,HCP,andTRACKTBI.
‘REFRESHCOUNTS’
Click‘REFRESHCOUNTS’toseetheup-to-datenumberofimagesdownloadedineachcollection.Thisishelpfulifdownloadsareinprocessorrecentlycompleted.
EditandShareImageCollections(ProjectLeaderAccessRequired)Imagescanbeselected(usingcheck-boxes)andmovedtoothercollectionsusingtheREGROUP(1)buttonordeletedusingtheREMOVE(2)button.SharecollectionswithCo-InvestigatorsusingtheSHARE(3)button.Onceacollectionhasbeenshared,itmaybe‘unshared’withthe‘UNSHARE’button(greyedoutinthescreenshot).
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D. DOWNLOADDATA
AllIDAprojectscontainimagingdatathatcanbedownloaded.SpecificprojectssuchasADNIandPPMIadditionallyprovidedClinicaldataintheformofCSVfiles,aswellasGeneticdata.ThesethreetypesofdataareaccessiblethroughtheDownloadMenu.
TheDownloadMenu
DownloadImages1. SelectImageCollectionsontheDownloadMenu.
a. Note–ImageCollectionsarealsovisiblewhenimageshavejustbeenaddedtothem.SeeCreatingImageCollections.
2. Selectthecheck-boxesoftheimagesyouwanttodownload,orusethe‘All’checkboxtoselectallimageswithinacollection.
3. Selectafileformattodownloadtheimagesas.4. Select1clickDownloadorAdvancedDownload(seespecificinstructionsbelow)5. TogeneratealistofallthedatainanImageCollection,selecttheCSVDownloadbuttonbelow.
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1-CLICKDOWNLOAD
Usethebuilt-infunctionalityofyourwebbrowsertoquicklydownloadallthefilesinyourcollectiontoasinglezipfile.Afterselectingapop-upwindowwithinformationaboutyourdownload(sizeandtimeestimate)willappear.ClickontheDownloadZipFilelinktostartdownloading.
ADVANCEDDOWNLOAD
TheAdvancedDownloadoptionwillallowyoutosplityourdownloadintomultiplefiles.
Click and selectagroupingoption fromthedropdownmenu.Youmayclickeach link todownloadthezipfilesoruseyourfavoriteDownloadManagersoftwaretooptimizeyourdownloadspeedandexperience.
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ABOUTDOWNLOADMANAGERS
SoftwareapplicationsknownasDownloadManagersmayhelpyoumanageyourIDAfiledownloads:theycanautomatedownloadsofmultiplefilesandcankeeptrackoflargefilesseamlesslywhileyoudootherthings or are away from your computer. Amajor advantage ofmostDownloadManagers is that if adownload is briefly interrupteddue topoor connectivity, that downloadwill continue from thepointwhereitwasinterruptedinsteadofrestartingfromthebeginning.
IDAdoesnotendorseorsupportanydownloadmanagersandisnotresponsiblefordownloaderrorsorsubsequentissuesresultingfromuseofanythird-partyproducts.However,IDAhastestedandsuggeststhefollowingfreeproductsforyourconsideration:
E. ARCHIVEIMAGES
Therearetwostepsinthearchiveprocess:de-identificationandfiletransmission.Thede-identificationstepremovesorreplacespotentiallyidentifyingsubjectinformationfromtheimageheaders.Next,aJavaappletde-identifiesthefiles,insertingauser-suppliedsubjectidentifierandremovingorreplacingotherpotentially identifying information. The user is given the opportunity to validate the de-identificationresults, prior to transmitting the images.Once the results of the de-identification process have beenvalidated,thefilesaretransmittedfromtheuser’slocalcomputertoLONI.UponarrivalatLONI,thedataarestoredinafault-tolerantstorageareanetworkandthedatabaseispopulatedwithrelevantmetadataattributes.
There are twomethods for uploading images – Single and Batch Archive, each with its own distinctadvantages.SeeSelectingArchiveMethod.
ThedataarchiveacceptsDICOMfiles(Type1headers),andfileswithlimitedheaderinformation,suchasAnalyze,MINC,andNIfTI(Type2files).Type2filesmayonlybearchivedafterthecorrespondingType1(raw)fileisarchived.ArchivingType2files,orprocessedimages,requiresadditionaluserinputtoprovideimagemetadata.
ProductName Platforms Site
jDownloader Linux,MacorWindows www.jDownloader.org
uGet LinuxorWindows www.ugetDM.com
FDM MacorWindows www.FreeDownloadManager.org
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SelectingArchiveMethod(SingleorBatchArchive?)Ifyouarearchivingasetofimagesfromonlyonesubject,allinthesameformat,SingleArchivewillbesuitable.Forlargerdatasetswithmultiplesubjects,BatchArchiveispreferable.Theschematicbelowoutlinesthemajordifferences.
TheArchiveMenuForallarchiveoptionsselecttheArchivemenuoption.
ArchiveRawImages(Type1)Beforeanyprocessedimagescanbeuploaded,theoriginalDICOMsmustbearchived.ThefollowingcategoriesoutlinehowtoSingleandBatcharchiveDICOMs.Note,mostuserswillonlybearchivingraw
•Single•Batch (Multiple)Archive Method
•Original (raw image files)•Processed (pre and post processed)Data Types
•Type 1 (DICOM)•Type 2 (ANALYZE, MINC, NIfTI)Image File Formats
•Remove potentially subject-identifying informationDe-Identify
•FileTransmission•File ArchivingArchive
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images.Onlyselectusersaregivenpermissionstouploadprocessedimages,andtheywillbetrainedbytheProjectSpecialist.
REQUIREMENTS:1. Placeallimagefilesforeachsubjectwithinasingledirectory(sourcedirectory)whichmay
containsubdirectories.Thesourcedirectorymustnotcontainmultipleimageformats.2. Createanemptydirectorywherethede-identifiedfileswillbewritten(targetdirectory)3. Thebrowserwindowmustremainopenduringtheentireuploadprocess.Closingthebrowser
windowcancelstheupload.Youmayminimizethewindow.SingleArchiveUsetheSingleArchiveprocesstouploadoneormorefilesfromasinglesubject.
NavigatetotheArchiveandReviewpagefromtheArchivemenu.
1. SelectyourProject/Site(1)fromthedropdownmenu.2. SelecttheSingleArchive(2)button.
YouwillbedirectedtotheDe-Identificationpage.
1. Selectthetypeofdatabeinguploaded–inthiscase,‘Original’(1).2. SelecttheVisitnumber,ifthisisanoption(2)3. ProvidetheSubjectID(3)youprovidereplacestheexistingPatientIDintheimagefile(s).Itis
recommendedthataseparatecrossreferenceoforiginalandreplacementsubjectidentifiersarekeptexternally.
4. SelecttheSourceDirectory(4)wheretheimagesarecontained5. SelecttheTargetDirectory(5)forde-identifiedfilestobewrittento.6. SelectCONTINUE(6)tobeginthede-identificationprocess.
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OntheVerifyandSubmitpage
1. Deselect(1)anyimageyoudonotwanttobearchived.Justdeselectthecorrespondingcheckbox.
2. SelectSUBMIT(2)tobeginthetransmissionprocess.Note:ThisisnotafeaturewithBatchArchive
Oncetransmissionhasbegun,aprogressbarwillshowthestatusoftheupload.
Oncecomplete,clickREVIEWUPLOADEDFILEStoviewalistofthearchivedimagesontheArchiveandReviewpage,orclickARCHIVEMOREtouploadfilesforanothersubject.Ifyouneedtocontinuearchivingfilesforseparatesubjects,considerusingtheBatchArchivefunctioninstead.
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BatchArchiveTheBatchArchiveprocessissimilartoSingleArchive,exceptthatmultiplesubjectsandimageseriescanbesubmittedinabatch.Batchescanbeofthesameordifferentfileformatsandmodalities.However,userscannotreviewtheresultsofthede-identificationprocesspriortothebatchupload.
NavigatetotheArchiveandReviewpagefromtheArchivemenu.
1. SelectyourProject/Site(1)fromthedropdownmenu.2. SelecttheBatchArchive(2)button.
3. ProceedtofollowtheDe-identificationstepsintheSingleArchivechapter.4. TheBatchArchivewillskiptheVerifyandSubmitstepthatisavailableinSingleArchive,and
directyoutotheImageDatabaseBatchQueuepage.5. SelectADDMORE(1)toaddmoreimagestotheBatch.Repeatthisprocessuntilyouhave
addedeverythingyouintendtoarchive.6. ClickSUBMIT(2)tobeginboththede-identificationandtransmissionprocesses.
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Oncetransmissionhasbegun,eachsubjectwillbede-identified,andthenarchived,consecutively.Aprogressbarwillshowthestatusofeachupload.
Oncecomplete,clickREVIEWUPLOADEDFILEStoviewalistofthearchivedimagesontheArchiveandReviewpage,orclickARCHIVEMOREtouploadfilesforanothersubject.Ifyouneedtocontinuearchivingfilesforseparatesubjects,considerusingtheBatchArchivefunctioninstead.
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F. GLOSSARY
AdvancedSearch:Advancedsearchallowsuserstosearchwithacombinationofsubject,study,andimagedescriptors.Userscansearchseveralmodalitiessimultaneouslyandsavesearchresults.Archiving:ThestorageofimagedataandmetadatadescriptorsforfutureretrievalBatch archive: Uploading data from multiple subjects simultaneously. Batches may be different fileformatsandmodalities.Collections:AnimageorgroupofimagesselectedfromresultsofaSimpleorAdvancedSearchandgivenameaningfuldescription(collectionname).Delete:Removingimagefilesfromarchive.De-identification:Removalorreplacementofcertainimageheadercontentstoprotecttheidentityofthesubject.DICOM:DigitalImagingandCommunicationinMedicine.DTI:DiffusionTensionImaging.EditMetadata:Modifyinginformationsuchassex,age,andweight,aswellasotherproject-specificattributes.FileswithTYPE1/comprehensiveheaders:Fileformats:DICOM,GE,Philips,HRRTandECAT.FileswithTYPE2/limitedheaders:Fileformats:Analyze,MINC.FMRI:FunctionalMagneticResonanceImaging.Imagemetadata:Informationcontainedintheimageheaderdescribingthesubjectandimage.MINC:MedicalImagingNEtCFD.MRA:MagneticResonanceAngiography.
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MRI:MagneticResonanceImaging.NIFTI:NeuroimagingInformaticsTechnologyInitiative.Originaldata:Rawimagesfilespre-orpost-processed.PET:PositronEmissionTomography.Processeddata:Imagedata filestransformedormodifies fromtheiroriginal form, i.e, registered,warpedorcorrecteddata.Seriesdescription:Anidentifier(name)giventoadataset.Sequencename:Sameasseriesdescription.SimpleSearch:SearchesbasedonalimitedsetofcriteriasuchassubjectID,researchgroup,sex,age,weight,modality,seriesdescription.Singlearchive:Uploadofdataforonesubjectatatime.Fileheadersmustbeofthesametypeforupload(allTYPE1orTYPE2).Sourcedirectory:Directoryorfoldercontainingthefilestobede-identified.Containssingleformat,singlesubjectimagesfilesonly.Study:Oneormorefilesfromthesamesubjectacquiredonthesamevisitandscanner.Targetdirectory:TheTargetDirectorycanbeanexistingfolderoranewdirectory.Atemporarylocationstocontainde-identifiesfiles,informationandacopyofthelogsoftheuploadprocess.Validation:Theprocessofverifyingresultsofde-identification,andremovingimageswhicharenottobeuploaded.ThevalidationbuttonappearsonlywiththeSingleArchiveprocess.