Difference between revisions of "Slicer3:Diffusion Editor"

From NAMIC Wiki
Jump to: navigation, search
m
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(28 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== Overview ==
+
<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Modules:Volumes:Diffusion_Editor-Documentation  here]</font></big>
The goal of this project is to add a Gradient Editor for DWI data in the Volumes module of Slicer3.
 
As the documentation of gradients in dicom data is not standardized, MRI scanners handle them differently. Because of that there is a big need to add/modify gradients manually.
 
=== Background - why specific editor features are needed ===
 
''TODO''
 
 
 
== Interface ==
 
This screenshots show the interface and its changes during the last months.
 
 
 
<gallery caption="Interface" widths="150px" heights="150px" perrow="4">
 
Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
 
Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
 
Image:DWI_Gradient_Editor_v3.jpg
 
Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements are no longer necessary
 
</gallery>
 
 
 
== How to use the editor==
 
*1.Step: Generate a Nrrd-header of your DWI data. Use the "Dicom to Nrrd" module in Slicer3 (Modules->Converters->Dicom to Nrrd).
 
**-> A .nhdr file will be created.
 
*2.Step: Use the output (.nhdr file) as an input of the Volumes module.
 
**-> The Gradient Editor will be enabled. If you load any other type of dataset the editor will be disabled.
 
 
 
=== What you can do with the Gradient Editor===
 
'''TODO: more details.'''
 
 
 
#'''Choose measurement frame'''.
 
## '''Negative''': Select the columns you want to negative.
 
## '''Swap''': Select two columns you want to swap.
 
## '''Rotate''': Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
 
## Set your own values.
 
#'''Define gradients'''.
 
## If the .nhdr file has the information about the gradients, the editor will put them in the text field.
 
## You can copy/paste your own gradients in the text field.
 
## You can load gradients from a plain text file or .nhdr file.
 
#'''Run test'''.
 
## Add a Fiducial List. To see if the chosen parameters are reasonable, you can run a test that automatically
 
### computes the Tensor and
 
### visualizes them by Tractography Seeding. (both with standard values)
 
#'''Cancel''': All parameters are restored to original.
 
 
 
== Status / Implementation Progress ==
 
The editor is now successfully integrated in the Volumes module of the trunk version of Slicer3.
 
*measurement frame (gui/load/change/save): 95%
 
*gradients (gui/load/change/save): 70%
 
*test (gui/...): 10% BIG TODO
 
*writing master thesis: 0% :-)
 
 
 
== Additional Information ==
 
 
 
Nrrd format: [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
 
 
 
DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]
 
 
 
DICOM for DWI and DTI : [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI]
 

Latest revision as of 17:37, 10 July 2017

Home < Slicer3:Diffusion Editor

Note: We are migrating this content to the slicer.org domain - The newer page is here