Difference between revisions of "Standard tasks provided through commands on the Utilities menu"

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=== Standard tasks provided through commands on the Utilities menu ===
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MIPAV provides a number of utilities that you can use to perform standard image-processing tasks such as converting image datasets to another image type, transforming images by copying, cropping, or rotating them, and changing image datasets by adding, removing, or reordering slices. To perform more complex tasks, MIPAV provides algorithms, which are covered in Volume 2 of the ''User's Guide''. This chapter explores the standard tasks.
  
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MIPAV provides a number of utilities that you can use to perform standard image-processing tasks such as converting image datasets to another image type, transforming images by copying, cropping, or rotating them, and changing image datasets by adding, removing, or reordering slices. To perform more complex tasks, MIPAV provides algorithms, which are covered in Volume 2 of the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">User's Guide.</font>''</span> This chapter explores the standard tasks.
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To access the standard image-processing tasks, you use the commands (refer to Table 1) on the Utilities menu in the MIPAV window.
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To access the standard image-processing tasks, you use the commands (refer to [MIPAV_Utilities.html#1221581 Table 2]) on the Utilities menu in the MIPAV window.
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<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">
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{| border="1" cellpadding="5"
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|+  <div class="TableTitle">Table 2. Standard tasks provided through commands on the Utilities menu in the MIPAV window </div>
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|+  <div class="TableTitle">Table 1.  Standard tasks provided through commands on the Utilities menu in the MIPAV window </div>
 
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<div class="CellBody">[MIPAV_Utilities.html#1189490 "Converting 3D to 4D images and vise versa" ]</div>
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<div class="CellBody">"Converting 3D to 4D images and vise versa" </div>
 
|
 
|
 
<div class="CellBody">Convert 3D to 4D</div>
 
<div class="CellBody">Convert 3D to 4D</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
 
<div class="CellBody">Convert 4D to 3D</div>
 
<div class="CellBody">Convert 4D to 3D</div>
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|-
 
|-
 
|
 
|
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<div class="CellBody">[MIPAV_Utilities.html#1189822 "Convert 4D to RGB" ]</div>
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<div class="CellBody">"Convert 4D to RGB"</div>
 
|
 
|
 
<div class="CellBody">Convert 4D to RGB</div>
 
<div class="CellBody">Convert 4D to RGB</div>
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|-
 
|-
 
|
 
|
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<div class="CellBody">[MIPAV_Utilities.html#1199862 "Extracting 3D subset from 4D" ]</div>
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<div class="CellBody">"Extracting 3D subset from 4D" </div>
 
|
 
|
 
<div class="CellBody">Extracting 3D Subset from 4D</div>
 
<div class="CellBody">Extracting 3D Subset from 4D</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1189690 "Removing time volumes" ]</div>
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<div class="CellBody">"Removing time volumes" </div>
 
|
 
|
 
<div class="CellBody">Remove Time Volumes</div>
 
<div class="CellBody">Remove Time Volumes</div>
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|-
 
|-
 
|
 
|
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<div class="CellBody">[MIPAV_Utilities.html#1213913 [MIPAV_Utilities.html#1213913 "Swapping the third and fourth dimensions" ]]</div>
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<div class="CellBody">"Swapping the third and fourth dimensions" </div>
 
|
 
|
 
<div class="CellBody">Swap DIMS 3 &lt;-&gt; 4</div>
 
<div class="CellBody">Swap DIMS 3 &lt;-&gt; 4</div>
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|-
 
|-
 
|
 
|
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<div class="CellBody">[MIPAV_Utilities.html#1203929 "Adding image margins" ]</div>
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<div class="CellBody">"Adding image margins"</div>
 
|
 
|
 
<div class="CellBody">Add Image Margins</div>
 
<div class="CellBody">Add Image Margins</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1006484 Copying images]</div>
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<div class="CellBody">Copying images</div>
 
|
 
|
 
<div class="CellBody">Clone (copy)</div>
 
<div class="CellBody">Clone (copy)</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1165547 "Converting image datasets to different data types" ]</div>
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<div class="CellBody">"Converting image datasets to different data types" </div>
 
|
 
|
 
<div class="CellBody">Convert Type</div>
 
<div class="CellBody">Convert Type</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1166931 "Converting grayscale images to RGB images" ]</div>
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<div class="CellBody">"Converting grayscale images to RGB images" </div>
 
|
 
|
 
<div class="CellBody">Grays to RGB</div>
 
<div class="CellBody">Grays to RGB</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1167348 "Converting RGB datasets to grayscale datasets" ]</div>
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<div class="CellBody">"Converting RGB datasets to grayscale datasets"</div>
 
|
 
|
 
<div class="CellBody">RGB to Gray</div> <div class="CellBody">RGB to Grays</div> <div class="CellBody">RGB to HSB</div>
 
<div class="CellBody">RGB to Gray</div> <div class="CellBody">RGB to Grays</div> <div class="CellBody">RGB to HSB</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1169542 "Correcting image spacing" ]</div>
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<div class="CellBody">"Correcting image spacing"</div>
 
|
 
|
 
<div class="CellBody">Correct Image Spacing</div>
 
<div class="CellBody">Correct Image Spacing</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1172273 "Cropping images" ]</div>
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<div class="CellBody">"Cropping images"</div>
 
|
 
|
 
<div class="CellBody">Crop Using Parameters</div> <div class="CellBody">Crop using VOI</div>
 
<div class="CellBody">Crop Using Parameters</div> <div class="CellBody">Crop using VOI</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1173255 "Masking (filling) images" ]</div>
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<div class="CellBody">"Masking (filling) images"</div>
 
|
 
|
 
<div class="CellBody">Fill Image</div>
 
<div class="CellBody">Fill Image</div>
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|-
 
|-
 
| rowspan="1" colspan="8" |
 
| rowspan="1" colspan="8" |
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<div class="CellHeading">[MIPAV_Utilities.html#1173868 "Flipping images" ]</div>
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<div class="CellHeading">"Flipping images"</div>
 
|-
 
|-
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"></div>
 
|
 
|
 
<div class="CellBody">Flip &gt; Horizontal</div>
 
<div class="CellBody">Flip &gt; Horizontal</div>
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|-
 
|-
 
|
 
|
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<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
 
<div class="CellBody">Flip &gt; Vertical</div>
 
<div class="CellBody">Flip &gt; Vertical</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
 
<div class="CellBody">Flip&gt;In Depth (invert slice order)</div>
 
<div class="CellBody">Flip&gt;In Depth (invert slice order)</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1207373 "Image Calculator" ]</div>
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<div class="CellBody">"Image Calculator"</div>
 
|
 
|
 
<div class="CellBody">Image Calculator</div>
 
<div class="CellBody">Image Calculator</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1296428 "Image Calculator-Bulk Images" ]</div>
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<div class="CellBody">"Image Calculator-Bulk Images"</div>
 
|
 
|
 
<div class="CellBody">Image Calculator-Bulk Images</div>
 
<div class="CellBody">Image Calculator-Bulk Images</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1177106 "Image Math" ]</div>
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<div class="CellBody">"Image Math"</div>
 
|
 
|
 
<div class="CellBody">Image Math</div>
 
<div class="CellBody">Image Math</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1180508 "Inverting the image" ]</div>
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<div class="CellBody">"Inverting the image"</div>
 
|
 
|
 
<div class="CellBody">Invert</div>
 
<div class="CellBody">Invert</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1180988 "Matching images" ]</div>
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<div class="CellBody">"Matching images"</div>
 
|
 
|
 
<div class="CellBody">Match Images</div>
 
<div class="CellBody">Match Images</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1182119 "Adding noise to images" ]</div>
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<div class="CellBody">"Adding noise to images"</div>
 
|
 
|
 
<div class="CellBody">Noise</div>
 
<div class="CellBody">Noise</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1204487 "Pad" ]</div>
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<div class="CellBody">"Pad" </div>
 
|
 
|
 
<div class="CellBody">Pad</div>
 
<div class="CellBody">Pad</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1182469 "Quantify Mask" ]</div>
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<div class="CellBody">"Quantify Mask"</div>
 
|
 
|
 
<div class="CellBody">Quantify Using Mask</div> <div class="CellBody">Quantify Mask(s)</div>
 
<div class="CellBody">Quantify Using Mask</div> <div class="CellBody">Quantify Mask(s)</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1184590 "Replacing pixel/voxel value in images" ]</div>
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<div class="CellBody">"Replacing pixel/voxel value in images"</div>
 
|
 
|
 
<div class="CellBody">Replace Pixe/Voxel Value</div>
 
<div class="CellBody">Replace Pixe/Voxel Value</div>
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|-
 
|-
 
| rowspan="6" colspan="1" |
 
| rowspan="6" colspan="1" |
−
<div class="CellBody">[MIPAV_Utilities.html#1185153 ][MIPAV_Utilities.html#1185153 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">"Rotating images" </font>'''</span>]</div>
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">"Rotating images" </font>'''</span></div>
 
|
 
|
 
<div class="CellBody">Rotate -&gt; X axis 90</div>
 
<div class="CellBody">Rotate -&gt; X axis 90</div>
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<div class="CellBody">Rotate -&gt; X axis <br />-90</div>
 
<div class="CellBody">Rotate -&gt; X axis <br />-90</div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"></div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"></div>
 
|
 
|
−
<div class="CellBody">Â </div>
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<div class="CellBody"> </div>
 
|-
 
|-
 
|
 
|
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1183350 "Concatenating images" ]</div>
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<div class="CellBody"> "Concatenating images"</div>
 
|
 
|
 
<div class="CellBody">Concatenate</div>
 
<div class="CellBody">Concatenate</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1186732 "Extracting slices/volumes" ]</div>
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<div class="CellBody">"Extracting slices/volumes"</div>
 
|
 
|
 
<div class="CellBody">Extract Slices/Volumes</div>
 
<div class="CellBody">Extract Slices/Volumes</div>
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|-
 
|
 
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−
<div class="CellBody">[MIPAV_Utilities.html#1006827 "Insert Missing Slices" ]</div>
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<div class="CellBody">"Insert Missing Slices" </div>
 
|
 
|
 
<div class="CellBody">Insert Missing Slices</div>
 
<div class="CellBody">Insert Missing Slices</div>
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|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1189070 "Inserting slices into image datasets" ]</div>
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<div class="CellBody">"Inserting slices into image datasets" </div>
 
|
 
|
 
<div class="CellBody">Insert Slice</div>
 
<div class="CellBody">Insert Slice</div>
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|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1189065 "Pad slices to power of 2" ]</div>
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<div class="CellBody">"Pad slices to power of 2"</div>
 
|
 
|
 
<div class="CellBody">Pad Slices to power of 2</div>
 
<div class="CellBody">Pad Slices to power of 2</div>
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|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1188247 [MIPAV_Utilities.html#1188135 "Randomizing image (slice) order" ]]</div>
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<div class="CellBody">"Randomizing image (slice) order" </div>
 
|
 
|
 
<div class="CellBody">Randomize Slice Order</div>
 
<div class="CellBody">Randomize Slice Order</div>
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|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1188247 "Removing images (slices) from datasets" ]</div>
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<div class="CellBody">"Removing images (slices) from datasets" </div>
 
|
 
|
 
<div class="CellBody">Remove Slices</div>
 
<div class="CellBody">Remove Slices</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1187813 "Replace blanks with averages" ]</div>
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<div class="CellBody">"Replace blanks with averages" </div>
 
|
 
|
 
<div class="CellBody">Replace blanks with averages</div>
 
<div class="CellBody">Replace blanks with averages</div>
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|-
 
|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1200790 "Replace Slices" ]</div>
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<div class="CellBody">"Replace Slices"</div>
 
|
 
|
 
<div class="CellBody">Replace Slices</div>
 
<div class="CellBody">Replace Slices</div>
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|-
 
|
 
|
−
<div class="CellBody">[MIPAV_Utilities.html#1201306 "Subtract VOI Background" ]</div>
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<div class="CellBody">"Subtract VOI Background"</div>
 
|
 
|
 
<div class="CellBody">Subtract VOI background</div>
 
<div class="CellBody">Subtract VOI background</div>
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<br /></font></div><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><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><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>
 
  
  
 
[[Recording utilities usage with the history feature]]
 
[[Recording utilities usage with the history feature]]

Latest revision as of 17:29, 22 February 2012

MIPAV provides a number of utilities that you can use to perform standard image-processing tasks such as converting image datasets to another image type, transforming images by copying, cropping, or rotating them, and changing image datasets by adding, removing, or reordering slices. To perform more complex tasks, MIPAV provides algorithms, which are covered in Volume 2 of the User's Guide. This chapter explores the standard tasks.

To access the standard image-processing tasks, you use the commands (refer to Table 1) on the Utilities menu in the MIPAV window.

Table 1. Standard tasks provided through commands on the Utilities menu in the MIPAV window

Task
Command
Scalar*
RGB
2D
3D
4D
2D
3D
4D
4D
"Converting 3D to 4D images and vise versa"
Convert 3D to 4D
N
Y
N
N
Y
N
Convert 4D to 3D
N
N
Y
N
N
Y
"Convert 4D to RGB"
Convert 4D to RGB
N
N
Y
N
Y
Y
"Extracting 3D subset from 4D"
Extracting 3D Subset from 4D
N
N
Y
N
N
Y
"Removing time volumes"
Remove Time Volumes
N
N
Y
N
N
Y
"Swapping the third and fourth dimensions"
Swap DIMS 3 <-> 4
N
N
Y
N
N
Y
"Adding image margins"
Add Image Margins
Y
Y
Y
Y
Y
Y
Copying images
Clone (copy)
Y
Y
Y
Y
Y
Y
Conversion Tools
"Converting image datasets to different data types"
Convert Type
Y
Y
Y
N
N
N
"Converting grayscale images to RGB images"
Grays to RGB
Y
Y
Y
N
N
N
"Converting RGB datasets to grayscale datasets"
RGB to Gray
RGB to Grays
RGB to HSB
N
N
N
Y
Y
Y
"Correcting image spacing"
Correct Image Spacing
N
Y
Y
N
N
N
"Cropping images"
Crop Using Parameters
Crop using VOI
Y
Y
Y
Y
Y
Y
"Masking (filling) images"
Fill Image
Y
Y
N
Y
Y
N
"Flipping images"
Flip > Horizontal
Y
Y
Y
Y
Y
Y
Flip > Vertical
Y
Y
Y
Y
Y
Y
Flip>In Depth (invert slice order)
N
Y
Y
N
Y
Y
"Image Calculator"
Image Calculator
Y
Y
Y
Y
Y
Y
"Image Calculator-Bulk Images"
Image Calculator-Bulk Images
Y
Y
Y
Y
Y
Y
"Image Math"
Image Math
Y
Y
Y
Y
Y
Y
"Inverting the image"
Invert
Y
Y
Y
Y
Y
Y
"Matching images"
Match Images
Y
Y
N
Y
Y
N
"Adding noise to images"
Noise
Y
Y
N
Y
Y
N
"Pad"
Pad
Y
Y
N
Y
Y
N
"Quantify Mask"
Quantify Using Mask
Quantify Mask(s)
Y
Y
Y
N
N
N
"Replacing pixel/voxel value in images"
Replace Pixe/Voxel Value
Y
Y
Y
Y
Y
Y
"Rotating images"
Rotate -> X axis 90
Y
Y
Y
Y
Y
Y
Rotate -> X axis
-90
Rotate.> Y axis -90
Y
Y
Y
Y
Y
Y
Rotate -> Y axis 90
Y
Y
Y
Y
Y
Y
Rotate -> Z axis 90
Y
Y
Y
Y
Y
Y
Rotate -> Z axis
-90
Y
Y
Y
Y
Y
Y
Slice Tools
"Concatenating images"
Concatenate
Y
Y
Y
Y
Y
Y
"Extracting slices/volumes"
Extract Slices/Volumes
N
Y
Y
N
Y
Y
"Insert Missing Slices"
Insert Missing Slices
N
Y
Y
N
Y
Y
"Inserting slices into image datasets"
Insert Slice
N
Y
Y
N
Y
Y
"Pad slices to power of 2"
Pad Slices to power of 2
N
Y
Y
N
N
N
"Randomizing image (slice) order"
Randomize Slice Order
N
Y
Y
N
Y
Y
"Removing images (slices) from datasets"
Remove Slices
N
Y
Y
N
Y
Y
"Replace blanks with averages"
Replace blanks with averages
N
Y
Y
N
N
N
"Replace Slices"
Replace Slices
N
Y
Y
N
Y
Y
"Subtract VOI Background"
Subtract VOI background
Y
Y
Y
Y
Y
Y
*Scalar includes the following image types: boolean, byte, unsigned byte, short, unsigned short, integer, long, float, and double.


Recording utilities usage with the history feature

Retrieved from "http://mipav.cit.nih.gov/pubwiki/index.php?title=Standard_tasks_provided_through_commands_on_the_Utilities_menu&oldid=42389"