handbook for electronic mri and clinical data...

HandbookforelectronicMRIandclinicaldatatransfer Version1.0

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ParallelstudyonMRIinNeuromyelitisOptica

HandbookforelectronicMRIandclinicaldatatransferVersion1.0fromJuly17,2017

DearfellowNMOSDresearchers,ThankyouforyourinterestinthePAMRINOstudy!PAMRINOisthepartnerstudytotheCollaborativeRetrospectivestudyonretinalOCTinNMOSD(CROCTINO)andwillcollectandanalyzeMRIdatafromNMOSDpatients.ThishandbookwillguideyouinyourclinicaldatauploadtoREDCapandMRIDICOMtransferviaTeamBeam.

ItisaprerequisitethatonlyanonymizeddataaretransferredtotheCROCTINO/PAMRINOStudyTeam.Assuch,youarerequiredtolabelalldatausinganindividualCROCTINO/PAMRINOIDforeachpatient/healthycontrol.TheprocessesofassigningtheCROTINO/PAMRINOID,preparationofyourMRIdata,andtransferoftheMRIandclinicaldatawillbeoutlinedinthismanual.

PleasedonothesitatetocontacttheCROCTINO/PAMRINOStudyTeamincaseyouhaveanyquestionsconcerningtheprojectat:

CROCTINO/PAMRINOStudyTeamPhone:+4930450539727Email:[email protected],[email protected]

ThePAMRINOproject(PIFriedemannPaul,Charité–UniversitätsmedizinBerlin,Germany)willinvestigateMRIchangesinNMOSDinalargemulticentersupportedbytheGuthyJacksonCharitableFoundation.TheauthorshippolicyforPAMRINOadvancesundertheaegisofGJCF-ICC.Specifically,whiletheactiveparticipants,e.g.datasetcontributors,willhavetheoptiontobeincludedthebylineauthorship,allICCmemberswillhavetheopportunitytoprospectivelyreviewandprovideinputtoanymanuscripts,andagreeordeclinetoberecognizedaspartofthebylineoraffiliatedauthorshipastheircontributionswarrant.AfterPAMRINOisfinished,allMRIdatasetswillbeavailablethroughtheNMOimagingrepository,NOIR.AllcollaboratorscangainaccessbyrequesttotheGuthyJacksonCharitableFoundation.Alldatauploadedneedstobeanonymizedandarenotallowedtocontainanypersonalinformation.Byuploadingdatayouconfirmthatthisisthecaseandthatyouhavetherightstouploadthedata.

Contents Page


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HandbookforelectronicMRIandclinicaldatatransfer 1

1. AssigningtheCROCTINO/PAMRINOID 3

2. MRIDICOMpreparation 4

2.1 DICOMsfromLocalPACS 4-5

2.2 DICOMmetadataanonymization 6

2.2.1 DownloadTudorAnonymizationTool 6

2.2.2 Anonymizationprocedure 6-9

2.2.3 Checkinganonymizationresults 9-12

2.2.4 SendinganonymizedMRIDICOMsusingTeamBeam 12-13

3. eCRF/Clinicaldataupload 14

3.1 REDCapTutorial 14-15


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1.AssigningtheCROCTINO/PAMRINOIDItisnecessarytoanonymizepatientdatathataretransferredtous.Assuch,youarerequiredtolabelalldatawithanindividualCROCTINO/PAMRINOIDforeachpatient.ThisIDconsistsofacodeforyourcenter(e.g.BERforBerlin),andunderscore,andconsecutivefour-digitnumbersforeachpatient(e.g.BER_0001,BER_0002,BER_0003,…).PleaseusethesameIDasinCROCTINOifthepatientisinboththeCROCTINOandPAMRINOstudies.Ifyoudonotknowyourcenter’sID,pleasecontactthePAMRINOStudyTeam.Werecommendstoringade-identifyinglistoftheCROCTINO/PAMRINOIDsusedforpatientdatafromyourcenter,asexemplifiedinthetablebelow.CROCTINO/PAMRINOID InternalID SubjectName Dateofbirth Group

BER_0001 ID04444 Doe,John 13/06/1971 NMOSD

BER_0002 ID05343 Dear,Jane 19/02/1980 NMOSD

BER_0003 ID09393 Skywalker,Luke 04/05/1955 NMOSD

BER_0004 ID07878 Simpson,Lisa 23/07/1970 NMOSD

BER_0007 ID09838 Cane,Candice 25/12/1981 HealthyControl

BER_0008 ID03435 Brown,Charlie 14/11/1973 HealthyControl

WewillbesendingyouanExceltemplateandanIDassignmentsheetforyourconvenience.


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2.MRIDICOMpreparationPleasesubmitonlyoriginalMRIscansasDICOMfilestoensurethatallscansundergothesamequalitycontrolandparametersarecalculatedandevaluatedusingthesameMRIanalysismethods.Forthis,weofferyoutheonlinedataserviceofourreadingcenter.Here,youcancomfortablytransferyourfilesasdescribedinthefollowingsections.BeforesendingBerlinyouranonymizedMRIDICOMs,adatatransferagreement(DTA)mustbemadebetweenyourcenterandthePAMRINOStudyTeamcenterinBerlin.PleasecontactusforfurtherinformationabouttheDTA.

2.1DICOMsfromLocalPACSInPAMRINO,wewillanalyzeparametersfromallMRIscansyourcenterhascollected,thus,allimagesthatareassociatedwithyourpatients/healthycontrolsmaybeused.ItismostcommonforMRIcenterstosavetheirMRIscansinapicturearchivingandcommunicationsystem(PACS).ThisiswhereyourDICOMsfromtheMRIaresavedtofromtheMRscannercomputer.TheseimagefilescanbedownloadedfromthePACStoanexternalcomputerthroughaninternetconnectionandaserverwhichiscenterspecific.Ifyoudonotknowhowtoexport/downloadMRIDICOMfiles,pleaseaskyourlocalMRItechnicianorimagingcenter.Fororganizeddatasharing,werecommendthefollowingprocedurefortheexport/downloadofyourMRIscans:

• CreateadirectoryonthecomputerwhereyouintendtodownloadtheMRIscans(e.g.C:\Desktop\PAMRINO_Export).ThencreateafolderforthepatientwhosedatayouintendtodownloadandnameitwiththeirCROCTINO/PAMRINOIDconsistingofyourthree-charactercenterIDandafour-digitconsecutivenumber(e.g.BER_0001).

• TheimagesfromthePACSsystemcanbeexported/downloadedaszippedfiles,whichcontainalltheMRIscansfromonepatientvisit(pleaserefertoFigure1).Savethe.zipfileintherespectivedirectoryyouhavecreatedbefore.PleasedoNOTchangetheimagefilesfromtherawDICOMfiles.

• PAMRINOisopentocollectinglongitudinaldata.Ifavailable,youcanexport/downloadyourpatientvisitsintotheoverarchingpatientdirectoryandcreatenewsubfoldersforeachvisit,namedwiththeCROCTINO/PAMRINOIDandanadditionalunderscoreandconsecutivenumberingforeachvisit(e.g.BER_0001_1,BER_0001_2,BER_0001_3,…)(pleaserefertoFigure1foranexampleofhowtocreatethefiledirectory).


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ExampleofMRIDICOMexport/downloadoptionsandfilestructuretouse.


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2.2DICOMmetadataanonymizationAlthoughyouhavesavedtheDICOMfilesinafilestructureusingtheCROCTINO/PAMRINOID(e.g.BER_0001_1),theMRIscanshavepatientinformationsavedinthemthatmustalsobeanonymized.Priortotransferringyourimagefilestous,wewouldsuggestusinganonline,openaccesstoolthathasbeenvalidatedbyourcenter,toanonymizethefieldsinyourDICOMheaders(wherethemetadataissaved).IfyourcenterhasamethodtoanonymizethemetadataintheDICOMheadersalready,pleasecontactusattheCROCTINO/PAMRINOStudyTeamtoinformusofyourcenter’sproceduretoensurethatallfieldsthatarerequiredtobechangedarecorrectlychanged/wiped.

2.2.1DownloadTudorAnonymizationTool

1. Usinganinternetbrowser,visitthesitehttp://www.santec.tudor.lu/project/dicom/downloadanddownloadthelatestversionoftheTudorDicomViewer(atthemomentversiondicom_viewer_1.9.30.zip).

2. Savethe.zipfileonyourPC/MaconyourDesktoporonthesamedriveasyourDICOMs.3. UnpacktheDicomViewer.zipfile:

a. PC:rightclickontheDicomViewer.zipfileandselect“Extractall”tounzipitb. Mac:doubleclickontheDicomViewer.zipfiletounzipit

4. OpentheextractedDicomViewerfolder.

2.2.2.Anonymizationprocedure

1. SincetheTudoranonymizertoolwilloverwritetheoriginalDICOMfiles,pleaseduplicatetheDICOM.zipfile:

a. PC:rightclickontheDICOM.zipfileandselect“Copy”;afterwardsrightclickintheoverarchingfolderandselect“Paste”

b. Mac:rightclickontheDICOM.zipfileandselect“Duplicate”ThiswillcreateacopyofyouroriginalDICOM.zipfileasshowninthisexample:

Oncethisstephasbeencompleted,followallstepsforanonymizationwithduplicated.zipfileonly.

2. PleaseunpacktheduplicatedDICOM.zipfile:

a. PC:rightclickontheDICOM.zipfileandselect“Extractall”tounzipitb. Mac:doubleclickontheDICOM.zipfiletounzipit


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3. GointheTudorDicomViewerfolderandstarttheanonymizerprogram:

a. PC:doubleclickonthe

“Dicom_viewer.exe”file

b. Mac:runthe“Dicom_Viewer.sh”fileinaterminalwiththecommand./Dicom_Viewer.shasshowninthefollowingexample:

a.

b.

b.


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4. ADicomViewerGUIwillopen.Pleaseclickonthe“AnonymizeDicomFiles”button:

5. Anotherwindowwillopen.Pleasefollowthesesteps:a. Clickthe“choose”buttonandbrowseforyourunpackedDICOMfolder(e.g.

“BER_0001_1–Copy”).b. EntertheCROCTINO/PAMRINOsubjectIDfollowedbythevisitnumberinthe

field“NEWPatientID”(e.g.“BER_0001_1”forsubjectBER_0001andthefirstvisit;“BER_0001_2”forthesecondvisit).

c. EntertheCROCTINO/PAMRINOsubjectIDinthefield“NEWPatientName”(e.g.“BER_0001”).

d. Unselectthecheckbox“removePatientAdditionalInformation”.e. Unselectthecheckbox“removeManufacturerInformation”.f. Unselectthecheckbox“renameFilesto_anon.dcm/_header.dcm”.g. Clickthe“run”button.Thebuttonwillbegrayedoutwhiletheprogramis

running.h. Waituntilthe“run”buttonisnotgrayedoutanymore.Afterwardsyoucanclose

thiswindow.

Stepsa.tog.arealsoshowninthefollowingscreenshot:


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2.2.3.CheckinganonymizationresultsTodoublecheck,iftheanonymizationprocedurehasworkedwell,youcanalsouseTudorDICOMViewer.NOTE:TheDICOMheaderscanbecheckedusinganyDICOMviewer.ThefollowingexampleisusingTudorDICOMViewerincaseyoudonothaveanotherDICOMviewer.


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Pleasefollowthesesteps:

1. IntheTudorDICOMViewerGUIclickthebutton“CompareDICOMHeaders”:

2. Youwillseeascreenlikethis:

a. b.


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Pleasefollowthesetwosteps:a. UnpacktheoriginalNOTanonymizedDICOM.zipfileasdescribedin2.2.2step1.

Clickthe“selectfile”buttonontherightside(a.)andbrowsefortheoriginal,NOTanonymizedDICOMfolder.

Makesurethatyoubrowsethroughthisfolderuntilyoufinda.dcmfile!Itdoesnotmatterwhichofthe.dcmfilesyouchoose.

b. Clickthe“selectfile”buttonontheleftside(b.)andbrowseforoneofthe.dcm

filesintheDICOMfolderyouhavejustanonymized(e.g“BER_0001_37492.dcm”).Browsethroughthisfolderandchoosethe.dcmfilewiththesamenameasyouhavechoseninstepa.(inthisexample“BER_0001_37492.dcm”).

3. YouwillnowseeacomparisonofthetwoDICOMheaders(anonymizedheadervs.originalheader)asshowninthefollowingexample.

Theleft-handsideshowstheoriginalDICOMmetadatahighlightedinred,wheretheinstitutioninformationshouldbechanged.Theright-handsideshowstheanonymizedDICOMmetadata,highlightedinred,wherethePatient’sNameandPatientIDhasbeenchangedtotheCROCTINO/PAMRINOIDforthatpatient,andthebirthdatehasbeenchangedtothefirstdayofthemonthandyear.


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4. Nowyoucancreatea.zipfileoftheanonymizedpatientDICOMfolder:a. PC::rightclickontheanonymizedDICOMfolderandselect“Sendto”->

“Compressed(zipped)folder”b. Mac:rightclickontheanonymizedDICOMfolderandselect“Compress”

5. Afteranonymization,pleasefollowsection2.3touploadtheanonymizedMRIdatavia

TeamBeamtotheCROCTINO/PAMRINOStudyTeam.

2.2.4SendinganonymizedMRIDICOMsusingTeamBeamTheanonymizedMRIDICOMsmustbetransferredtotheCROCTINO/PAMRINOStudyTeamthroughasecuredatatransfermethodovertheinternet.ThereforeweprovideTeamBeam,aneasy-to-useonlineplatformforsecureimagedatatransfer.AfteradataagreementhasbeenmadebetweenyourcenterandBerlin,pleasevisitthePAMRINO-TeamBeamwebsite:https://neurodial.teambeam.de/pamrinoandfollowtheinstructionsbelow.Allmandatorystepsareinbold.Steps1-7arehighlighted

usinggreenlabelledarrowsinthefigureonthenextpage.

1. Selectyourpreferredlanguageontherighttopcorner.

2. Enteryourname.

3. Enteryouremailaddress.

4. EntertheCROCTINO/PAMRINOsubjectID(e.g.BER_0001)forthecurrentsubject.If

youdon’tknowhowtonameyoursubjects,[email protected]

5. Ifyouwant,youcanleaveusamessagehere.Otherwise,youcanleavethisfieldblank.

6. SelectyouranonymizedMRIzippedfilesbyclickingthe“Browse”button.Alternatively,youcandrag-and-dropthefilesintothespacebelowthe“Browse”button.

PleaseonlychooseMRIsfromonepatienttotransferatatime.Youmaychooseallvisitsforthesamepatient,butnotmultiplepatientfilesatonce.Importantnote:Pleasede-identifyandrenameyourMRIfileswiththerespectiveCROCTINO/PAMRINOIDasdescribedinthemanualbeforeupload!

7. Transfertheselectedimagesbyclickingthe“Send”button.


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TeamBeamimagetransferGUIfortheCROCTINO/PAMRINOStudyTeam.Pleasefollowsteps1–7totransferyourMRIDICOMstoBerlin.Pleasenote:WewillnotacceptordownloadanyfilessenttousthatarenotMRIimages(i.e.noPDFs,orotherdocuments).


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3.eCRFs/ClinicalDataUploadAweb-basedplatform(REDCap)forsharingdemographicandclinicaldataofthesubjectsisusedfordatacollection.PleaseaccessthefollowingwebsiteforfillingtheelectronicCaseReportForms(eCRFs)usinganyinternetbrowser(e.g.InternetExplorer,Firefox,Chrome,Opera,etc.):https://redcap.utahdcc.org/redcap/

3.1REDCapTutorialHaveyourCenter-IDready(senttoyoubyEmail),aswellastheCROCTINO/PAMRINOSubjectIDsforyourpatients(Center-ID,underscore,followedbyfourconsecutivenumbers,e.g.BER_0001).ToaccesstheCROCTINO/PAMRINOREDCapproject,youarerequiredtogetanaccountfromtheDataCoordinationCenter(DCC)oftheUniversityofUtah.Ifyoudonothaveanaccountyet,pleasefillintheEDCUserAgreementform(sendtoyoubyEmailandalsoavailableonourwebsitehttp://www.neurodial.de/nmosd),scanit,andsendittopamrino@neurodial.de.Wewillthencreateanaccountforyourcenterassoonaspossible.Thefollowingstepscanalsobeseeninourvideotutorialunder“Files&Documents”onourwebsite.AfterloggingintoREDCap,pleasefollowthesesteps:

1. Click“MyProjects”.

2. ChoosetheCROCTINO/PAMRINOprojectbyclicking“CROCTINO/PAMRINO”.

3. Select“Add/EditRecords”fromtheleftsidenavigationmenu.

4. Selectthecorrectarmyoursubjectbelongsto:a) forNMOSDpatients,select“Arm1:NMOSDpatients”b) forhealthycontrols,select“Arm2:HealthyControls”

5. EnteraCROCTINO/PAMRINOsubjectID(e.g.BER_0001)nextto“EnteraneworexistingCROCTINO/PAMRINOSubjectID”asshownbelowandpressthe“Enter”buttononyourkeyboard.

ThisfigureshowshowtochooseapatientrecordtocreateoreditanexistingpatientrecordinREDCap.


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6. AfterwardsyoucanstartfillingintheeCRFsforthissubject.

Pleasenotethatrecordscanbesavedatanypointandrevisedatadifferenttimepoint.

7. PleaseleaveFormStatus(“Complete?”)on“Incomplete”ifyouplantocontinuelater.Onceyouaredonefillingitout,setFormStatuson“Unverified”asshownbelow.

The“FormStatus”eCRFshouldbekepton“Unverified”,suchthatourreadingcentermaycheckforrecordcompletenessorforanyerrorsandcontactyouifanyproblemsarefound.

8. Pleaserepeatsteps3-7untilyouhavefilledalleCRFsforallsubjectsandtheircorrespondingvisits.NOTE:EachMRIDICOMsetshouldbeassociatedwithclinicalvisitdatawithin+/-3monthsofthescandate.

Thankyouagainforparticipationandfeelfreetocontactusifyouhaveanyquestionsorcomments!CROCTINO/PAMRINOStudyTeamPhone:+4930450539727E-Mail:[email protected]:http://www.neurodial.de/NMOSD