Slicer3:FAQ - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:34:35Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Meier at 22:28, 21 December 2010

2010-12-21T22:28:37Z

Meier at 22:27, 21 December 2010

2010-12-21T22:27:18Z

Show changes

Meier: /* Registration result is wrong or worse than before? */

2010-11-23T17:08:24Z

Registration result is wrong or worse than before?

Meier: /* Can I manually adjust or correct a registration? */

2010-11-23T17:08:05Z

Can I manually adjust or correct a registration?

Meier: /* How do I register a DWI image dataset to a structural reference scan? (Cookbook) */

2010-11-23T17:04:32Z

How do I register a DWI image dataset to a structural reference scan? (Cookbook)

Meier: /* How do I register a DWI image dataset to a structural reference scan? (Cookbook) */

2010-11-23T17:03:26Z

How do I register a DWI image dataset to a structural reference scan? (Cookbook)

Meier: /* Can I manually adjust or correct a registration? */

2010-11-23T17:00:39Z

Can I manually adjust or correct a registration?

Meier at 16:57, 23 November 2010

2010-11-23T16:57:52Z

Show changes

Meier: /* What's the difference between the various registration methods listed in Slicer? */

2010-11-23T16:53:56Z

What's the difference between the various registration methods listed in Slicer?

← Older revision		Revision as of 02:34, 27 November 2019
Line 1:		Line 1:
−	'''This page has been deprecated. Please refer to the [~~http://www.slicer.org/slicerWiki/index.php/~~Slicer-3-6-FAQ '''new Slicer 3.6 FAQ here]'''	+	'''This page has been deprecated. Please refer to the [[Slicer-3-6-FAQ\|'''new Slicer 3.6 FAQ here]]'''

	= User FAQ : installation & general use =		= User FAQ : installation & general use =

← Older revision		Revision as of 22:28, 21 December 2010
Line 1:		Line 1:
		+	'''This page has been deprecated. Please refer to the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ '''new Slicer 3.6 FAQ here]'''
		+
	= User FAQ : installation & general use =		= User FAQ : installation & general use =

@@ Line 111: / Line 111: @@
 **'''too many/too few DOF''': the degrees of freedom (DOF) determine how much motion is allowed for the image to be registered. Too few DOF results in suboptimal alignment; too many DOF can result in overfitting or the algorithm getting stuck in local extrema, or a bad fit with some local detail matched but the rest misaligned.  Consider a stepwise approach where the DOF are gradually increased. [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] and [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated] provide such pipelines; or you can nest the transforms manually. A multi-resolution approach can also greatly benefit difficult registration challenges: this scheme runs multiple registrations at increasing amounts of image detail. The [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution module] performs this task.
 **'''inappropriate algorithm:''' there are many different registration methods available in Slicer. Have a look at the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration '''Registration Method Overview'''] and consider one of the alternatives. Also review the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' in the Registration Case Library] to see which methods were successfully used on cases matching your own.
-**you can adjust/correct an obtained registration manually, within limits, as outlined [[Projects:SlicerFAQ:RegistrationAdjust|here]].
+**you can adjust/correct an obtained registration manually, within limits, as outlined [[Slicer3:FAQ#Can I manually adjust or correct a registration?|'''in this FAQ''']].
 == How many sample points should I choose for my registration? ==

@@ Line 57: / Line 57: @@
 *'''Problem:''' obtained registration is insufficient
 *'''Explanation:''' The automated registration algorithms (except for  fiducial and surface registration) in Slicer operate on image intensity and try to move images so that similar image content is aligned. This is influenced by many factors such as image contrast, resolution, voxel anisotropy, artifacts such as motion or intensity inhomogeneity, pathology etc, the initial misalignment and the parameters selected for the registration.
-*'''Fix:''' you can adjust/correct an obtained registration manually, within limits. As outlined below. Your first try however should be to obtain a better automated registration by changing some of the input and/parameters and then re-run. Some guidelines on this are listed [[Slicer3:FAQ#Registration result is wrong or worse than before?|'''here''']]
+*'''Fix:''' you can adjust/correct an obtained registration manually, within limits. As outlined below. Your first try however should be to obtain a better automated registration by changing some of the input and/parameters and then re-run. Some guidelines on this are listed [[Slicer3:FAQ#Registration result is wrong or worse than before?|'''in this FAQ''']]
 **'''Manual Adjustment''': If the transform is linear, i.e. a rigid or affine transform, you can access the rigid components (translation and rotation) of that transform via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module].
 ***#In the ''Data'' module, drag the image volume inside the registration transform node

@@ Line 51: / Line 51: @@
 *'''Explanation:''' DWI images are often acquired as EPI sequences that contain significant distortions, particularly in the frontal areas. Also because the image is acquired before or after the structural scans, the subject may have moved in between and the position is no longer the same.
 *'''Fix:''' obtain a baseline image from the DWI sequence, register that with the structural image and then apply the obtained transform to the DTI tensor. The two chief issues with this procedure deal with the difference in image contrast between the DWI and the structural scan, and with the common anisotropy of DWI data.
 * you can find example cases in the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraDTI '''DWI chapter of the Slicer Registration Case Library'''], which includes example datasets and step-by-step instructions. Find an example closest to your scenario and perform the registration steps recommended there.
 == Can I manually adjust or correct a registration? ==

@@ Line 185: / Line 185: @@
 == What's the difference between the various registration methods listed in Slicer? ==
 Most of the registration modules use the same underlying ITK registration algorithm for cost function and optimization, but differ in implementation on parameter selection, initialization and the type of image toward which they have been tailored. To help choose the best one for you '''based on the method or available options''', an [http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration#Registration_in_3D_Slicer overview of all registration methods] incl. [http://www.slicer.org/slicerWiki/index.php/Registration:Categories a '''comparison matrix''' can be found here]. <br>
-To help choose '''based on a particular image type and content''', you will find many example cases incl. step-by-step instructions and discussions on the particular registration challenges in the [[Projects:RegistrationDocumentation:UseCaseInventory|'''Slicer Registration Library''']]. The library is organized in several different ways, e.g. consult this [[Projects:RegistrationDocumentation:RegLibTable|'''sortable table''' with all cases and the method used]].<br>
+To help choose '''based on a particular image type and content''', you will find many example cases incl. step-by-step instructions and discussions on the particular registration challenges in the [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory '''Slicer Registration Library''']. The library is organized in several different ways, e.g. consult this [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable '''sortable table''' with all cases and the method used].<br>
 There is also a brief overview within Slicer that helps distinguish: Select the ''Registration Welcome'' option at the top of the Modules/Registration menu.