Difference between revisions of "Documentation/4.0/Modules/PETStandardUptakeValueComputation"

From Slicer Wiki
Jump to: navigation, search
(Created page with '<!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- ---------------------------- --> <!-- ---------------------------- --> {{doc…')
 
(Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887)
 
(12 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 +
<noinclude>{{documentation/versioncheck}}</noinclude>
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-header}}
 
{{documentation/{{documentation/version}}/module-header}}
Line 8: Line 9:
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
 
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
Author: FIRSTNAME LASTNAME, AFFILIATION<br>
+
Author: Wendy Plesniak, SPL<br>
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
+
Contributor1: Ron Kikinis, SPL<br>
Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
+
Contributor2: Nicole Aucoin, SPL<br>
Contact: FIRSTNAME LASTNAME, <email>john@doe.org</email><br>
+
Contact: Wendy Plesniak, <email>wjp@bwh.harvard.edu</email><br>
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-isomics.png|Isomics, Inc. <- Replace this logo with yours
+
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
|Image:Logo-splnew.jpg|Surgical Planning Laboratory  <-Replace this logo with yours
+
|Image:NAMIC 380x463.jpg|NA-MIC
 
}}
 
}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
  
<!-- ----------------------------------------------------------------- -->
+
<!-- ---------------------------- -->
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION -->
+
{{documentation/{{documentation/version}}/module-section|Module Description}}
<!-- ----------------------------------------------------------------- -->
+
Computes the standardized uptake value based on body weight.  
{{note}}The section above is generated using the following wiki code:
+
[[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] gives more details on the algorithm.
<pre>
 
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
 
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
 
Author: FIRSTNAME LASTNAME, AFFILIATION<br>
 
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
 
Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
 
Contact: FIRSTNAME LASTNAME, <email>john@doe.org</email><br>
 
{{documentation/{{documentation/version}}/module-introduction-row}}
 
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
 
|Image:Logo-isomics.png|Isomics, Inc. <- Replace this logo with yours
 
|Image:Logo-splnew.jpg|Surgical Planning Laboratory  <-Replace this logo with yours
 
}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
 
</pre>
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
  
 +
{{documentation/{{documentation/version}}/module-description}}
  
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
{{documentation/{{documentation/version}}/module-section|Module Description}}
+
{{documentation/{{documentation/version}}/module-section|Use Cases}}
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
 
  
<!-- ----------------------------------------------------------------- -->
+
This command line module was developed for a special use case in which many different VOIs were specified on the fused structural and PET images; SUV maximum, SUV minimum, SUV mean were computed for each of these labels and the resulting quanitative measures were output to a comma-separated value (csv) file of the user's choosing.  
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION -->
 
<!-- ----------------------------------------------------------------- -->
 
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre>
 
  
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
+
Since various study parameters for the datasets are required for these measurements, a pointer to the DICOM directory is also provided to the computation.
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>
 
  
Using this later template, the final syntax would be:
+
This module does not visualize the functional and structural dataset. Instead, it saves all measurements to the csv file as well as showing the following quantitative measures in Slicer's interface: label name, label value, SUV max, SUV mean, SUV minimum.
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
  
 
+
{|
<!-- ---------------------------- -->
+
|[[Image:Slicer4-SUV-1.jpeg|thumb|280px|PET and CT volumes with SUV computation]]
{{documentation/{{documentation/version}}/module-section|Use Cases}}
+
|}
Most frequently used for these scenarios:
 
 
 
* Use Case 1:
 
* Use Case 2:
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
Line 78: Line 48:
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
  
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
+
{|
 
+
|[[Image:Slicer4-SUV-2.jpeg|thumb|280px|GUI]]
{|style="width: 100%"
+
|{{documentation/{{documentation/version}}/module-parametersdescription}}
|
 
* Input panel1:
 
** First input
 
** Second input
 
* Parameters panel:
 
** First parameter
 
** Second parameter
 
* Output panel:
 
** First output
 
** Second output
 
* Viewing panel:
 
| align="right" |
 
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
 
|-
 
|
 
* Input panel2:
 
** First input
 
** Second input
 
* Parameters panel:
 
** First parameter
 
** Second parameter
 
* Output panel:
 
** First output
 
** Second output
 
* Viewing panel:
 
| align="right" |
 
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
 
 
|}
 
|}
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality
+
* The Slicer3 PETCTFusion module formed the basis of this module.
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
+
Publications related to this module:
For extensions: link to the source code repository and additional documentation
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
+
{{documentation/{{documentation/version}}/module-developerinfo}}
 
 
 
 
<!-- ----------------------------------------------------------------- -->
 
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION -->
 
<!-- ----------------------------------------------------------------- -->
 
{{note}}The section above is generated using the following wiki code:
 
<pre>
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
 
</pre>
 
 
 
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre>
 
 
 
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
 
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>
 
 
 
Using this later template, the final syntax would be:
 
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
<!-- ----------------------------------------------------------------- -->
 
  
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
{{documentation/{{documentation/version}}/module-footer|category=Example}}
+
{{documentation/{{documentation/version}}/module-footer}}
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Latest revision as of 07:33, 14 June 2013

Home < Documentation < 4.0 < Modules < PETStandardUptakeValueComputation

For the latest Slicer documentation, visit the 4.10 page.


Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Wendy Plesniak, SPL
Contributor1: Ron Kikinis, SPL
Contributor2: Nicole Aucoin, SPL
Contact: Wendy Plesniak, <email>wjp@bwh.harvard.edu</email>

Surgical Planning Laboratory  
NA-MIC  

Module Description

Computes the standardized uptake value based on body weight. references gives more details on the algorithm.

Computes the standardized uptake value based on body weight. Takes an input PET image in DICOM and NRRD format (DICOM header must contain Radiopharmaceutical parameters). Produces a CSV file that contains patientID, studyDate, dose, labelID, suvmin, suvmax, suvmean, labelName for each volume of interest. It also displays some of the information as output strings in the GUI, the CSV file is optional in that case. The CSV file is appended to on each execution of the CLI.


Use Cases

This command line module was developed for a special use case in which many different VOIs were specified on the fused structural and PET images; SUV maximum, SUV minimum, SUV mean were computed for each of these labels and the resulting quanitative measures were output to a comma-separated value (csv) file of the user's choosing.

Since various study parameters for the datasets are required for these measurements, a pointer to the DICOM directory is also provided to the computation.

This module does not visualize the functional and structural dataset. Instead, it saves all measurements to the csv file as well as showing the following quantitative measures in Slicer's interface: label name, label value, SUV max, SUV mean, SUV minimum.

PET and CT volumes with SUV computation

Tutorials

Links to tutorials that use this module

Panels and their use

GUI
Parameters:
  • Image and Information
    • PET DICOM volume path: Input path to a directory containing a PET volume containing DICOM header information for SUV computation
    • Input PET Volume: Input PET volume for SUVbw computation (must be the same volume as pointed to by the DICOM path!).
    • Input VOI Volume: Input label volume containing the volumes of interest
  • Output
    • Output (csv) file: A file holding the output SUV values in comma separated lines, one per label. Optional.
    • Output Label: List of labels for which SUV values were computed
    • Output Label Value: List of label values for which SUV values were computed
    • SUV Max: SUV max for each label
    • SUV Mean: SUV mean for each label
    • SUV Minimum: SUV minimum for each label

Similar Modules

  • The Slicer3 PETCTFusion module formed the basis of this module.

References

Publications related to this module:

Information for Developers