Package com.xinapse.image.template

Class HeadTemplate

java.lang.Object
com.xinapse.image.template.HeadTemplate
public abstract class HeadTemplate extends Object
Access to the built-in and head template images. Some of these templates are from the Montreal Neurological Institute, and are copyrighted. The following copyright notice is provided as a condition of inclusion in this software package.

Copyright © 1993—2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided “as is” without express or implied warranty. The authors are not responsible for any data loss, equipment damage, property loss, or injury to subjects or patients resulting from the use or misuse of this software package.

  • Field Details

    • MS_PD_IMAGE_NAME

      public static final String MS_PD_IMAGE_NAME
      The name of the proton-density-weighted MS template image.
      See Also:

  • Method Details

    • getMSPDHeadTemplate

      public static WritableImage getMSPDHeadTemplate(boolean reverseSlices) throws IOException
      Returns the built-in proton density weighted head template image.
      Parameters:
      reverseSlices - if the image should be returned with the slice order reversed.
      Returns:
      the built-in proton density weighted template image.
      Throws:
      IOException - if the template image cannot be read.

    • getMSLesionProbTemplate

      public static WritableImage getMSLesionProbTemplate(boolean reverseSlices) throws IOException
      Returns the built-in MS lesion probability template image.
      Parameters:
      reverseSlices - if the image should be returned with the slice order reversed.
      Returns:
      the built-in MS lesion probability template image.
      Throws:
      IOException - if the template image cannot be read.

    • getMSLesionCorrelTemplate

      public static WritableImage getMSLesionCorrelTemplate(boolean reverseSlices) throws IOException
      Returns the built-in MS lesion correlation template image.
      Parameters:
      reverseSlices - if the image should be returned with the slice order reversed.
      Returns:
      the built-in MS lesion correlation template image.
      Throws:
      IOException - if the template image cannot be read.

    • getTemplateImage

      public static WritableImage getTemplateImage(WeightingType weightingType) throws IOException
      Returns the a built-in template image of the specified weighting type.
      Parameters:
      weightingType - the type of image weighting for the template.
      Returns:
      the built-in template image.
      Throws:
      IOException - if the template image cannot be read.

    • getGMProbTemplate

      public static WritableImage getGMProbTemplate() throws IOException
      Returns the built-in grey-matter probability template image.
      Returns:
      the built-in grey-matter probability template image.
      Throws:
      IOException - if the greay-matter probability image cannot be read.

    • getWMProbTemplate

      public static WritableImage getWMProbTemplate() throws IOException
      Returns the built-in white-matter probability template image.
      Returns:
      the built-in white-matter probability template image.
      Throws:
      IOException - if the white-matter probability image cannot be read.

    • getCSFProbTemplate

      public static WritableImage getCSFProbTemplate() throws IOException
      Returns the built-in csf probability template image.
      Returns:
      the built-in csf probability template image.
      Throws:
      IOException - if the csf probability image cannot be read.

    • getLVProbTemplate

      public static WritableImage getLVProbTemplate() throws IOException
      Returns the built-in lateral ventricle probability template image.
      Returns:
      the built-in lateral ventricle probability template image.
      Throws:
      IOException - if the lateral ventricle probability image cannot be read.

    • getLesionProbTemplate

      public static WritableImage getLesionProbTemplate() throws IOException
      Returns the built-in lesion probability template image (which has been warped to the same space as the T1-weighted template image).
      Returns:
      the built-in lesion probability template image.
      Throws:
      IOException - if the lesion probability cannot be read.

    • getICBMMSPDHeadTemplate

      public static WritableImage getICBMMSPDHeadTemplate(boolean reverseSlices) throws IOException
      Returns the built-in ICBM proton density weighted head template image.
      Parameters:
      reverseSlices - if the image should be returned with the slice order reversed.
      Returns:
      the built-in ICBM proton density weighted template image.
      Throws:
      IOException - if the template image cannot be read.

    • getICBMMSLesionProbTemplate

      public static WritableImage getICBMMSLesionProbTemplate(boolean reverseSlices) throws IOException
      Returns the built-in MS lesion probability image matched to the ICBM template.
      Parameters:
      reverseSlices - if the image should be returned with the slice order reversed.
      Returns:
      the built-in MS lesion probability template image matched to the ICBM template.
      Throws:
      IOException - if the image cannot be read.

    • getICBMTemplateImage

      public static WritableImage getICBMTemplateImage(WeightingType weightingType) throws IOException
      Returns the built-in ICBM template image of the specified weighting type.
      Parameters:
      weightingType - the type of image weighting for the template.
      Returns:
      the built-in ICBM template image.
      Throws:
      IOException - if the template image cannot be read.

    • getICBMGMProbTemplate

      public static WritableImage getICBMGMProbTemplate() throws IOException
      Returns the built-in ICBM grey-matter probability template image.
      Returns:
      the built-in ICBM grey-matter probability template image.
      Throws:
      IOException - if the ICBM grey-matter probability image cannot be read.

    • getICBMWMProbTemplate

      public static WritableImage getICBMWMProbTemplate() throws IOException
      Returns the built-in ICBM white-matter probability template image.
      Returns:
      the built-in ICBM white-matter probability template image.
      Throws:
      IOException - if the ICBM white-matter probability image cannot be read.

    • getICBMCSFProbTemplate

      public static WritableImage getICBMCSFProbTemplate() throws IOException
      Returns the built-in ICBM csf probability template image.
      Returns:
      the built-in ICBM csf probability template image.
      Throws:
      IOException - if the ICBM csf probability image cannot be read.

    • getICBMLVProbTemplate

      public static WritableImage getICBMLVProbTemplate() throws IOException
      Returns the built-in lateral ICBM ventricle probability template image.
      Returns:
      the built-in lateral ICBM ventricle probability template image.
      Throws:
      IOException - if the ICBM lateral ventricle probability image cannot be read.

    • getICBMLesionProbTemplate

      public static WritableImage getICBMLesionProbTemplate() throws IOException
      Returns the built-in lesion probability template image (which has been warped to the same space as the T1-weighted ICBM template image).
      Returns:
      the built-in lesion probability template image.
      Throws:
      IOException - if the lesion probability cannot be read.

    • getICBMICCMask

      public static WritableImage getICBMICCMask() throws IOException
      Returns the built-in ICBM intra-cranial cavity mask.
      Returns:
      the built-in ICBM intra-cranial cavity mask image.
      Throws:
      IOException - if the ICBM intra-cranial cavity mask image cannot be read.

    • getICBMLabelsImage

      public static WritableImage getICBMLabelsImage() throws IOException
      Returns the built-in ICBM labels image.
      Returns:
      the built-in ICBM labels image.
      Throws:
      IOException - if the ICBM labels image cannot be read.

    • getICBMLabels

      public static Set<ICBMLabel> getICBMLabels() throws IOException
      Returns the built-in ICBM labels.
      Returns:
      the built-in ICBM labels.
      Throws:
      IOException - if the ICBM labels cannot be read.

    • getIccMesh

      public static com.xinapse.geom3d.TessellatedSphere getIccMesh() throws IOException
      Returns a pre-calculated surface mesh of the intra-cranial cavity for any of the template images (the T1, T2 or PD templates).
      Returns:
      a surface mesh of the ICC.
      Throws:
      IOException - if the mesh cannot be found because a jar file is missing, or the mesh is missing from the jar file.