DTI Pipeline and Generating graphs: Difference between pages

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Diffusion tensor imaging (DTI) analyzes the tissues that have an internal fibrous structure, which is analogous to the anisotropy of some crystals (e.g.neural axons of white matter or muscle fibers in the heart). In those tissues, the diffusion of water displays anisotropy in certain directions. That means that molecules of water diffuse more rapidly in the direction aligned with the fibrous structure, and more slowly in the direction perpendicular to it. Thus, the measured rate of diffusion will differ depending on the fiber direction and an observer's point of view.
MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"<br />


In diffusion-weighted imaging (DWI), at least 3 gradients are applied in 3 different directions, which is sufficient to estimate the trace of the diffusion tensor. From the diffusion tensor, diffusion anisotropy measures such as the fractional anisotropy (FA) eigenvalues and eigenvectors can be computed and displayed. The principal direction of the diffusion tensor can be also used [[DTI pipeline interface#VisualizationTab |to visualize the white matter connectivity of the brain]]. DTI has been proven to be very useful to diagnose vascular strokes in the brain and in other clinical applications.
=== Generating contour VOI graphs ===
Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs. <br />


'''Note:''' this diffusion model is a rather simplified model of the diffusion process. It assumes that diffusion within each image voxel is linear and homogeneous.  
'''To generate 2D contour VOI graphs'''<br />
1 Open an image.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br />


== Introduction ==
The DTI pipeline of MIPAV prepares [http://www.mr-tip.com/serv1.php?type=db1&dbs=Diffusion%20Tensor%20Imaging diffusion weighted images (DWIs)] and computes voxel-wise diffusion tensors ([http://en.wikipedia.org/wiki/Diffusion_MRI#Diffusion_tensor_imaging DT]) for the further analysis of diffusion tensor imaging (DTI) data, see [[DTI Color Display| MIPAV DTI Color Display]]. The pipeline computes maps of diffusion [http://en.wikipedia.org/wiki/Diffusion_MRI#Measures_of_anisotropy_and_diffusivity eigenvalues] and [http://en.wikipedia.org/wiki/Diffusion_MRI#Measures_of_anisotropy_and_diffusivity eigenvectors]. It also determines an anatomical correspondence between DTI and structural MRI images (T2) of the same sample.


== MIPAV DWI pipeline overview ==
{| border="1" cellpadding="5"
 
|+ '''Figure 10. Contour VOI Graph window '''
[[File:DtiPipelineWikiSmall.jpg‎ |400px|thumb|right|MIPAV DTI Pipeline schematic]]
|-
 
| rowspan="1" colspan="3" |
=== Brain MRI introduction ===
[[Image:windowContourVOIGraph.jpg]]
Brain MRI is usually performed with a 1.5- or 3- T MRI machine, with a gradient strength in the range of 20-60 mT/m and a slew rate of 120 T/m/s. Parameters for a single-shot spin-echo echo-planar imaging (EPI) sequence include: a repetition time (TR) of 6000 ms, an echo time (TE) of 100 ms, a field of view (FOV) of 24 cm. These parameters are typically used to obtain 3- to 5-mm axial or coronal sections with a 5-mm intersection gap. The acquisition matrix is usually 96 × 96 with a reconstruction matrix set to 128 × 128. The DWIs are obtained by using 4 linearly increasing b values in 6-7 non-collinear directions (bmax ~ 703-1000 s/mm2). In addition, a T2-weighted (T2W) reference image is obtained without diffusion weighting. Read more: [http://www.ajnr.org/content/26/6/1455.full], [http://radiology.rsna.org/content/217/2/331.full].
|-
 
| rowspan="4" colspan="1" |
=== Determining an anatomical correspondence ===
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
between DTI and structural MRI images of the same sample. In MIPAV we use [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=941749&tag=1 an image-based registration scheme] mainly because i) it doesn't require [http://www.mr-tip.com/serv1.php?type=db1&dbs=High%20Field%20MRI a field map], which is usually not available for DWIs,  and ii) it allows one to correct for artifacts produced by a patient motion. For more information, refer to [http://ee.sharif.edu/~miap/Files/Medical%20Image%20Registration.pdf], [http://www.sciencedirect.com/science/article/pii/S0165027007002270].
| rowspan="1" colspan="2" |
 
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Graph</font>'''</span>-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </div>
At least one of the following images is required as a reference in DTI pipeline:
|-
 
| rowspan="1" colspan="2" |
*'''[http://www.mr-tip.com/serv1.php?type=db1&dbs=T2%20Weighted%20Image T2 image]''' - MIPAV uses the T2 as a reference image because it is usually less distorted and has a higher signal-to-noise ratio (SNR) than DWIs.  
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Save Graph</font>'''</span>-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
|-
| rowspan="3" colspan="1" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delete Function</font>'''</span>-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.</div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Copy Function</font>'''</span>-Copies a function that is currently displayed in the window.</div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</div>
|-
| rowspan="3" colspan="1" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Range to Default</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span></div>
|-
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Graph to Original</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span>. </div>
|-
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help Topics</font>'''</span>-Displays online help topics.</div>
|}


*'''B0''' - which is a DWI volume with no gradient applied. It can be used instead of T2, if T2 is not available.
<br />
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window. <br />
*Right click on the VOI and then select Graph &gt; Boundary Intensity.<br />
*The Contour VOI Graph window (Figure 10) opens.<br />


MIPAV aligns all other images to the reference image (either T2  or B0 volume) by optimizing [[Cost functions used in MIPAV algorithms | the cost function]], which represents the measure of how well the images are spatially aligned.  
'''To generate 3D contour VOI graphs'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window. <br />
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window.<br />
*Right-click on the VOI and then select Graph &gt; Boundary Intensity. <br />
The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary. <br />


'''Note:''' In MIPAV, we use the term "cost function" to refer to [[Cost functions used in MIPAV algorithms |the negative cost function]].
=== Generating intensity graphs ===
Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).<br />


=== MIPAV DTI pipeline outline ===
'''To generate 2D intensity graphs'''<br />
<ol>
1 Open an image.<br />
<li>The user [[DTI pipeline interface#ImportData | uploads a DWI image]] and [http://en.wikipedia.org/wiki/Spin-spin_relaxation_time T2 image] to the pipeline using the Import Data panel. A DWI image can be acquired from many different MRI scanners (including [http://www.healthcare.philips.com/us_en/products/mri/ Philips], [http://www.medical.siemens.com/webapp/wcs/stores/servlet/CategoryDisplay~q_catalogId~e_-1~a_categoryId~e_12754~a_catTree~e_100010,1007660,12754~a_langId~e_-1~a_storeId~e_10001.htm Siemens], [http://www.gehealthcare.com/euen/mri/index.html GE], etc.) and in [[Supported Formats | various formats]]. MIPAV reads the gradient information from the image header, or from the B-matrix file uploaded by the user. The gradient (or B-matrix) information is then displayed in the Gradient table. For the list of image types and how MIPAV reads the header information, refer to [[#ImageTypes | Image Types]] section.</li>
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br /><
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
Select VOI &gt; Graph in the MIPAV window and either of the following:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the VOI region. <br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
Right-click on the VOI and then select Graph and one of the following commands:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
* ''2.5D Total Intensity with Threshold'' -TBD. <br />
* ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.


<li>In the Pre-processing step, the B0 volume in DWI is detected (or entered by user), and then rigidly aligned to the T2 image. The DW image is then registered to rigidly aligned B0 using the[[Optimized automatic registration 3D | Optimized Automatic Registration 3.5 D]] algorithm. These steps are necessary to perform a motion correction and eddy current distortion correction.</li>
{| border="1" cellpadding="5"
 
|+ '''Figure 11. Intensity Graph window '''
<li>In the EPI Distortion Correction step, MIPAV calculates deformation vector fields for rigidly aligned B0 and T2, which came from the Pre-processing step. MIPAV then uses both: the transformation matrices obtained in the Pre-processing step, and deformation vector field values to create a corrected DWI image.</li>
 
<li>MIPAV then calculates a diffusion tensor using pre-processing DWI and the gradient/B-value information  and a mask image uploaded by the user.</li>
 
<li>MIPAV uses the tensor information to create a tensor statistics, including ADC, color map, eigenvalue, eigenvector, FA, RA, and volume ratio images.</li>
 
<li>MIPAV creates a 3D visualization of fiber bundle tracts in the brain's white matter using the information from the previous step. The user can save fiber tracts information as <span style="font-family:courier">[[Image formats descriptions#VtkXml |.vtk]]</span> and <span style="font-family:courier">[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion .dat]</span> files. See also: [[Image formats descriptions]].
</ol>
 
<div id="ImageTypes"></div>
 
== Image types ==
 
{|style="color:black; background-color:#F8F8F8;" border="1" cellpadding="10" class="wikitable"
! align="left"| Image file type
! align="left"| Auto Population of Bvals
! align="left"| Auto Population of Gradients
! align="left"| Auto Population of Bmatrix
! align="left"| Philips Gradient Creator Utility
|-
|-
|Philips PAR/REC V3 &V4
|
|Yes
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
|Yes
|
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Graph</font>'''</span>-Opens a PLT file that contains graph data.</div> <div class="CellBody">When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </div>
|Yes
| rowspan="2" colspan="1" |
[[Image:VOIGRaphMOdifyPointsVis.jpg]]
|-
|-
|Philips PAR/REC 4.1 &4.2
|
|Yes
<div class="CellBody"> </div>
|Yes
|
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Save Graph</font>'''</span>-Saves the graph data in a PLT file. </div> <div class="CellBody">When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</div>
|Yes
|-
|-
|Philips DCM V3 &V4
|
|Yes
<div class="CellBody"> </div>
|Yes
| rowspan="1" colspan="2" |
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</div>
|Yes
|-
|-
|Philips DCM 4.1 &4.2
|
|Yes
<div class="CellBody"> </div>
|Yes
| rowspan="1" colspan="2" |
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
|Yes
|-
|-
|Siemens Mosaic DCM, see also [[#ImportDataOutput | output files]]
|
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
|No
| rowspan="1" colspan="2" |
|Yes
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delete Function</font>'''</span>-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.</div>
|No
|-
|-
|Nifti w/ Philips Par File
|
|Yes
<div class="CellBody"> </div>
|Yes
| rowspan="1" colspan="2" |
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</div>
|Yes
|-
|-
|GE DCM
|
|Yes
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
|Yes
| rowspan="1" colspan="2" |
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</div>
|No
|-
|-
!align="left"|Text File Type
|
!align="left"| Auto Population of Bvals
<div class="CellBody"> </div>
!align="left"| Auto Population of Gradients
| rowspan="1" colspan="2" |
!align="left"| Auto Population of Bmatrix
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Range to Default</font>'''</span>-TBD.</div>
!align="left"| Philips Gradient Creator Utility
|-
|-
|fslBvalGrad.txt
|
|Yes
<div class="CellBody"> </div>
|Yes
| rowspan="1" colspan="2" |
|No
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Graph to Original</font>'''</span>-TBD.</div>
|No
|-
|dtiStudioBvalGrad.txt
|Yes
|Yes
|No
|No
|-
|mipavStandardBvalGrad.txt
|Yes
|Yes
|No
|No
|-
|dcm2nii.bvec
|Yes
|Yes
|No
|No
|-
|fslBmatrix.txt
|No
|No
|Yes
|No
|-
|mipavStandardBmatrix.txt
|No
|No
|Yes
|No
|-
|-
|
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
| rowspan="1" colspan="2" |
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help Topics</font>'''</span>-Displays online help topics.</div>
|}
|}


== MIPAV DTI pipeline interface ==
'''To generate 3D intensity graphs of all slices in a dataset at a specific point'''<br />
1 Open an image.<br />
2 Draw a point VOI on the image (Figure 12).<br />
3 Select the VOI.<br />
4 Do one of the following:<br />
*Select the Propagate VOI to all slices icon.<br />
*Select VOI &gt; Propagate &gt; To All Slices. <br />
*Right-click on the VOI, then select Propagate &gt; To All Slices (Figure 12).<br />
5 Right-click on the VOI and select Show VOI Graph (Figure 12).<br />


''Main article: [[DTI pipeline interface]].''
{| border="1" cellpadding="5"
|+ '''Figure 12. Point VOI'''
|-
|
<div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000">  <br /></font></div>


The MIPAV DTI Pipeline interface contains 6 tabs:
<br clear="all" />


*In the [[DTI pipeline interface#ImportData |Import Data]] the user uploads DW and T2 image (optional), and the gradient information (optional). MIPAV could also read the gradient information from the image header. The Phillips Gradient Creator will then calculate the gradient table based on the information provided.
{|
*In the [[DTI pipeline interface#PreProcessing | Pre-processing tab]], the user is asked to specify the parameters required for aligning B0 to T2, and then DWI to the rigidly aligned B0, and also parameters for motion correction and eddy current distortion correction.
|
* In the [[DTI pipeline interface #EPIDistortionCorrection | EPI Distortion Correction]], the user enters parameters needed for calculation of deformation vector fields for rigidly aligned B0 and T2 from the Pre-processing step.  
[[Image:PointVOIPropagate.jpg]]
* In the [[DTI pipeline interface #TensorEstimation |Tensor Estimation tab]], the user uploads the mask image, selects the tensor estimation algorithm and specifies the output options.
|}
* In the [[DTI pipeline interface#TensorStatistics |Tensor Statistics]] the user can upload the tensor image and specify which kind of images (e.g. ADC, color map, Eigen value, Eigen vector, FA, RA, and Volume Ratio) he/she would like to have as an output.
* In the [[DTI pipeline interface#VisualizationTab |Visualization]], the user can  upload images needed for a 3D visualization of fiber bundle tracts in the brain's white matter using the provided information. The user can then save fiber tracts information as [[Image formats descriptions#VtkXml |.vtk and .dat]] files.
 
== DTI Pipeline Tutorials ==
 
Refer to [[DTI Pipeline Tutorials]].


TBD.
'''To generate 3D intensity graphs of specific areas'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon.<br />
3 Select the VOI. Then, do one of the following:<br />
*a Select VOI &gt; Graph and either of the following in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
*b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
** ''2.5D Total Intensity with Threshold'' -TBD.<br />
** ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.<br />


== See also: ==
*[[Understanding MIPAV capabilities]]
*[[Developing new tools using the API]]
*[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]]
*[[Cost functions used in MIPAV algorithms]]
*[[Interpolation methods used in MIPAV]]
*[[DTI Color Display]]
*[[DTI Estimate tensor]]
*[[Optimized automatic registration 3D]]


[[Category:Help:Stub]]
[[Customizing the appearance of graphs - Modify graph dialog box]]
[[Category:Help:Algorithms]]

Revision as of 20:22, 21 February 2012

MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"

Generating contour VOI graphs

Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs.

To generate 2D contour VOI graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.


Figure 10. Contour VOI Graph window

WindowContourVOIGraph.jpg

File
Open Graph-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.
Save Graph-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.
Copy Function-Copies a function that is currently displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-[TBD]
Reset Graph to Original-[TBD].
Help
Help Topics-Displays online help topics.


3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right click on the VOI and then select Graph > Boundary Intensity.
  • The Contour VOI Graph window (Figure 10) opens.

To generate 3D contour VOI graphs
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window.
3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right-click on the VOI and then select Graph > Boundary Intensity.

The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary.

Generating intensity graphs

Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).

To generate 2D intensity graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.
< 3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:
Select VOI > Graph in the MIPAV window and either of the following:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the VOI region.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.

Right-click on the VOI and then select Graph and one of the following commands:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • 2.5D Total Intensity with Threshold -TBD.
  • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.

Figure 11. Intensity Graph window
File
Open Graph-Opens a PLT file that contains graph data.
When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.

VOIGRaphMOdifyPointsVis.jpg

Save Graph-Saves the graph data in a PLT file.
When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-TBD.
Reset Graph to Original-TBD.
Help
Help Topics-Displays online help topics.

To generate 3D intensity graphs of all slices in a dataset at a specific point
1 Open an image.
2 Draw a point VOI on the image (Figure 12).
3 Select the VOI.
4 Do one of the following:

  • Select the Propagate VOI to all slices icon.
  • Select VOI > Propagate > To All Slices.
  • Right-click on the VOI, then select Propagate > To All Slices (Figure 12).

5 Right-click on the VOI and select Show VOI Graph (Figure 12).

Figure 12. Point VOI


PointVOIPropagate.jpg

To generate 3D intensity graphs of specific areas
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon.
3 Select the VOI. Then, do one of the following:

  • a Select VOI > Graph and either of the following in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
    • 2.5D Total Intensity with Threshold -TBD.
    • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.


Customizing the appearance of graphs - Modify graph dialog box

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