Projects:RegistrationDocumentation:UseCaseAdvertisement - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:04:24Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier at 14:28, 22 April 2010

2010-04-22T14:28:27Z

Meier at 14:27, 22 April 2010

2010-04-22T14:27:05Z

Meier at 14:24, 22 April 2010

2010-04-22T14:24:59Z

Meier: /* Limitations/Disclaimer */

2010-04-22T14:23:53Z

Limitations/Disclaimer

Meier: /* Procedure */

2010-04-22T14:23:33Z

Procedure

Meier: /* What We Will Do */

2010-04-22T14:20:56Z

What We Will Do

Meier at 13:50, 15 April 2010

2010-04-15T13:50:50Z

Meier: /* Procedure */

2010-03-17T22:35:09Z

Procedure

Meier at 22:49, 26 February 2010

2010-02-26T22:49:40Z

@@ Line 42: / Line 42: @@
 *1. if you have not yet done so, browse/search the [[Projects:RegistrationDocumentation:UseCaseInventory|Registration Case Library]]  for a scenario similar to yours. If you find one matching in organ, modality and contrast, try out the parameter settings and procedures suggested there. If that fails, go to step 2.
 *2. Drop us a line with the following info: the image type and size of your case, the registration objective, if avail. criteria for evaluating a good registration, time constraints if you have any
-*3. If you can provide us with fiducial pairs that define a good registration, we will use them in optimization efforts. You can use the 3DSlicer ''Fiducials'' module to select one or more pairs of points that should line up. [[Projects:RegistrationDocumentation:RegistrationFiducials|Step by step guidelines for picking fiducial pairs are here ]] and [http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.4 Detailed documentation on the fiducials module is here].
+*3. If you can provide us with fiducial pairs that define a good registration, we will use them in optimization efforts. You can use the 3DSlicer ''Fiducials'' module to select one or more pairs of points that should line up. [[Projects:RegistrationDocumentation:RegistrationFiducials|Step by step guidelines for picking fiducial pairs are here ]] and [https://www.slicer.org/wiki/Modules:Fiducials-Documentation-3.4 Detailed documentation on the fiducials module is here].
 ---!>

@@ Line 7: / Line 7: @@
 ==Registration in 3D Slicer- <big>'''Call for Datasets for the Registration Case Library'''</big> ==
 Let us help you turn your registration problem into a success story. If you have an interesting or vexing registration problem that is not yet covered in [[Projects:RegistrationDocumentation:UseCaseInventory|the Library]] , send us your '''one''' case: we will try to register it for you and design a tailored registration approach you can use. We then add the '''anonymized''' data to the library and build a guided step-by-step tutorial for it. This is a time and resource limited service available until '''July 1, 2011'''.  If interested drop a line to '''meier at bwh.harvard.edu'''.   We'll take it from there.
 == What We Will Do ==
-* we will seek the best possible registration obtainable with the most recent version of 3DSlicer.
+* we will seek the best possible registration obtainable with the most recent version of 3DSlicer, and send you the final result as well as the procedure and parameters.
 * we will post the anonymized image data as a new case in our [[Projects:RegistrationDocumentation:UseCaseInventory|Slicer Registration Case Library]].
 * an acknowledgment of your lab as the data source is posted, if desired with a link to your institution and/or related research papers
@@ Line 33: / Line 38: @@
 **for some high-resolution structural head MRI we may have apply additional "defacing" (i.e. masking of image parts of the face and/or ears) before posting. This removal applies only to image content of facial features that might be recognizable as a 3D rendering. We will do this for you. Only the defaced data is kept.
 <!---

@@ Line 33: / Line 33: @@
 **for some high-resolution structural head MRI we may have apply additional "defacing" (i.e. masking of image parts of the face and/or ears) before posting. This removal applies only to image content of facial features that might be recognizable as a 3D rendering. We will do this for you. Only the defaced data is kept.
-===Procedure===
+==What You Will Need To Do ==
-* until '''July 1, 2011''': just send us an Email with a brief description of the problem, send to '''meier at bwh.harvard.edu'''.   We'll take it from there. All you will  have to do is save your image data as NRRD or NIFTI files and provide a brief description of the registration problem.
+* just send us an Email with a brief description of the problem, send to '''meier at bwh.harvard.edu'''.   We'll take it from there.
 <!---
 *1. if you have not yet done so, browse/search the [[Projects:RegistrationDocumentation:UseCaseInventory|Registration Case Library]]  for a scenario similar to yours. If you find one matching in organ, modality and contrast, try out the parameter settings and procedures suggested there. If that fails, go to step 2.

@@ Line 6: / Line 6: @@
 ==Registration in 3D Slicer- <big>'''Call for Datasets for the Registration Case Library'''</big> ==
-Let us help you turn your registration problem into a success story. If you have an interesting or vexing registration problem that is not yet covered in [[Projects:RegistrationDocumentation:UseCaseInventory|the Library]] , send us your '''one''' case: we will try to register it for you and design a tailored registration approach you can use. We then add the '''anonymized''' data to the library and build a guided step-by-step tutorial for it. This is a time and resource limited service available until '''July 1, 2011'''.
+Let us help you turn your registration problem into a success story. If you have an interesting or vexing registration problem that is not yet covered in [[Projects:RegistrationDocumentation:UseCaseInventory|the Library]] , send us your '''one''' case: we will try to register it for you and design a tailored registration approach you can use. We then add the '''anonymized''' data to the library and build a guided step-by-step tutorial for it. This is a time and resource limited service available until '''July 1, 2011'''.  If interested drop a line to '''meier at bwh.harvard.edu'''.   We'll take it from there.
 == What We Will Do ==

@@ Line 29: / Line 29: @@
    investigator in  such a manner that subjects cannot be identified, directly or through identifiers linked
    to the subjects.
-:*if you are unsucessful in anonymizing the data as described above, let us know and we'll walk you through it.
+**''anonymization'' is easy: load your data into slicer. Save it as ''NRRD'' file (in the Save dialog box, make sure 'nrrd' is selected as filetype for all output images). This will save only the raw image data + voxelsize and image orientation. No other data re. subject, scanner or institution are present in the NRRD file. For details see our [[Projects:RegistrationDocumentation:Anonymization|'''Anonymization Instructions''']]
-*for some high-resolution structural head MRI we may have apply additional "defacing" (i.e. masking of image parts of the face and/or ears) before posting. This removal applies only to image content of facial features that might be recognizable as a 3D rendering. We will do this for you. Only the defaced data is kept.
+**if you are unsucessful in anonymizing the data as described above, let us know and we'll walk you through it.
 ===Procedure===

@@ Line 10: / Line 10: @@
 == What We Will Do ==
 * we will seek the best possible registration obtainable with the most recent version of 3DSlicer.
-* we will post the anonymized image data as a new case in our [[Projects:RegistrationDocumentation:UseCaseInventory|Slicer Registration Case Library]]. Your case will receive its own page, similar to [[this]].
+* we will post the anonymized image data as a new case in our [[Projects:RegistrationDocumentation:UseCaseInventory|Slicer Registration Case Library]].
 * the exact workflow of obtaining the registration will be posted alongside the data as a guided step-by-step tutorial
 * the parameters for successful registration will also be posted as a loadable custom "Registration Preset" file that you can load directly into slicer and apply on your data
 * if you can provide us with fiducial pairs or other criteria that define a good registration, we will use them in optimization efforts. You can use the 3DSlicer ''Fiducials'' module to select one or more pairs of points that should line up. Detailed instructions below.
 * [[Projects:RegistrationDocumentation:UseCaseExample1b|'''example of what the final shared product will look like''']]
 ===Limitations/Disclaimer===
-*we will assist only with 3DSlicer registration software.
+*we can assist only with 3DSlicer registration software.
-*we will register only 1 case. If you have a batch we hope the rest will perform similarly.
+*if you have a study of N cases, pick a typical one or a hard one. We can register only 1 or 2 cases of the same type. But if you have outliers that do not perform as the rest these are welcome.
 *this is a time-limited service, available in a first trial until ''''July 1, 2011'''.
-*we cannot guarantee a particular result or a specific turnaround time
+*depending on workload, we try to get you something within a few weeks, but we cannot guarantee a particular result or a specific turnaround time.
-*all shared data-sets must be anonymized. High-resolution structural head MRI may have to be posted with applied ''defacing'', i.e. removed image content of facial features that might be recognizable as a 3D rendering.
+*all shared data-sets are '''anonymized''':
-*Sharing anonymized data in most cases is IRB exempt based on Code of Federal Regulations  45 CFR 46.101(b), which lists as exemption category 4:
+**Sharing anonymized data in most cases is IRB exempt based on Code of Federal Regulations  45 CFR 46.101(b), which lists as exemption category 4:
    Unless otherwise required by department or agency heads, [...] the following categories are exempt [...]: <br>
 .Research involving the collection or study of existing data, documents, records , pathological specimens,
@@ Line 30: / Line 29: @@
    investigator in  such a manner that subjects cannot be identified, directly or through identifiers linked
    to the subjects.
-:*if you do not have the ability to anonymize the data we may, with some limitations, be able to do that for you also, but  you will need to obtain an IRB approval for us to be allowed to perform the anonymization for you from your institution and enter a direct collaborative agreement with us.
+:*if you are unsucessful in anonymizing the data as described above, let us know and we'll walk you through it.
-*if your case pairing of images is already presented in the library, we expect that you have tried the approach & settings presented there already. If to no avail we will gladly consider it.
+*for some high-resolution structural head MRI we may have apply additional "defacing" (i.e. masking of image parts of the face and/or ears) before posting. This removal applies only to image content of facial features that might be recognizable as a 3D rendering. We will do this for you. Only the defaced data is kept.
 ===Procedure===
-*0. until '''July 1, 2011''': just send us an Email with a brief description of the problem, send to meier at bwh.harvard.edu.   We'll take it from there.
+* until '''July 1, 2011''': just send us an Email with a brief description of the problem, send to meier at bwh.harvard.edu.   We'll take it from there.
 *1. if you have not yet done so, browse/search the [[Projects:RegistrationDocumentation:UseCaseInventory|Registration Case Library]]  for a scenario similar to yours. If you find one matching in organ, modality and contrast, try out the parameter settings and procedures suggested there. If that fails, go to step 2.
 *2. Drop us a line with the following info: the image type and size of your case, the registration objective, if avail. criteria for evaluating a good registration, time constraints if you have any
 *3. If you can provide us with fiducial pairs that define a good registration, we will use them in optimization efforts. You can use the 3DSlicer ''Fiducials'' module to select one or more pairs of points that should line up. [[Projects:RegistrationDocumentation:RegistrationFiducials|Step by step guidelines for picking fiducial pairs are here ]] and [http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.4 Detailed documentation on the fiducials module is here].

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation|back to Registration Main Page]]
-[[Image:SlicerRegistrationLibrary_Ad.png|left|800px|Slicer Registration Case Library: Call for Example Datasets]]<br>
+[[Image:SlicerRegistrationLibrary_Ad.png|left|600px|Slicer Registration Case Library: Call for Example Datasets]]<br>
 ==Registration in 3D Slicer- <big>'''Call for Datasets for the Registration Case Library'''</big> ==