Modules:DiffusionMRIWelcome-Documentation-3.6 - Revision history

Kikinis: /* 1. Convert DWI data into nrrd format */

2011-04-27T02:55:30Z

1. Convert DWI data into nrrd format

2010-12-16T12:47:54Z

Recommended Workflow in 3D Slicer

2010-12-16T12:47:24Z

Filter the DWI for noise reduction

2010-12-16T12:45:21Z

Diffusion MRI in 3D Slicer

2010-12-16T12:41:37Z

Diffusion MRI in 3D Slicer

2010-12-09T20:00:00Z

2010-05-21T21:30:52Z

First: Convert the Diffusion Weighted Images (DWI) from DICOM to NRRD

2010-05-21T21:29:52Z

First: Convert the Diffusion Weighted Images (DWI) from DICOM to NRRD

2010-05-21T21:27:53Z

Estimate the DT from the DW image

2010-05-21T19:44:13Z

DWI Filtering

@@ Line 13: / Line 13: @@
 ==1. Convert DWI data into nrrd format==
 <big><big>'''As first step for handling your DICOM format DWI data, use the DicomToNrrd module to convert your DWI data from DICOM to NRRD format.'''</big></big>
-* Then load the nrrd format data into Slicer using the File->Add Volume dialog. See [[Modules:DicomToNRRD-3.6|here]] for a list of supported DWI formats.
+* Then load the nrrd format data into Slicer using the File->Add Volume dialog. See [[Modules:DicomToNRRD-3.6|here]] for a '''list of supported DWI formats'''.
 * See [[Slicer-3.6-Load-Overview|here]] for an overview over the process of loading data into Slicer.
 ==2. Filter the DWI for noise reduction==
 * Begin with the [[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Modules:Joint Rician LMMSE Image Filter]]

@@ Line 11: / Line 11: @@
 =Recommended Workflow in 3D Slicer=
-==Convert DWI data into nrrd format==
+==1. Convert DWI data into nrrd format==
 <big><big>'''As first step for handling your DICOM format DWI data, use the DicomToNrrd module to convert your DWI data from DICOM to NRRD format.'''</big></big>
 * Then load the nrrd format data into Slicer using the File->Add Volume dialog. See [[Modules:DicomToNRRD-3.6|here]] for a list of supported DWI formats.
 * See [[Slicer-3.6-Load-Overview|here]] for an overview over the process of loading data into Slicer.
-==Filter the DWI for noise reduction==
+==2. Filter the DWI for noise reduction==
 * Begin with the [[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Modules:Joint Rician LMMSE Image Filter]]
 * Several other filters are available, but we have found this one to be easy to use and the defaults should work on human brains.
-==Estimate Tensors==
+==3. Estimate Tensors==
-==Perform Tractography==
+==4. Perform Tractography==
 = Diffusion MRI Modules =

@@ Line 16: / Line 16: @@
 * See [[Slicer-3.6-Load-Overview|here]] for an overview over the process of loading data into Slicer.
 ==Filter the DWI for noise reduction==
+* Begin with the [[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Modules:Joint Rician LMMSE Image Filter]]
 ==Estimate Tensors==

@@ Line 10: / Line 10: @@
 |}
 <big><big>'''As first step for handling your DICOM format DWI data, use the DicomToNrrd module to convert your DWI data from DICOM to NRRD format.'''</big></big>
 * Then load the nrrd format data into Slicer using the File->Add Volume dialog. See [[Modules:DicomToNRRD-3.6|here]] for a list of supported DWI formats.
 * See [[Slicer-3.6-Load-Overview|here]] for an overview over the process of loading data into Slicer.
 = Diffusion MRI Modules =

@@ Line 10: / Line 10: @@
 |}
-<big><big>'''As first step for handling your DICOM format DWI data, use the DicomToNrrd module to convert your DWI data from DICOM to NRRD format.'''</big></big>  Load the nrrd format data into Slicer using the File->Add Volume dialog. See [[Modules:DicomToNRRD-3.6|here]] for a list of supported DWI formats.
+<big><big>'''As first step for handling your DICOM format DWI data, use the DicomToNrrd module to convert your DWI data from DICOM to NRRD format.'''</big></big>
 = Diffusion MRI Modules =

@@ Line 9: / Line 9: @@
 For a brief description of the common diffusion MRI processing pipeline please follow this [[ #Diffusion Processing Pipeline|link ]].
 |}
 = Diffusion MRI Modules =

@@ Line 49: / Line 49: @@
 # Click on '''Input Dicom Data''' and select the directory where your the DICOM files corresponding to your DWI images are stored.
 # Click on '''Output Directory''' and select the directory where you want to store the resulting NRRD file.
-# Fill in '''Output Filename''' the name of the file, for instance: ''dwi.nhdr''.
+# Fill in '''Output Filename''' the name of the file, for instance: ''dwi.nrrd''. You must include the extension.
 # Press the Apply button.

@@ Line 45: / Line 45: @@
 ===First: Convert the Diffusion Weighted Images (DWI) from DICOM to NRRD===
 In order to use 3D Slicer to process the Diffusion Weighted Images obtained from a Diffusion Tensor imaging protocol, we must convert them to the NRRD format as follows:
-[[Image:DWIDicomToNrrdGUI.jpg|thumb|280px|left|[[Modules:DicomToNRRD-3.6|'''Dicom To Nrrd''']] module]]
+[[Image:DWIDicomToNrrdGUI.png|thumb|280px|left|[[Modules:DicomToNRRD-3.6|'''Dicom To Nrrd''']] module]]
 # Select the [[Modules:DicomToNRRD-3.6|'''Dicom To Nrrd''']] module from the '''Converters''' module category.
 # Click on '''Input Dicom Data''' and select the directory where your the DICOM files corresponding to your DWI images are stored.

@@ Line 69: / Line 69: @@
 #;'''Output Baseline Volume'''
 #;'''Otsu Threshold Volume'''
-#:to their corresponding ''Create new...'' option.
+#:to their corresponding ''Create new...'' option. You can then use the '''rename''' option if you do not like the default file names.
 #Press the '''Apply''' button.
 ===Third: Perform a tractography study===

@@ Line 11: / Line 11: @@
 = Diffusion MRI Modules =
-== DWI Filtering ==
+== DWI Denoising==
 [[Image:DenoisingIllustration.png|center|thumb|upright=4.|Result of the different DWI filtering algorithms. From left to right: Original images,
 [[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]];