How to apply fileprefix.svreg.map.nii.gz in other neuroimaging software?

Forums Forums Surface and Volume Registration (SVReg) How to apply fileprefix.svreg.map.nii.gz in other neuroimaging software?

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    • #1535
      cclan
      Participant

      Dear BrainSuite Experts

      Is it possible to apply one of the volume output files of svreg, fileprefix.svreg.map.nii.gz, in other neuroimaging software, such as FNIRT or antsRegistration for normalisation?
      If so, how could this be done?
      Are there specific script of functions to change between the deformation field files used in BrainSuite and in these different programs?

      For instance, if I have a PET parametric image that is already affine-coregistered with the T1 image, how can I utilize the svreg map to warp this PET parametric image into the atlas space?

      Thank you very much!

      Chen-Chia

    • #1536
      Anand Joshi
      Moderator

      You can apply the deformation map stored in that file using svreg_apply_map.sh script that should be in <BrainSuite18a>svreg/bin folder.
      The usage is described here.
      #13 here http://brainsuite.org/processing/svreg/svreg_modules/

      The map in svreg is stored in a slightly different format than the one in fnirt, so svreg_apply_map shoudl be used for the svreg map and FSL’s function for applying maps from fnirt.

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