View source for Projects:RegistrationDocumentation:UseCaseInventory

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= The Slicer Registration Case Library =
{| style="color:#000000; background-color:#aaaaaa;" cellpadding="10" cellspacing="0" border="0"
|Welcome to the 3DSlicer Registration Case Library. This page is under continuous development as we add and refine case examples of image registration within 3DSlicer. The goal is for you to find here a case similar enough to your particular image registration problem to provide you with registration parameters, strategies and tutorials. The library is growing by virtue of '''user contributions'''; if you have an interesting case please consider our ''Call for Datasets'' on the right.  Successful registration strategies; algorithm choice and parameters vary greatly for different image contrast and content. Each listed case comprises a test dataset to try yourself,  a guided step-by-step '''tutorial''' that will show you how to register the case with 3DSlicer, the solution transform so you can compare, and a custom ''Registration Parameter Presets'' file with optimized registration parameters that you can load directly into slicer. 
|
|[[Image:SlicerRegistrationLibrary_Ad.png|right|300px|link=Projects:RegistrationDocumentation:UseCaseAdvertisement|Slicer Registration Case Library: Call for Example Datasets]] <br>
[[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''Consider adding your case to the library''']]
|}

Library organized by structure below. [[Projects:RegistrationDocumentation:RegLibTable|'''Library as sortable table see here.''']] 

== BRAIN ==

{| cellpadding="6" cellspacing="2" 
|align="center" |[[Image:Registration_HLogo_IntraMRI.png| 135px |link=Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraMRI]]
|align="center" |[[Image:Registration_HLogo_IntraDTI.png| 135px |link=Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraDTI]]
|align="center" |[[Image:Registration_HLogo_IntrafMRI.png| 135px |link=Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraFMRI]]
|align="center" |[[Image:Registration_HLogo_IntraPET.png| 135px |link=Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraPETCT]]
|-
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraMRI|'''Same Subject Brain MRI''' ]] collection contains '''structural'''MRI of the same subject, e.g. aligning follow-up to baseline or a T1w and a PDw image.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraDTI|'''Same Subject  DTI''' ]] collection contains cases of registering a DTI dataset with an anatomical reference, such as a high-resolution MRI.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraFMRI|'''Same Subject  fMRI''' ]] collection contains cases of registering a fMRI dataset with an anatomical reference, such as a high-resolution MRI.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraPETCT|'''Same Subject  PET/CT/MRI''' ]] collection contains cases of registering a PET or CT dataset with an MRI or CT.
|-
|align="center" |[[Image:Registration_HLogo_InterMRI.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:BrainInterMRI]]
|align="center" |[[Image:Registration_HLogo_InterPET.png‎| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:BrainInterPETCT]]
|align="center" |[[Image:Registration_HLogo_Atlas.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:BrainAtlas]]
|
|-
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainInterMRI|'''Different Subject Brain MRI''' ]] collection contains cases of co-registering MRI of (many) different subjects into a common space. This often includes non-rigid registration (image warping).
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainInterPETCT|'''Different Subject PET/CT''' ]] collection contains cases of registering PET/SPECT/CT images from different subjects, e.g. aligning a SPECT perfusion atlas with an MRI.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:BrainAtlas|'''Different Subject Brain Atlas''' ]] collection contains cases of registering an atlas to a single subject or building atlases from a collection of subjects.
|
|}

== OTHER ==


{| cellpadding="6" cellspacing="2" 
|align="center" |[[Image:Registration_HLogo_Abdominal.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:Abdominal]]
|align="center" |[[Image:Registration_HLogo_Knee.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:Musculoskeletal]]
|align="center" |[[Image:Registration_HLogo_WholeBody.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:WholeBody]]
|align="center" |[[Image:Registration_HLogo_Animal.png| 135px |link= Projects:RegistrationDocumentation:UseCaseInventory:Animal]]
|-
|The [[Projects:RegistrationDocumentation:UseCaseInventory:Abdominal|'''Abdominal/Thoracic''' ]] collection contains cases of breast and abdominal MRI/CT/PET, e.g. for therapeutic assessment or interventional guidance.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:Musculoskeletal|'''Musculoskeletal''' ]] collection contains cases of aligning musculoskeletal images, e.g. aligning knee MRI images.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:WholeBody|'''Whole Body PET/CT''' ]] collection contains cases of registering different modalities of whole body imaging.
|The [[Projects:RegistrationDocumentation:UseCaseInventory:Animal|'''Animal MRI/CT''' ]] collection contains cases of aligning animal datasets.
|}

== TECHNICAL ISSUES ==
COMING SOON, case help for the following issues :
*Images with incorrect spatial orientation
*Distorted images (incorrect or missing voxel sizes)
*Image pairs with non-matching spatial 
*Images with incorrect datatype
*Images with clipped FOV


== How to get started ==
*1. browse/search the library for a case similar to yours. The library is organized by organ (brain vs. non-brain), modality (MR, CT, PET), intra- vs. inter-subject). Each case also has a list of keywords, so you may try a direct search for a case matching yours.
*2. If you find a good match, continue with 3. below. If you cannot find a good match, consider our  [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''Call for Datasets & Registration Service''']]. 
*3. from the case description page, follow the links to download the data, preset file and tutorials.
*4. run the tutorial on your machine with your installation of slicer (v3.6 or higher recommended)
*5. load the preset file and try those settings on your own data
*5. if you do not get a satisfactory registration results with the presets, have a look at the ''Registration Challenges'' and ''Key Strategies''  section on the download page of your case. You will find recommendations there on how to venture forth. Try the recommended adjustments.
*6. if still unsuccessful you may have a case of interest to the library. [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''Consider adding your case to the library for a free registration''']].  Also consider posting a message to the [http://www.slicer.org/pages/Mailinglist slicer user group].
*7. if successful we'd also love to hear:  [[Projects:RegistrationDocumentation:UseCaseAdvertisement|''' We gladly add your case with full acknowledgment to the library''']].

== Source & Format ==
Data is collected from a variety of sources. Most we hope to originate from user contributions. Because we want to focus on the registration problem and not be distracted by image format or other data management issues, the datasets listed here are reformatted as NiFTI files. Cases under construction may be listed, and when complete a download link is added.  
*[[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''Call for Datasets''']]
*[[Projects:RegistrationDocumentation:RegLibList|Full List of Registration Library Cases]]
*[[Projects:RegistrationDocumentation:RegLibTable|Sortable Table of Library Cases]]
*[[Projects:RegistrationDocumentation:RegLibDataList|List of downloadable Registration Library data files]]
* All image data is anonymized, i.e. there is no identifying or patient specific information in any of the posted data. We do not keep identifiers, so we cannot retrace. 
*Options for the download location is a direct link to a download page from the main  [http://www.slicer.org/pages/UserOrientation 3Dslicer user page] or XNAT Central. The former seems preferable, since the general XNAT GUI appears too complex for a simple 1-case download. We expect most users to download only 1 or 2 files closest to their particular use case, not entire study sets. Such download should be acessible with 1-2 clicks, as with other slicer resources. 
*[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|How to Load/Save Registration Parameter Presets]]
*Disk usage: Likely these example sets will grow no larger than 10GB. Estimating 50-80MB per case would allow  60-100 cases within a 5GB space. 
*If desired, links & contact info to the contributor lab are provided.
*Links here also from the  [[Data|NA-MIC resource page]].To be updated when moving.
*[[Projects:RegistrationDocumentation:UseCaseList| list of use case candidates]]
*For a list/overview of registration options '''by method''' see [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration#Registration_in_3D_Slicer the '''3DSlicer Registration Portal Page''']
[[Category:Registration]]