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| − | == 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.
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| − | 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.
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| − | === Background (why specific editor features are needed) ===
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| − | ''TODO'' | |
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| − | == Interface ==
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| − | This screenshots show the interface and its changes during the last months.
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| − | <gallery caption="Interface" widths="150px" heights="150px" perrow="4">
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| − | Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
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| − | Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
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| − | Image:DWI_Gradient_Editor_v3.jpg
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| − | Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements are no longer necessary
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| − | </gallery>
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| − | | |
| − | == How to use the editor==
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| − | *1.Step: Generate a Nrrd-header of your DWI data. Use the "Dicom to Nrrd" module in Slicer3 (Modules->Converters->Dicom to Nrrd).
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| − | **-> A .nhdr file will be created.
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| − | *2.Step: Use the output (.nhdr file) as an input of the Volumes module.
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| − | **-> The Gradient Editor will be enabled. If you load any other type of dataset the editor will be disabled.
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| − | | |
| − | === What you can do with the Gradient Editor===
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| − | ''TODO: more details.''
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| − | #'''Choose measurement frame'''.
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| − | ## '''Negative''': Select the columns you want to negative.
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| − | ## '''Swap''': Select two columns you want to swap.
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| − | ## '''Rotate''': Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
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| − | ## Set your own values.
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| − | #'''Define gradients'''.
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| − | ## If the .nhdr file has the information about the gradients, the editor will put them in the text field.
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| − | ## You can copy/paste your own gradients in the text field.
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| − | ## You can load gradients from a plain text file or .nhdr file.
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| − | #'''Run test'''.
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| − | ## Add a Fiducial List. To see if the chosen parameters are reasonable, you can run a test that automatically
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| − | ### computes the Tensor and
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| − | ### visualizes them by Tractography Seeding. (both with standard values)
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| − | #'''Cancel''': All parameters are restored to original.
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| − | | |
| − | == Status / Implementation Progress ==
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| − | The editor is now successfully integrated in the Volumes module of the trunk version of Slicer3. | |
| − | *measurement frame (gui/load/change/save): 95%
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| − | *gradients (gui/load/change/save): 95%
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| − | *test: 50%
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| − | ** tensor estimation with existing clm: 80%
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| − | ** tractography fiducial seeding: 10%
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| − | *writing master thesis: 5% :-)
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| − | | |
| − | == Additional Information ==
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| − | 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]
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| − | DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]
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| − | 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]
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