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LONI Image Data Archive User Manual

1. DLDemsm criprtinn MPRAGE Herian IE 13105 11101 465 Dr zwamni Vycemt Cera Foldsr 13105111291455PAD 0006 MAT br Zi DETAILS gt lf the subject has other studies already archived a list of previously archived images and their dates appears Click Select for the desired study Study information must be provided only if an existing study is not selected For Analyze and MINC source files can be in a shared directory Image protocol information must be provided for each image series For 3 D images if archiving multiple files in the same source directory use batch archive and select specific image files rather than subdirectories YYYY 38
2. a gt Subject Research Group Sex Scan Date visit Ave Study modasty image Type Series Description Series UCLA 0001 Control F 8 04 1997 21 MRI Original 5 20 Spin Echo EDR GR 4 Original Long TE FSE 1 Original Long FSE 2 Original Short TE FSE 2 p Provide a reason on the REASON FOR DELETION box 1 gt Click COPY TO ALL 2 if the reason for deletion is the same for all files gt Click DELETE IMAGES 3 The images listed below have been selected for deletion Delete kanes You must supply a reason for each selection you delete Remove Selection 7 sl Copy To All Type Reason Here 7 image Type Sere Dacian 4 UCLA 0001 F 80411007 21 MRI Original Head Sag 20 Spin Type reason here Echo EDR GR gt remove the image from the delete list click REMOVE SELECTION 4 28 LONI Image amp Data Archive gt Click PRINT OUT THE RECEIPT to print a copy of the deletion list for your records Deleted by jessica yarosgloni ucla edu Jun 17 2013 02 12 21 0700 The images below have been removed from the LONI Image Data Archive Please print this page for your records Close Print out the receipt Research Group E Image Type Description Reason for deletion UCLA_0001 Control F 8 04 1997 21 MRI Original Long TE FSE 2 fovexty PROJECT SUMMARY The Project Summary su
3. gt Click SAVE QUERY 3 I save Query eee z Enter a name for the query Enter the query description Click the SAVE QUERY button to save this query or Click the CANCEL button to return to the results page without saving the query EN 2011 LOMI All rights reserved 12 LONI Image amp Data Archive DETAILS gt a search has been saved a drop down list appears on the Advanced Search submenu To run a saved query select the query from the saved query drop down list LONI Image Data Archive PAD LONI 5 ARCHIVE DOWNLOAD MANAGE LONI Home Advanced Search mage Database Advanced Search Choose saved query or Specify your selection criteria in the form below Hold down Ctrl amp Click to select or deselect multiple options Wild cards are permitted in fields marked with a in the form below For example UCLA retums records where the value begins with UCLA SAVED QUERY gt Select saved query d SUBJECT INFORMATION ae search Displayed by default Leave blank unless searching for a specific subject Subject id C IMAGE COLLECTIONS OVERVIEW The Collections Interface provides access to existing collections and their individual components Users can view remove regroup or download single images and entire collections This level of interaction applies both to personal collections and s
4. 3042008 Downloaded 2 tibi 20 presentalion B Sag 1 seventeens ucia30s 2 My Shared Collections Offer Shared Collections A dialogue box appears It is possible to grant different access levels to other users who can view your collection Guest is the minimum access level to view the collection LONI Image amp Data Archive Choose the user access level for your collection then click SHARE 2 images selected Share Collection e 15 Choose the permissions that others need access your collection E Minimum Level Guest 18 Leader Manager To remove other users access to your collection click UNSHARE COLLECTION The collection is no longer seen by others Edit Collection Unshare Collection Export Met Acq Date Format Downloaded 4 04 1995 IMG 3 05 2009 To remove an image from your collection click the checkbox beside the image 1 or click the All checkbox 2 to remove the entire collection then click REMOVE 3 COLLECTIONS TIONS Expand a by clicking en emm icing f select Ai chbed ANALYZE the symbol Choras an action to perform on selected Bem C a iC ollectim MAS oA imaga edected Chae Collection Ir aperi Metariata My Collecbons morons o gt n S
5. LONI IMAGE amp DATA ARCHIVE USER MANUAL Laboratory of Neuro Imaging Dr Arthur W Toga Director June 2013 LONI Image amp Data Archive INTRODUCTION The LONI Image amp Data Archive IDA is a user friendly environment to archive search share track and disseminate neuro imaging data It accommodates MRI fMRI PET MRA DTI and other imaging modalities A flexible data de identification engine and encrypted file transmission help ensure compliance with patient privacy regulations All data are stored on redundant servers with daily and weekly on and off site backups Archiving data in the IDA is simple secure and requires no specialized hardware or software The IDA automatically extracts relevant metadata from de identified image files and allows data to be searched within moments of archival Once archived data can be downloaded and or streamed into the LONI Pipeline workflow environment for processing and analysis Integration of the LONI Debabeler file format translation engine allows users to download image data in a number of common file formats IMAGE amp DATA ARCHIVE IDA Institute for Neuroimaging and Informatics Keck School of Medicine University of Southern California 2001 North Soto Street SSB 102 Los Angeles CA 90033 Phone 323 442 7246 Fax 323 442 0137 https ida loni usc edu For questions or problems with the IDA please e mail dba loni usc edu ACKNOWLEDGEMENTS This work was
6. or no headers TIFF TGA etc must contain a single series for a single subject in single directory Headerless files must contain a sequential slice number within the name ANALYZE files assumed io be in SPM orientation CONTINUE dim C Record diagnostics to file When the de identification step is complete a list of de identified files is shown along with the de identified header information 21 LONI Image amp Data Archive gt Toremove any images uncheck the Selected box beside the image 1 Note This feature is not an option with Batch Archival page 24 Click SUBMIT to transmit the de identified images 2 Choosing DISCARD cancels the upload and returns to the previous page 3 ll Verify amp Submit Data STEP TWO VERIFY amp SUBMIT DATA THE VERIFY PROCESS LETS YOU CONFIAM THE ACCLHACY OF THE DE4OENTEIED RE ORR Toe AND CESeLectT DATA SETS BEFORE Yow Suse THEM TO THE LONI ASCHE FOS STORAGE Review he de idenbied metadata below If you need to make corrections please use the Back bution in your browser window to return to the penous page Review tested data sets in the box below Uncheck the box beside any data set which you dent want submitted such or scout Chck ihe SUBMIT bunon to start ihe Gaia transmission process Sequence Name Numberofimages Selected PAD DOOS Cirde
7. study and image descriptors Users can Search several modalities simultaneously and save search results Archiving The storage of image data and metadata descriptors for future retrieval Batch archive Uploading data from multiple subjects simultaneously Batches may be of different file formats and modalities Collections An image or group of images selected from the results of a Simple or Advanced Search and given a meaningful description collection name Delete Removing image files from the archive De identification Removal replacement of certain image header contents to protect the identity of the subject DICOM Digital Imaging and Communication in Medicine DTI Diffusion Tensor Imaging Edit Metadata Modifying information such as sex age and weight as well as other project specific attributes Files with TYPE 1 comprehensive headers File formats DICOM GE Philips HRRT and Files with TYPE 2 limited headers File formats Analyze MINC FMRI Functional Magnetic Resonance Imaging Image metadata Information contained the image header describing the subject and image MINC Medical Imaging NetCFD MRA Magnetic Resonance Angiography MRI Magnetic Resonance Imaging LONI Image amp Data Archive NIfTI Neuroimaging Informatics Technology Initiative Original data Haw image files not pre or post processed PET Positron Emission Tomography Processed
8. Choose an action to perform on selected items 6 Collections Collection ucla30s 0 images selected Share Collection Export Metadata My Collections Subject Group Sex Age Visit Modality Description Type AcqDate Format Downloaded o MArsd 3 UCLA 1231 Control 63 0 MRA 2122 03 Original 9 05 2006 DCM Pod tof fi3d tra Multislab MIP UCLA_1131 Control M 21 0 MRA Original 9 14 2007 DCM Instead to download select images or entire collections by selecting the checkbox beside an image 1 or checking the All box 2 Search 26 COLLECTIONS CTIONS Expand a collection by clicking on Select items below by clicking the select box es As Archived ANALYZE the symbol Choose an action to perform on selected items REMOVE REGROUP powNLoAD O MINC Collections xj Collection MArs4 2 images selected Share Collection Export Metadata Collections 2 Subject Group Sex Modality DescriptionType AcqDate Format Downloaded Ni MArs4 2 21 0002 Control 19 0 MRI 1 Original 4 04 1995 IMG 3 05 2009 NotDownloaded control M 22 0 MRI rrr Original 3 11 1995 IMG 3042009 Downloaded 2 brin1 20 gt presentation 6 sag2 1 seventeens 6 ucla30s 2 My Shared Collections Age Visit gt Choose file down
9. Scout __ 0005 Scout PAD 0005 Circe Scout PAD 0005 Aud amp orgHam PAD 0005 HanGirretabon PAD 0005 MerbGeneraton PAD O005 JExtemasOraer PAD DOOS Gculomotor pen PAD 0005 Matched Bandatdcth Hi gt DISCARD SUBMIT dug Compress n es before transmituag REVIEW DE IDENTIFIED HEADER INFORMATION De ldenzzz ied Filet Attributes The progress bar shows the status of the file transmission step gt Once the file transmission is complete click REVIEW UPLOADED FILES to view the results of the archiving process gt Orclick ARCHIVE MORE to upload more files TRANSMIS SION RESULTS Progress Your Connection Speed Modem DSL T1 LAN Ir 4 dcm ploading file 257 805 PAD PAD 0005 MR VerbGeneration br raw 20110705121124505 70 dcm Uploading file 258 805 PAD PAD 0005 MR VerbGeneration br raw 20110705121124926 76 dcm FW UPLOADED FILES ARCHIVE MORI CANCEL TYPE 2 FILES ARCHIVING INSTRUCTIONS Analyze MINC Available to users with higher access levels REFER TO THE APPENDIX FOR INFORMATION ABOUT HOW TO ARCHIVE ANALYZE AND MINC FILES PLEASE CONTACT DBA LONLUSC EDU FOR OTHER FILE FORMATS 22 LONI Image amp Data Archive BATCH ARCHIVE INSTRUCTIONS The Batch Archive process is similar to Single Archive except that multiple subjects and image series can be submitted in a batch Batches can be of the same or different file formats and modalities However users cannot rev
10. The IDA system requires a computer with internet access newer web browser software IE Netscape Mozilla Safari Chrome Java plug in version 1 5 or higher and a valid user account IDA Menu Overview LONI Image Data Archive PAD LONI PROJECTS SEARCH ARCHIVE DOWNLOAD MANAGE LONI Home Projects e All View participant gender and research group distribution on public projects and other private projects you are permitted to access Public projects such as PAD are available to all users e Individual Projects View project information and participant gender distribution from your project Search e Simple Image Search Database queries based on a limited set of subject and image parameters e Advanced Image Search Database queries using a more extensive list of parameters Limited to authorized users on a project by project basis Archive e Archive Files De identify images to remove potentially identifying subject information and securely transmit files to be stored in the LONI Image amp Data Archive Download e Image Collections Download individual images or entire collections e Study Data Download study data for selected projects Manage e Edit metadata Provide or modify subject related information such as sex age and weight e Delete data Remove images from the LONI Image and Data Archive Available to users with higher access levels e mage QC Quality control of imaging data Available to users with
11. To access processed images use the Advanced Search SEARCH AND DOWNLOAD DATA GRAPHIC OVERVIEW Search Collections Download cones E Perform simple or advanced selected searches items to new or existing collections Download from personal or shared collections View images Select items from results list Download multiple image and file formats SIMPLE SEARCH Choose SIMPLE SEARCH on the SEARCH menu LONI Image Data Archive PROJECTS ARCHIVE DOWNLOAD Advanced Search MANAGE LONI Home Note Available menu options vary based on project and user access level LONI Image amp Data Archive Enter the search criteria and click SEARCH IDA Search LEGEND Projects Research Groups Modalities Help View Collections Image Status Data Collections Enter your selection criteria usin the form below SUBJECT INFORMATION _ IMAGE INFORMATION Leave blank unless searching for a specific Modality MRI Subject I subject Sex Both Series Description Age Equals years Weighting Slice Thickness Equals mm Acquisition Plane SEARCH RESULTS Order By andihenby Image Count 500 Click VIEW to see an image using the IDA Image Viewer IDA Search LEGEND Projects Research Groups Modalities Help View Collections Image Status Data Colle
12. data Image data files transformed modified from their original form i e registered warped or corrected data Series description An identifier name given ta a data set Sequence name Same as series description Simple Search Searches based on a limited set of criteria such as subject ID research group sex age weight modality series description Single archive Upload of data for one subject at a time File headers must be of the same type for upload all TYPE 1 or TYPE 21 Source directory Directory or folder containing files to be de identiied Contains single format single subject image files only Study One or more files from the same subject acquired on the same visit and scanner Target directory The Target Directory can be an existing folder or a new directory A temporary location to contain de identified files information and a copy of the logs of the upload pracess Validation The process of verifying results of de identification and removing images which are not to be uploaded The validation button appears only with the Single Archive process XML Extensible Markup Language A language framework created 1996 by the W3C to allow structured information to be shared and stored on the internet in an easily readable text format 33 LONI Image amp Data Archive H APPENDIX AML FILES When an image file is downloaded an XML file containing metadata describing the subject
13. higher access levels e Project Summary View project upload and download summary information Available to users with higher access levels e Manage user access Grant or modify user s privileges Available to project leaders Note Available submenus vary depending on project and user access level LONI Image amp Data Archive USER REGISTRATION If you do not have a user account click REGISTER on the Image amp Data Archive Log In page https ida loni usc edu Emad Panwa Register Forgot Password LONI The LONI Image Data Archive IDA is a user friendly environment for archiving searching sharing tracking and disseminating neuroimaging and related clinical data The IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MEI MRA DTI and other imaging modalities A exible data de identification engine and encrypted file transmission help ensure compliance with patient privacy regulations All data stored on redundant servers with daily and weekly on and off site backups Archiving data in the IDA is simple secure and requires no specialized hardware software or personnel All that is required is a computer with internet access and web browser software The IDA automatically extracts relevant metadata from the de identified image files allowing data to be searched within moments of archival Once archived data may be downloaded and or streamed
14. ms WalghtingsT1 Note Processed images display an additional section describing information such as package name process name program name etc 11 LONI Image amp Data Archive SAVE QUERIES Any search generated with the Advanced Search can be saved and re used Users can query the database with saved searches for repeated use in analysis and comparison Click SAVE QUERY on the Advanced Search Results tab advanced Search Results 10 record s matched your search criteria Subject 56 Image Status User Quarantine Subject Id L CLA 1234 Image Type Original Maximum Image count 300 Click SAVE QUERY to save the query Click ADD TO COLLECTION to add selected image sets to your collection Click NEW SEARCH to retum to the search page bm m mee 7 gre field I Matched Bandwidth Hi Res 210 F SAG DOUBLE ECHO 7j SAG MPRAGE 8 CHANNEL SAG MPRAGE 8 CHANNEL F SAG MPRAGE 8 CHANNEL E SAG MPRAGE 8 CHANNEL F SAG MPRAGE 8 CHANNEL Three Plane Loc trufisp Click here to select all series on this page Note To select an individual image series dick the select box under IMAGE or dick the box under STUDY or SUBJECT t select all series in the study or for the subject Click RESET to uncheck the checkboxes on this page RESET 1 Previous Mexi ADD TO COLLECTIO The Save Query pop up appears gt Provide a new query name 1 and description 2
15. of neuroimeaeging research projects across North Arnernca and Europ and accommodaies MEI PET MRA DTI and other maging modalities A flexible data de Identihc ation engine and encrypted nie transmission help ensure compliance with patient privacy regulations All data are stored on redundant servers with daily and weekly on and off site backups Archiving data in the IDA is simple Secure and requires no specialized hardware software or personnel All thai is reguired is a computer wih intemel access and web browser software The IDA automatically extracts relevant metadata from the de identified image files allowing dala to be searched within moments of archival Once archived data may be downloaded and or streamed into the LONI Pipeline processing environment Integration of the LOM tle format transiation engine allows users to download image data in a number of fle formats in addition to the original Me formal ES EB ALOT NEWS DOCUMENTATION SOFTWARE DATA Image Data Storage Protection amp Sharing amp Footure nstructions Anno unmcmmern Saber Lue dadentficali n J If you are experiencing difficulty with access notify dba loni usc edu umma individuals and their families The complexity and heterog Select a project from the Projects menu 1 The Projects menu displays a description of the project 2 project related links 3 and a chart showing par
16. sponsored in part by grants from the National Institutes of Health Grants U54 21613 P41 RR013642 U01 AGO24904 and M01 00865 and through the generous support of the High Q Foundation LONI Image amp Data Archive IMAGE amp DATA ARCHIVE OVERVIEW 4 User Registration 5 Image amp Data Archive Log In 6 B SEARCH 7 Simple Search 7 View Images 9 Advanced Search 9 Save Searches 12 C IMAGE COLLECTIONS 13 Create Image Collections 14 View and Download Images 15 share Collections 17 D ARCHIVE 19 Single Archive Instructions 21 Type 1 Files Archiving Instructions e g DICOM GE Philips HRRT ECAT 21 Type 2 Files Archiving Instructions Analyze MINC 22 Batch Archive Instructions 23 Processed Image Archive Instructions 24 DOWNLOAD 24 Steps to Download Imaging Data 254 Download Study Data 255 F MANAGE 266 Edit Metadata 276 Delete Data 287 Project Summary 29 Manage Users Error Bookmark not defined 30 G GLOSSARY 32 H APPENDIX 34 XML Files 34 Type 2 Files Archiving Instructions Analyze MINC 36 dO us us LONI Image amp Data Archive A IMAGE 8 DATA ARCHIVE OVERVIEW The LONI Image amp Data Archive IDA provides an integrated and safe environment to archive neuro imaging data The archive protects data from unauthorized access and allows investigators to share data For questions or problems with the IDA please e mail dba loni usc edu System Requirements
17. type in TE c 4 ms Select Value Select Other to type in TR PERPEN E ms Select Value Select Other to type in TI TRI 2 238 SelectValue Select Other to type Select Value Select Other to type in EORR Select Value select Other to type in Flip Angle DR Vana Select Value Select Other to type in NES sumt DATA 37 LONI Image amp Data Archive On the Verify amp Submit Data screen click SUBMIT to archive the de identified images or DISCARD to cancel the upload and return to the previous page Verify amp Submit Data STEP TWO VERIFY E SUBMIT DAT A 2 Tau vigRSEY FPEnDRCIESHS LETE TOA CDOBNTIHBERE Tee AOU COME iT ION AMD DESELECT DATA SETS YOu SUMMIT THERE Po Te LOST ARCHIE POR STO OE Atita he d metadata below B you noed bo Make connections please use ne Back Dumpn iw your proves ors wirdos b pugae Advi ie lished daln sais inte Dx Lieneck m box Desicdae amy dala sel which you uA a A3 B DEAD Click ima SLT Suen 1 3 iei eara Pande pioces v T DE BEC uj eet IE Sequence Nama Mumbeererimages iran oone M PLAGE lz sunm dmm Compress floes beter transmitting REVIEW HEADER ENECHIMATLIN LOHI De ZIuseztifimed Film
18. 9 LONI Image amp Data Archive Click the UPLOAD SUMMARY tab to view a breakdown of images by Modality MRI PET DTI Image Type original ar processed orImage Status available User Quarantine Failed GC Selectthe checkboxes above the pie charts to view individual or combined breakdowns At least one category mustbe selected For example the interface below displays the quantity of differing image modality types collected overtime Curwntoad Summary Upload Lestngs p ee RISSESDGR EUG Rogo US GEB dem irae picid by Modasty Carey PES BETA CVT eration Cpu tuque be ta A eee ty Dec Cada DD caes for 0857 E DET L i i Y i 55 1 3 22 i 1 F LA D n amamus zm ETI uq ps bier MANAGE USERS The Manage Users submenu allows project leaders to manage permissions for team members and associated collaborators Users must register for an account before they can be granted access to a project Refer User Registration page 5 for information on how to create an account 30 LONI Image amp Data Archive Grant New User Access Select a project from the PROJECTS menu Click MANAGE USERS on the Manage menu Enter the users email in the text box 1 Click FIND 2 wow ww User access 5 dalprmnad by com
19. EVIEW BATCH QUEUE THE IMAGE STUDIES LISTED BELOW HAVE BEEN PREPARED FOR BATCH DE IDENTIFICATION AND UPLOAD Click ADD MORE to add another study to the queue or SUBMIT ta archive this baich now REMEMBER to leave your browser window open until all uploads are complete and you have been retumed to this page or the Archive amp Review page Click CLEAR to dear the batch queue AN logs will be deleted 1 CANCEL Subject Data Type Research Group Source Status Date E I Remowe PAD 0006 Original Control DAwanittest data UCLAD1017 S0 Queued 742 41 remove PAD 0007 Original Control Dwanitest data I CLAD1017 S0 Queued AAT DETAILS gt Once files are archived click Review Uploaded Files to view a list of all the successfully archived images Or click Archive More to upload more files Zs LONI Image amp Data Archive PROCESSED IMAGE ARCHIVE INSTRUCTIONS Archiving processed images requires the inclusion of an XML file that describes the processing provenance and the link to the image s from which it is derived This method is best suited to large batch archival Please contact dba loni usc edu for more information about using XML files DOWNLOAD The DOWNLOAD menu allows users to manage and download image collections and download study data STEPS TO DOWNLOAD IMAGING DATA gt Perform a Simple or Advanced search gt Form an image c
20. PE 1 FILES ARCHIVING INSTRUCTIONS e g DICOM GE Philips HRRT ECAT PREREQUISITES e Place all image files for each subject within a single directory Source directory which may contain subdirectories The source directory must not contain multiple image formats e Create an empty directory where the de identified files will be written target directory NOTE The browser window must remain open during the entire upload process Closing the browser window cancels the upload You may minimize the window HOW TO ARCHIVE TYPE 1 FILES E G DICOM GE PHILIPS HRRT ECAT Choose ARCHIVE FILES from the Archive menu LONI Image Data Archive PAD LONI PROJECTS SEARCH MANAGE LON Home aa gt select your Project Site from the drop down menu 1 Click SINGLE ARCHIVE 2 Archive and Review PROJECT INFORMATION Select Project PAD NotApplicable ARCHIVE FILES The data archival process involves two basic steps 1 De identifj tne header file by replacing any fields that identify the subject such as Patient Name and ID and 2 Transmit image data securely from the local site to LON To archive a single study click SINGLE ARCHIVE button Hse 7 To archive multiple studies in batch mode click the BATCH ARCHIVE button E BATCH ARCHIVE NOTE not open mustiple IDA browser windows while archiving data VIEW RECENTLY ARCHIVED VOLUMES Click on the VIEW bu
21. R Enter a name for the collection Ok Cancel 16 LONI Image amp Data Archive The new regrouped collection appears Search COLLECTIONS CTIONS Expand a collection by clicking on Select items below by clicking the select box es As Archived 0 ANALYZE the symbol Choose an action to perform on selected items 9 Collections 2 Collection MArs43 0 images selected Collections MArS4 1 Subject Group Sex Visit Modality DescriptionType AcqDate Format Downloaded NI 10022 0001 Control 22 0 MRI T1 FFE Original 3 11 1995 IMG 3 04 2009 D c Not Downloaded 0 Downloaded 1 MArs43 1 Not Downloaded 0 SHARE COLLECTIONS Click SHARE COLLECTION if you want to allow other users to view your collections ACTIONS Expand a collection by ticking on ale tems below by clicking the select box es nc C asarchived ANALYZE z a DA Ihe symbol SEDE ANITA SEI NDS EO LTD wien wine Collection MArs4 2images selected Share Collection Export Metadata Wy Collections Subject Group Sex Age Vist Modality DescriptionType MArs4 2 PAD 000 M 19 1 rre 4041095 IMG 305 2000 ni NotDownloaded 0 pio Control 22 0 Original 3411995 MG
22. SubjectID 1856 Sex Male Study Date 11 06 2008 Age 39 0 Subject Weight 8444 Handedness R ProjectPhase 2 NEW SEARCH DELETE DATA Use the Delete submenu to permanently remove an image study series or subject from the archive There is a delay time of approximately seven days from when the user deletes an image until it 15 permanently removed from the archive Note only users with higher access levels are permitted to delete data Click DELETE DATA on the MANAGE menu LONI Image Data Archive IDATE LONI PROJECTS SEARCH ARCHIVE pownLoap LONI Home Edit Metadata Delete Data Manage Project Project Summary Manage Users 27 LONI Image amp Data Archive Provide a subject ID a study date and or series description on the Search tab and click SEARCH Enter your selection criteria using the form below SUBJECT INFORMATION You may use the wild card character in the Subject ID amp Series Description For example enter UCLA to search for all Subject IDs beginning with UCLA Subject ID UCLA 0001 Study Date Equals Image Type V Original V Processed 9 Post processed Series Description gt delete an individual image check the checkbox beside SERIES DESCRIPTION 1 column gt Alternatively check the STUDY 2 box to delete all images within a study gt PROCEED TO DELELETE 1 IMAGE 3 2 2 1011 lt prev 4 next Proceed to delete 1 image _
23. Y 2 0 SAGITTAL Q1 view SAGDUALTSEOLD WAY 20 SAGITTAL Q1 view SAGDUALTSEOLDWAY PD 2 0 SAGITTAL Q1 SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 view SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 view MNI_0504 Control F 5 25 2002 41 MRI SAGDUALTSEOLDWAY PD 2 0 SAGITTAL Q1 view SAGDUALTSEOLDWAY 2 0 SAGITTAL SAGDUALTSEOLDWAY 2 0 SAGITTAL Q1 view SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 view SAGDUALTSEOLDWAY PD 2 0 SAGITTAL Q1 view SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 view SAGDUALTSEOLDWAY PD 2 0 SAGITTAL Q1 0502 Control F 5 25 2002 45 MRI SAGDUALTSEOLDWAY 2 0 SAGITTAL Q1 view gt Enter a name for the collection or select an existing collection name 1 gt Click OK 3 cking the select boxes 9 As Archived arm on selected items C C imanes sele te i hare Collection Ex Regroup Collection xl d Select a existing collection OR Enter a name for the collection 2 Ok Cancel LONI Image amp Data Archive gt Anew window displays the collection contents gt To view the image click on the DESCRIPTION link gt Anew window opens Click VIEW under Acquisition Protocol not shown Search COLLECTIONS CTIONS Expand a collection by clicking on Select items below by clicking the select box es As Archived 0 ANALYZE the symbol
24. and other information is placed in the root of the download directory For processed data the file also includes processing provenance The contents of the XML file vary depending on project AML file example z xml version 1 0 encoding UTF 8 idaxs xmins htip loni usc edu ida idaxs xmins xsi htip eww w3 org 2001 ML Schema instance xsps mAxs 2 0 XSD gt project xmins xmas oroiectideniifier CEM cription International Consoriuin for Brain Mapping projectDescription siteKev 8 nE subj ntifier USC 0004 subjectidentifier LAS Terr lt subjectsex gt F lt subjectsex gt lt subjectinfo item DX 5 zvisit ifter Month G visitidentifier assess ment name MMSE name MMSE TOTAL SCORE 7 Score attribute MIMSCORE 724 00 assessmentScore icomponent assessment assessment name COR gt component TOTAL SCORE lt assessmentscore attribute COGL OBA 0 50 assessmentSc zicomponent zlassessment assessment name NEUROPSYCHIATRIC INVENTORY QUESTIONNAIRE NPI Q component name NEUROPSYCHIATRIC INVENTORY Q TOTAL SCORE zassessmentscore attribute NPISCORE 72 00 assessmentScore gt zicomponent assessment assessment name FUNCTIONAL ASSESSMENT QUESTIONNAIRE component name FAQ TOTAL SCORE lt assessmentscore attribute AQTOTA 2 00 lt as
25. binalion of she and access an existing users access level by clicking on the adi button orta add a new USE access enter ua users emal address in fe New User section below NEW USER ACCESS Emir users email MODIFY USER ACCESS Access Lewel gt Choose a site in the DEFINE USER ACCESS section 1 Select the user access level 2 e Manager permission to search view download and archive data edit metadata delete images and manage user access e Leader permission to search view download and archive data as well as edit metadata e Member permission to search view download and archive data e Guest permission to search view and download data gt Click UPDATE 3 select the new users site and access level from the drop down lists and click Update or click Cancel to return to the previous page DEFINE USER ACCESS usergloni ucla edu Project Wide 2011 LONI All nights reseved gt To repeat the process for another project choose a different project from SELECT NEW PROJECT Change Existing User Access Click the MANAGE USERS submenu from the MANAGE menu Click either EDIT ar REMOVE beside the user whose access level is to be modified Select SITE and or ACCESS LEVEL from the drop down boxes Click UPDATE YYYY LONI Image amp Data Archive G GLOSSARY Advanced Search Advanced Search allows users to search with a combination of subject
26. bmenu is a multi layered environment which allows authorized users to view the project upload and download summary information Summaries can be exported as CSV files into Excel spreadsheets Project Management Summary requires Flash player to display charts Tables in Project Management Summary are viewable without a Flash player Select a project from the Project menu click Manage then PROJECT SUMMARY There are three sub sections Upload Summary Download Summary and Upload Listings LONI Image Data Archive IDATE PROJECTS SEARCH ARCHIVE DOWNLOAD M LONI Home Edit Metadata Delete Data Image QC Manage Project Project Summary Manage Users Use the UPLOAD LISTINGS shown below or DOWNLOAD SUMMARY tabs to view statistics on archived files or downloaded data respectively gt Specify a date range 1 and click Refresh 2 gt download this data select Export CSV 3 Upload Summary Download Summary 52018 S From June 2013 To July 020131 feires Export 1011 prev next 3 Field Strength Weighting Series Description 6172013 UCLA_8888 T1 30 FLASH 20 Flip 6112013 UCLA_9999 T1 3D FLASH 20 Flip 6 1 2013 UCLA_2223 T1 23D FLASH 20 Flip 6 1 2013 UCLA 2222 T1 3D FLASH 20 Flip 6 1 2013 UCLA 1111 T1 3D FLASH 20 Flip 6 1 2013 UCLA 2345 T1 3D FLASH 20 Flip 6 1 2013 UCLA_1234 T1 3D FLASH 20 Flip 2
27. ct box es As Archived ANALYZE the symbol Choose an action to perform on selected items NiFTI GO Collections 2 Collection 0 images selected My Collections MArs4 2 Mot Downloaded 0 Downloaded 2 4 brin1 20 presentation 6 sag2 1 seventeens B ucla30s 2 My Shared Collections Other Shared Collections To move an image or group of images to a new or different collection check the appropriate checkbox beside the image s 1 and click REGROUP 2 Search COLLECTIONS CTIONS Expand a collection by clicking on Select items below by clicking the select box es As Archived ANALYZE the symbol Choose an action to perform on selected items O MINC 1 Collections z Collection MArs4 2 images selected My Collections lt mes Subject Group Sex Age Visit Modality DescriptionType AcqDate Format Downloaded mim 15 BET nicl Ocamloaded tt PAD_0002 Control 19 0 MRI T1 FFE Original 4 04 1995 IMG 3 05 2009 Not Downloaded 0 a pot Control M 22 0 MRI meee Original 3 11 1995 IMG 30472009 Downloaded 2 A dialogue box appears Select an existing collection or enter a new name for the collection 1 and click OK 2 cking the select box es 9 As Archived orm on selected items 2 Iw C aes selected 111 share Collection Regroup Collection Select a existing collection j O
28. ctions 3 image sets match your criteria Sex Both Modality MAI Image count 500 Your access level ADNI DBA ADNIP MANAGER APOE MEMBER GUEST CRYO MANAGER GEMS DBA GIBT MANAGER HVLMS LEADER ICBM MANAGER PAD LEADER SFIC MEMBER SIMS DBA Access to data is controlled by each project s leader Click the Projects link above for additional information 1011 lt prev next gt TTITISESISSTONTESZ NI Control PAD 0001 M 34111995 22 MRI n sema ww A PAD 0002 Control 404995 19 MRI TH FFE T 10 SAGITTAL A ww PAD 0005 Control 3484995 19 MRI TFE n 10 SAGITTAL A Clicking the view icon lauches the LONI Image Viewer The viewer requires a Java enabled browser with Java Plug in 1 4 2 or newer installed LONI Image amp Data Archive VIEW IMAGES The IDA Image Viewer provides a multi dimensional reconstruction of the image data Users can view an image in different orientations flip vertical and horizontal planes and adjust brightness and contrast Currently the image viewer works on 3 D images only Only the first time point appears on 4 D images To view different slices drag one of the red bars on the SELECT SLICE section 491177 Image Viewer IMAGE INFORMATION Site Project PAD Subject 105 00071 Series Description T1 FFE SELECT ORIENTATION SAGITTAL CORONAL AXIAL SELECT SLICE 4 128 256 Cha
29. e page 14 gt Toview image header information imaging protocol select an image DESCRIPTION 3 This will open the IMAGE DATA DETAILS interface Displaying Results 1 20 of 8135 1 image selected Select Add To Collection MAGE Select Subject ID Sex Select Age Select View Description 7 UNI 0101 7 240 1 3 0102 23 0 pound TA FFE MNI_O703 220 Mw T1 FFE _0104 35 0 1 MINI_O105 31 0 TI FFE 0106 310 TLAT 1 0107 210 ew T1 FFE MI 0108 26 0 MNI 0108 M 19 0 MiEW TA FFE Mtl 0110 280 T1 FFE MI 0111 F 26 0 La TH FFE MNI 0112 23 0 Aw T4 FFE MINI 0113 F 240 FFE MI 0114 200 1 On the IMAGE DATA DETAILS page display an image by selecting VIEW The image will open the IDA image viewer page 9 Image Data Details LEGEND Projects Research Groups Modalities Help View Collections Image Status Subject ID MNI 0101 Modality MRI Research Group Control Image Type Onginal Sex Female image File Type Image Volume Visit N A image Status AVAILABLE view um Imaging Protocol Acquisition Planez SAGITTAL Acquisition Type 3D Coilz Field Strengthz1 5 tesla Flip Angle 30 0 degree ManufacturerzPhilips Matrix Xz 172 0 pixels Matrix Yz25 Spacing Yz 1 0 mm Pulse Sequences Slice Thicknessz 1 0 mm TE 10 0 ms TIz0 0 ms TR 18 0
30. elow This unprecedented effort is expected to facilitate 35 Male discovery science and comparisons across samples ERI cei 102 Gender Mumbar of Subjacts bs Le Lu E E Pa EA 4 nds mm 4 accordance with HIPAA guidelines and 10 00 Functional M d x el ge Lair E 1 5 2 Femele 1 sle a Conneclomes Proleg IHDI protacols all datasets are i gt i anonymous with no protected health information included Page Cliek on a pie slice to change ihe 1212 RELATED Line E ms A Age Group Central Autism Export C Vj z 11 153 155 12 18 251 234 19 29 128 102 30 29 3 40 48 50 59 50 59 ABIDE Weeere Hus INDI Fesai duh im C du LONI Image amp Data Archive B SEARCH Users can search for images based on subject and image related criteria view images form collections and download images There are two types of image searches Simple search and Advanced search The Simple Search performs a basic database query on subjects and images providing information such as subject age sex and image modality or series description The Advanced Search supports a more extensive exploration of the database and provides additional information about subjects and images To download images perform a Simple or Advanced Search add the images to a data collection then download
31. ex Age Wel Medai DescripiionTyse Aco Dais Format Dovinioaded EE gt brit 2 PAD QUU2 18 0 Mg Orignal 40471995 pnis RM Ez Fiii PAD QUOT 22 ME Trrp 3211095 Ius 344 2009 O prezariabon 15 t 588 11 spyaritaan 8 claws My Shared Collachons ther Shared Codecton LONI Image amp Data Archive D ARCHIVE There are two steps in the archive process de identification and file transmission The de identification step removes or replaces potentially identifying subject information from the image headers During the file transmission step the de identified files are securely transmitted to LONI and stored in the data archive The data archive accepts DICOM GE Philips HRRT and ECAT files Type 1 headers and files with limited header information such as Analyze and MINC Type 2 files Archiving Type 2 files requires some user input to provide image metadata ARCHIVE PROCESS GRAPHIC OVERVIEW e Single Archive Batch Multiple Method e Original raw image files e Processed pre and post processed e Type 1 DICOM GE Philips HRRT ECAT e Type 2 ANALYZE MINC e Remove potentially subject identifying information Identify File Archiving 19 LONI Image amp Data Archive SINGLE ARCHIVE INSTRUCTIONS Use the Single Archive process to upload one or more files from a single subject TY
32. hared collections those created by other users to which the user has access Users can create collections with an unlimited number of images It is not necessary to perform a search to access previously created collections Collections can be restructured by adding or removing images Features Access Personal data collections Download Any number of images with a single request Download images in a number of file formats including the originally archived format or an alternate format of the user s choice Analyze NIfTI 4D MINC Track downloaded not downloaded images Access shared collections Created by other users 13 4 LONI Image amp Data Archive CREATE IMAGE COLLECTIONS AND DOWNLOAD Use the Image Collections submenu to manage and download data selected through Simple and Advanced Searches Create new collections add to previously created collections or change collections as needed Use collections for viewing downloading and sharing imaging data Perform a Simple or Advanced Search see page 7 gt the Search Results page choose images by checking the Select box beside the image s 1 gt Click ADD TO COLLECTION 2 2 10f21 lt prev 2225672910 11 12 13 1415 next gt ADD TO COLLECTION 0500 Contro 5 25 2002 62 MRI SAG DUAL TSE OLD WAY SAGITTAL views SAG DUAL TSE OLD WAY PD 2 0 SAGITTAL Q1 VIEW SAGDUALTSEOLDWAY PD 2 0 SAGITTAL Q1 view SAG DUAL TSE OLD WA
33. iew the results of the de identification process prior to the batch upload Click BATCH ARCHIVE on the Archive and Review page PAD LONI Archive Files PROJECTS SEARCH ARCHIVE DOWNLOAD MANAGE Archive and Review PROJECT INFORMATION Select Project Mol Applicable ARCHIVE FILES The data archival process imoives basic steps 1 De identiify the header file by replacing any fields that identify the subject such as Patent Name and iD and 2 Tranemi image data securely Mom the local site t LORI To archive 4 single study cick ihe SINGLE ARCHIVE button To archive multiple studies in batch mode click the BATCH ARCHIVE bution denen MOTE Do nat open multiple IDA browser windows while archiving data VIEW RECENTLY ARCHIVED VOLUMES lick on the VIEW Button fo visualize ihe volumetric representation of pour uploaded Mas Click on the REFRESH buon 1o update ihe volume list PE secus arcane rerreese DERES De see ty Ho cor lages Wierw Download PAD 000 gre_ficld_map 5a Tue 07 05420111 Ww CHIAVE CAII PAD ODUS gre field map Tue OF S014 vE Follow the instructions the Single Archive section gt On the Batch Queue page click ADD MORE 1 to add more studies Repeat this process for each study series or subject to be archived gt Click SUBMIT 2 to de identify and upload all files image Database Batch Queue R
34. ific information Age years Equals gt Axsessmanis 7 r3 7 image imaging Protocol CBM L 18 4 image Status Processing 5bsdy Date Equals 7 Original Archive Date Equals Pre processed Post processed Image Description i Image Saparade mutia image 113 by commas ag 11231456 12146 Subject en jon zu PST leis SUNT ERA STATUS l Desplay in resa Available User Quarantine IRS MIFAA Quarantine Flagged for Failed OC RESET SEARCH DEFINITIONS gt Original data refers to raw image files gt Processed data refers to registered or warped data e g segmentations gt Toselect more than one item in a drop down click each item while holding down the control key on PC or Command key on Mac 10 LONI Image amp Data Archive Advanced Search Results The Search Results tab displays information about image sets matching the search criteria Users can view and add these results to collections and save search parameters page 12 The Series Description of each image is a link to the detail page which provides additional information about the image such as weighting pulse sequence acquisition type etc Users can also view images from the Image Protocol Details page Check the checkbox beside VIEW 1 and then select ADD TO COLLECTION 2 to add images to a collection This is a necessary step before downloading the image s se
35. into the LONI Pipeline processing environment Integration of the LOM Debabeler file format translation engine allows users to download image data in a number of file formats in addition to the original file format Image Data Storage Protection amp Sharing New Features Debabaler Announcements Collaboration De identicaton Debablet FAQ Inspector Downloads Complete the form to create a new account then click the REGISTER button Create New Account m your Emas asaos 7 7 57 memamen E you have LOM account ute your LONI user name PERSONAL ORMA THON 2p 7 cem 1 I ywou have a webs piese enter tne URL here ed fekis me denoted try an astesishba n Once you click Regitter well send you an e mail message containing your temporary pas sword To endure your temporary Pattword is recewed you may need to add ucla edu to your gate sender ict i LON TERMS OF USE On the Log in page provide your email address and password LONI Image amp Data Archive Image amp Data Archive Log In Note Password Lexam LONI Image Data Archive ABOUT NEWS DOCUMENTATION SOFTWARE DATA LONI Home The LOM Image Data Archive IDA amp a user friendly environment for archiving searching sharing tracking and disseminating neuroimaging and related clinical data 15 utilized for dozens
36. load format either as originally archived or converted to MINC Analyze or 4D by choosing the corresponding button in the Actions section 1 Click DOWNLOAD 2 gt Anew window opens Provide the download location The files will download to the selected location Search MNT NA TR rts _ COLLECTIONS Expand a by Select below br cricang fre select braier 0 ANALYZE the an achan ba parim en ENE arima o HRE Collections E MArsA mags selected are Enpa Maiadas MeColetiens T Group Ma Age Vedb Mosh Despina Downbeaded Arum Pan 0002 Cord M 1 MAL Digina 41011135 MG 30572008 E D m PAD no Contre 1 LEE Gigna 3111995 MG 30408 Dewnlaaded 2 bent 20 pesenan sag 0 15 LONI Image amp Data Archive DETAILS gt Converting file formats adds slightly to the overall download time gt For each image downloaded an XML file containing metadata about the subject and the image is placed in the root of the download directory e See Appendix for an example of an XML file To view a collection click on the collection name Data Collections COLLECTIONS CTIONS Expand a collection by clicking on Select items below by clicking the sele
37. m MMSE 2 was selected gt Click DOWNLOAD 3 When the pop up window appears choose to open or save the file LONI mage Data Archive IDATE LONI PROJECTS SEARCH ARCHIVE RRO IRURE MANAGE LONI Home Study Data Image Collections Download Study Data v Assessments Assessments Neuropsychological Download Meuropsychological Select Items gt Subject Charactensiics ALL 4 ALL ly Woe mui NPI 2011 LONI All rights reserved 25 LONI Image amp Data Archive F MANAGE The MANAGE menu allows project leaders and users with higher access levels to manage projects edit metadata delete data perform image quality control view project summaries and manage other users Note not all options are available to all projects users LONI Image Data Archive IDATE amp LONI PROJECTS Edit Metadata Delete Data SEARCH ARCHIVE DOWNLOAD Image QC Manage Project LONI Home Project Summary Manage Users EDIT METADATA The Edit Metadata submenu allows authorized users to add or modify subject related information such as sex age and weight gt Click Edit Metadata on the Manage menu gt Search for a specific subject in a particular site by providing Subject ID and Site Name then click SEARCH Enter the Subject ID to search for a specific subject or select a Site Name to search for all subjects in that site You may also use both the S
38. nge Slice Number BRIGHTHESS amp CONTRAST Brightness ee a o Drag mouse in the image area to pan 4 i Contrast ADVANCED SEARCH Use the Advanced Search to query the database using a more extensive list of elements than the Simple Search Choose additional elements or image types original or processed data and set the sort order of the results The availability of elements varies according to project and user access level You may save queries to be reused Choose ADVANCED SEARCH from the SEARCH menu LONI Image Data Archive SFIC LONI provects EGR DOWNLOAD LONI Home Simple Search LONI Image amp Data Archive Complete the form sections gt To display specific categories in the SEARCH CRITERIA check the corresponding checkbox in SEARCH OPTIONS 1 gt Todisplay specific information on the Results menu the next page check DISPLAY IN RESULTS 2 Some items display by default gt Click SEARCH 3 Search Criteria RI L Spaai selection criberia using fw 01805505 on fma hen Wild cards are permitted in fields marked wit a star belma For example VELA retams results mar begin pEARCH Enhas Previous Downloads SEARCH SECTION De Projects ADHI ProciPhasa m 7 ER E E z Tu Emm I nuo i Susjed SubjectiD Separate multiple Suben 175 y commas 7 Su amp jed Spec
39. ollection Download There are two ways to access and manage existing Collections in the IDA gt Select IMAGE COLLECTIONS on the Download menu LONI f Image Data Archive IDATE PROJECTS SEARCH ARCHIVE E MANAGE LONI Home Study Data Image Collections gt Orclick DATA COLLECTIONS on the Simple or Advanced Query menu Data Collections Enter your selection criteria using the form below SUBJECT INFORMATION IMAGE INFORMATION I sex Bon SeriesDescription Age Equals Ej years Weighting 2 Slice Thickness mm Acquisition Plane Order By and then by Image Count 500 8 Note Refer to the Create collections section page 14 for information on how to create and manage collections before downloading imaging data 24 LONI Image amp Data Archive DOWNLOAD STUDY DATA Clinical and research data are available for downloading on selected projects Select DOWNLOAD then STUDY DATA from the menu LONI Image Data Archive IDATE LONI PROJECTS SEARCH ARCHIVE M MANAGE LONI Home Study Data Image Collections The Download Study Data page displays a list with available categories to the left gt Click on a category to display a list of csv files available for downloading In the example below the category ASSESSMENTS 1 was selected gt Click on the checkbox beside the item s In the example below the ite
40. op down list Define Study STEP 1A DEFINE STUDY THE DEFINE STUDY PROCESS LETS YOU ADD DATA TO AN EXISTING STUDY OF DESCRIBE A HEY STUDY Selec imaging modality from the drop down menu amp Select an existing shady or e Adda how shudy by describing new study attributes and cicking the SUBIT DATA Busan SELECT MODALITY W S eee 36 LONI Image amp Data Archive Provide the study information and click SUBMIT DATA DEFINE HEW STUDY Study Date 2011 07 12 jectAge 22 Years SubjectWeight 120 Post Mortem Mo Maa gt Provide the Image Metadata information gt To save the information provided for reusing at a later date click SAVE PROTOCOL 1 Click SUBMIT DATA 2 REQUIRED INFORMATION DEJ SAVEPROTOCOL Sequence Name MPRAGE Weighting SelectValue Select Other to type in sauce ee SelectValue Select Other to type in Acquisition Plane Select Value Select Value Select Other to type in uptrend Select Value Select Other to type in Matrix 2 SelectValue Select Other to type in puse Select Value Select Other lo type in Pixel Select Value Select Other to type in Manufacturer Select Value Select Other to type in Mfg Model Select Value Select Other to type in Fen oer nie Select Value Select Other to type in ME ACQUISITION Acquisition Type Select Value Pulse Sequence Select Value Select Other to
41. rati value 1 value xiseries istudy xisubject project idaxs gt 35 LONI Image amp Data Archive 2 FILES ARCHIVING INSTRUCTIONS Analyze MINC Please contact peA gLONI usc Eepu for other file formats gt On the Archive and Review tab choose SINGLE archive PAD SEL OHI PROJECTS SEARCH ARCHIVE Archive EROVEHL ORI l Archive and Review PROJECT INFORMATION Prace Applicable ARCHIVE FILES Tha achiral rocas s pretties Two 1 Dae idenbfs Tae haria Bie Es replacing am fields hal ident the Euch as Patent fame ID and 2 Tina rel image dab securely hom ihe local site bo LOHI To anche a saga study click Ina ARCHIVE ER unii m To are amp ludisa in Saft moda cick ma sena ncn HOT Gs nel ID bidet eo ale RIAA dai VIEW ARCHIVED VOLUMES Chick on ee STEW GuHoniaviruako Pee repre cf your uploaded Biss Cbck on REFRESH io update fie ieee ligt 10 SERIE Dt soe nog Ho or Dam Mies Dceundoad PAD uS gne map 54 Tus WEF CH D Pap Ost gre figi3 map E4 Tus 07705 2011 wrl p Gull gt Provide subject identification select Source and Target Directories Select a modality from the dr
42. sessmentscore zicomponent assessment gtudy studvldentifier 88 5 studyIdentifier subiectAgez 59 9800 subiectAge ageQualifier Y ageQualifier weightage 84 5000 lt weightKg gt F postMortem gt 5 lt senes RI modality imaginaProtocol ou UlD 32108 mmageulD LONI Image amp Data Archive descnption MP RAGE description protocol emm gt protocol tarm 4ceaursition TYPE 3D protocol protocol tarm VVEIGHTING gt T1 protocal gt protocol term PuLse SEQuence RM protocol gt protocol term SticE THICKNESS 71 20000 protocol protocol term 7 3 92400 protocol protocol term TR 8 91600 protocol protocol term 7 1000 00000 protocol protocol term Con SHRBRAIN protocol zprotocol term FLiP AwGLE 8 00000 protacol protocol term AcQuisiTiaN PLANE SAGITTAL protacol protocol term Ma X 256 00000 protocol protocol term Ma Tam Y 2586 00000 protacol protocol term gt 166 00000 protocal gt protocol SPACING X 70 937 50 x protocol protocol Pixet SPACING Y 70 93750 protocol protocol term M4ANUEACTURER GE MEDICAL SY STEMS protacol protocol term MFG MopEer 7 SIGNA EACITE protocol protocol SELD STRENGTH 71 50000 protocol iprotocoL Term imaqeRating ratingD escriptianz 1
43. ticipant distribution 4 You may view a break down of the distribution based on research group and gender by selecting the checkbox in the corresponding chart 5 To remove an individual group from the participant distribution chart click on the corresponding section of the pie chart i ABIDE LONI SEARCH PROJECTS DOWNLOAD Autism Brain Imaging Data Exchange Introduction Export POF Participant Distribution Age Visit Rd Autism spectrum disorders 45D are qualitative impairment in reciprocal social communication a5 well as by repetitive restricted an reotyped behaviors Previously considered rare now recognized to occur in more than 1 of children causing immense suffering te characterized by 500 Ww Research Group Auton eneity of ASD make it necessary to obtain large scale samples which are difficuli to attain in any individual lab In response the Control Autism Brain Imaging Datla Exchange ABIDE hereby provides 3 previously collected resting state functional magnetic resonance A Contra 573 Autism 39 imaging R MRI datasets from 529 indmiduals with ASD and 573 typical controls for the purpose of data sharing in the broader scientific community This grass roaat initiative involved 16 international sites sharing 20 samples yielding 1112 datasets composed of DOM of MRI data and an extensive amay 100 of phenotypic information common across nearly all sites see 1323 Female b
44. tton to visualize the volumetric representation of your uploaded files Click on fhe REFRESH button to update the volume list SEE REFRESH LONI Image amp Data Archive On the DE IDENTIFY page gt Provide a Subject ID gt Click Source Directory Browse to find the directory which contains the file s to be uploaded or provide the directory path then click Select Source File Directory gt Repeat the process to select a target directory to contain the de identified files To upload files without validating de identification results check the Bypass Validation Steps box not recommended for first time users Click CONTINUE to begin the de identification process To automatically record any issues during the archive process check the box near Record diagnostics to file You will be prompted to provide a location to store the diagnostics file Note this is an optional step Please follow the instructions outlined above Project PAD NA Bypass validation steps Select Data Type Original XML Subject ID 10 characters allowed identifier to replace Patient ID Source Directory BROWSE Location of original files Target Directory BROWSE Location for target files NOTE Source Directory for file formats with complete headers DICOM GE ECAT eic may contain multiple series from single subject Source Directory for file formats with limited headers ANALYZE MINC
45. ubject ID and the site name to search for a specific subject in a particular site SUBJECT INFORMATION Subject You may use the wild card character in the Subject ID For example enter UCLA to search for all Subject IDs beginning with UCLA SiteName Select CU RESET SEARCH Click UPDATE beside the subject to be edited Your search returned 5 record s Press the UPDATE button beside the entry you wish to update OR press the NEW SEARCH button to return to the search page Subject ID Sex Study Date Age Subject Weight Select UCLA_1231 Male 09 05 2006 63 0 77 18 UPDATE e 09 05 2006 63 0 77 18 UPDATE 09 05 2006 63 0 74 91 UPDATE 09 05 2006 63 0 74 91 UPDATE 09 05 2006 63 0 74 91 UPDATE 1 Previous NEW SEARCH LONI Image amp Data Archive Change the desired information then click UPDATE SUBJECT INFORMATION STUDY INFORMATION Study Date Subject iD Age Years Sec Mse m Weight 7 18 Kg PROJECT SPECIFIC INFORMATION Handedness Ro Alphanumeric character Project Phase Unknown type NEW SEARCH UPDATE Notes Items grayed out cannot be changed gt Project specific Information may need to be entered for each new subject The Updated Results page displays the edited record information Below is your updated result Clickthe NEW SEARCH button to return to the search page and search for more subjects Clickthe BROWSE button to return to the results page BROWSE

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