DTI in MNI space

This topic contains 5 replies, has 2 voices, and was last updated by  Anand Joshi 2 months, 2 weeks ago.

  • Author
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  • #635

    LucaF
    Participant

    I want to co-register the BDP results in the MNI space.
    Do you have any suggestions about the software and the procedure that I could use?
    Thanks
    Luca

  • #638

    Anand Joshi
    Moderator

    Hi Luca,
    Can you please describe what you would like to do? The image analysis of diffusion tensors is done by BDP and TrackConnect and you would not need coregistration of the results to the MNI space.
    http://brainsuite.org/tutorials/dtiexercise/
    http://neuroimage.usc.edu/neuro/Resources/TractConnect

    If you do need to transform your data to a common MNI space,
    you can apply inverse map generated by svreg as follows:
    Use svreg_apply_map.sh binary provided with svreg. Here is how I would do this on Linux, though the corresponding binaries are available in Linux, Windows and Mac, so similar command will work.

    /home/ajoshi/BrainSuite16a1/svreg/bin/svreg_apply_map.sh subname.svreg.inv.map.nii.gz fa_map.nii.gz out_fa.nii.gz /home/ajoshi/BrainSuite16a1/svreg/BrainSuiteAtlas1/mri.bfc.nii.gz

    thanks,
    Anand

  • #639

    LucaF
    Participant

    Thanks Anand,
    I need to reconstruct connections from spherical ROI in MNI coordinates from ODF.
    I have to do it at single subject level, but it would be better also to have a mean ODF from all of my subject co-register in the MNI space and then study also connections of the same ROI at population level in an MNI template (for example ICBM152). Do you have any suggestions how I can use the brainsuite output with other software in order to achieve my goal.
    Luca

  • #640

    Anand Joshi
    Moderator

    I think the best way is to demarcate the spherical ROIs on the BrainSuiteAtlas1. If you already have the ROIs in MNI space, then you have to somehow merge them with BrainSuiteAtlas1. BrainSuiteAtlas1 is in MNI space, so it should be easy.
    Make a custom atlas with all the ROIs that you would be using.

    http://brainsuite.org/processing/svreg/creating-custom-atlases/

    And then proceed with the BrainSuite, SVReg and BDP sequences as usual. The new ROIs will be incorporated into your analysis.

    • This reply was modified 6 months, 3 weeks ago by  Anand Joshi.
  • #698

    LucaF
    Participant

    Dear Anand,
    I tried many times, but I noticed that my subject brain is not in the same space as Atlas1. Could you tell me how can coregistered my subject with diffusion and than with BrainsuiteAtlas1?
    Thank you very much,
    Luca

  • #723

    Anand Joshi
    Moderator

    Hi Luca,
    Did you try the command as mentioned above?
    You should run the subject with SVReg and with BrainSuiteAtlas1 as the atlas. Then run
    /home/ajoshi/BrainSuite16a1/svreg/bin/svreg_apply_map.sh subname.svreg.inv.map.nii.gz fa_map.nii.gz out_fa.nii.gz /home/ajoshi/BrainSuite16a1/svreg/BrainSuiteAtlas1/mri.bfc.nii.gz

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