Transform the individual label file to standard space

Forums Forums Surface and Volume Registration (SVReg) Transform the individual label file to standard space

This topic contains 4 replies, has 2 voices, and was last updated by  bokkyuki@usc.edu 4 years, 4 months ago.

  • Author
    Posts
  • #111

    bokkyuki@usc.edu
    Participant

    Hello,

    I tried to transform individual label file to standard atlas space. Could you provide an explanation for this process?

    Thank you,

  • #117

    bokkyuki@usc.edu
    Participant

    Hello, thank you for your reply. I am trying to identify stroke lesion. So I want to make a label of stroke lesion on each individual, and transform the lesion label to standard atlas space to compare the lesions among different stroke patients.

  • #118

    Anand Joshi
    Moderator

    I am not sure what can be done by putting lesions into common space? If you want to perform measurements of lesions, such as size etc, then you can do that in the original space itself.

    If you really have to transform the lesion labels to a common space, then you can do that using the inverse map stored in SVReg directory (subbasename.svreg.inv.map.nii.gz).

    You can use matlab with the utility functions available from

    http://neuroimage.usc.edu/neuro/Resources/BST_SVReg_Utilities
    assuming your subbasename is name of the subject prefix, including path.

    e.g. if your subject file is c:\Users\ajoshi\Downloads\sub01\sub01.nii.gz then subbasename would be c:\Users\ajoshi\Downloads\sub01\sub01

    and

    atlasbasename=C:\Program Files\BrainSuite15b\svreg\BrainSuiteAtlas1\mri

    The following matlab code should do the warping.
    vmap=load_nii_z(‘subbasename.svreg.inv.map.nii.gz’);
    vw=load_nii_z(‘atlasbasename.label.nii.gz’);
    vlab=load_nii_z(‘subbasename.label.nii.gz’)

    vw.img=interp3(vlab.img,vmap.img(:,:,:,2),vmap.img(:,:,:,1),vmap.img(:,:,:,3),’nearest’);

    save_nii(vlab,’warped_labels.nii.gz’);

    • #122

      bokkyuki@usc.edu
      Participant

      Hi,

      Thank you so much for your support. The reason why I am trying to convert the individual image to standard space is to identify the lesion location, and compare the location among participants.

      Anyway, the code is working very well.

  • #115

    Anand Joshi
    Moderator

    Hi, Can you please explain more what you are trying to do? Are you trying to transform the individual anatomy to common atlas space? SVReg performs registration of subject and atlas and warps atlas to match the subject. The labels from warped atlas are then transferred to the subject anatomy. Can you please explain more about what you are trying to do?

    • This reply was modified 4 years, 4 months ago by  Anand Joshi.

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