Caret:Documentation:CaretNiftiExtension

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Caret's NIFTI Volume File Extension

Caret add's an extension to the NIFTI volume file. The extension is in XML and described below.

The extension code for Caret is 30.

XML Tags in the Caret Extension

  • CaretExtension - The root tag.
    • Comment - A comment associated with the file.
    • Date - The date and time of when the file was written. This is in ISO Format.
    • Volume Information - There is one Volume Information element for each volume stored in the NIFTI Volume File. The attribute Index indicates the index of the Volume that this data is associated.
      • Comment - A comment associated with the volume the that may be entered by the user in Caret's Graphical User Interface.
      • GuiLabel - A label displayed in the Graphical User Interface that the user uses to select the associated volume for display or other operations.
      • LabelTable - This optional element is present if the Volume contains label data. It is a GIFTI LabelTable element.
      • PaletteColorMapping - This optional element describes how voxels are mapped to colors using a color palette.
      • StudyMetaDataLinkSet - A link into Caret's StudyMetaData File.
      • VolumeType - The type of volume. Possible values are Anatomy, Functional, Label, RGB, Segmentation, and Vector.

Example of the Caret Extension

<CaretExtension>
   <Comment>Written by John</Comment>
   <Date><![CDATA[2010-02-05T12:15:07]]></Date>   
   <VolumeInformation Index="0">      
      <Comment><![CDATA[Created by CARET]]></Comment>      
      <GuiLabel><![CDATA[brodmann]]></GuiLabel>
      <LabelTable>   
         <Label Index="0" Red="0.667" Green="0.667" Blue="0.667" Alpha="0.000"><![CDATA[???]]></Label>   
         <Label Index="1" Red="0.667" Green="0.667" Blue="0.667" Alpha="1.000"><![CDATA[???_not_used]]></Label>
         <Label Index="2" Red="0.784" Green="0.882" Blue="1.000" Alpha="1.000"><![CDATA[LOBE.TEMPORAL]]></Label>
         <Label Index="3" Red="0.706" Green="0.706" Blue="0.941" Alpha="1.000"><![CDATA[LOBE.LIMBIC]]></Label>
         <Label Index="4" Red="1.000" Green="0.784" Blue="0.784" Alpha="1.000"><![CDATA[LOBE.OCCIPITAL]]></Label>
         <Label Index="5" Red="0.784" Green="1.000" Blue="0.784" Alpha="1.000"><![CDATA[LOBE.PARIETAL]]></Label>   
         <Label Index="6" Red="1.000" Green="0.902" Blue="0.784" Alpha="1.000"><![CDATA[LOBE.FRONTAL]]></Label>   
         <Label Index="7" Red="1.000" Green="0.902" Blue="0.784" Alpha="1.000"><![CDATA[CUT]]></Label>
      </LabelTable>
      <StudyMetaDataLinkSet>
         <StudyMetaDataLink>
            <pubMedID><![CDATA[ProjID20071119100596200000]]></pubMedID>
            <tableNumber><![CDATA[]]></tableNumber>            
            <tableSubHeaderNumber><![CDATA[]]></tableSubHeaderNumber>
            <figureNumber><![CDATA[]]></figureNumber>
            <panelNumberOrLetter><![CDATA[]]></panelNumberOrLetter>
            <pageReferencePageNumber><![CDATA[]]></pageReferencePageNumber>
            <pageReferenceSubHeaderNumber><![CDATA[]]></pageReferenceSubHeaderNumber>
         </StudyMetaDataLink>      
      </StudyMetaDataLinkSet>
      <PaletteColorMapping Version="1">
        <ScaleMode>MODE_AUTO_SCALE</ScaleMode>
        <AutoScalePercentageValues>98.0 2.0 2.0 98.0</AutoScalePercentageValues>
        <UserScaleValues>-100.0 0.0 0.0 100.0</UserScaleValues>
        <PaletteName>PSYCH</PaletteName>
        <InterpolatePalette>false</InterpolatePalette>
        <DisplayPositiveData>true</DisplayPositiveData>
        <DisplayZeroData>false</DisplayZeroData>
        <DisplayNegativeData>true</DisplayNegativeData>
        <ThresholdTest>THRESHOLD_TEST_LESS_THAN</ThresholdTest>
        <ThresholdType>THRESHOLD_TYPE_OFF</ThresholdType>
        <ThresholdFailureInGreen>false</ThresholdFailureInGreen>
        <ThresholdNormalValues>-1.0 1.0</ThresholdNormalValues>
        <ThresholdMappedValues>-1.0 1.0</ThresholdMappedValues>
        <ThresholdMappedAvgAreaValues>-1.0 1.0</ThresholdMappedAvgAreaValues>
        <ThresholdDataName>Label.nii.gz</ThresholdDataName>
      </PaletteColorMapping>
      <VolumeType>Label</VolumeType>   
   </VolumeInformation>
</CaretExtension>
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