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Translation in Native Atlas Build

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Translation in Native Atlas Build4

Tagged: Atlases, Native Space

Viewing 9 posts - 1 through 9 (of 9 total)
  • Author
    Posts
  • 01/06/2017 at 12:32 AM #1877
    neuropsyched
    Participant

    When building a native atlas and rendering in 3D I’m getting a large linear translation error that looks like this.

    Has anyone encountered this issue before? Any thoughts?

    Thanks in advance.

    01/06/2017 at 12:42 AM #1878
    andreashorn
    Keymaster

    Hi there,

    two questions:
    1. Did you check co-registration and normalization and did both look correct?
    2. Did you by chance use FNIRT (FSL)? Because it could be that the inverse FSL routine is currently not working correctly.
    -> If not, which normalization method did you use?
    How many preoperative files did you use (i.e. was it only the T1 or is there additional data in your project)?

    Best, Andy

    01/10/2017 at 10:01 PM #1899
    neuropsyched
    Participant

    Hi Andy,

    Coregistration and normalization look good. No FSL routines were used. I used ANTs for coregistration and normalization. I have a single preop mri (anat_t1.nii) and a single postop mri (postop_tra.nii).

    sorry for the broken link. image here

    • This reply was modified 4 years ago by neuropsyched.
    • This reply was modified 4 years ago by neuropsyched.
    01/10/2017 at 10:06 PM #1902
    andreashorn
    Keymaster

    This is really weird.

    What you could do is delete /patient/atlas/native folder and retry to visualize just to make sure this will be generated again as flawed as before.
    If this doesn’t help, if possible, could share the subject with me so I can try to replicate here?

    Best, Andy

    01/11/2017 at 3:46 AM #1904
    neuropsyched
    Participant

    I’ll give it a try and get back to you.

    It almost looks as though the atlas is being registered to the original anat_t1.nii.

    Are the anatomy slices in the 3d viewer taken from the normalized preop images (glanat.nii)? I have Preop MRI selected in the drop down of the Anatomy Slice controller. Is it possible that the atlas is being resliced into the original anat_t1 space?

    01/11/2017 at 3:52 AM #1905
    andreashorn
    Keymaster

    Sure, if you are visualizing in native space, it’s all in native space, i.e. the original anat_t1.nii will be visualized, as well.

    01/11/2017 at 11:58 PM #1907
    andreashorn
    Keymaster

    Hi neuropsyched,

    sorry, I think this really was a visualization bug – it showed the MNI space backdrop but the atlas in native space. Atlas file should be fine, visualization of the backdrop not.

    Please exchange this file:
    https://dl.dropboxusercontent.com/u/18255196/ea_assignbackdrop.m

    Best, Andy

    01/15/2017 at 8:50 AM #1915
    akapp
    Participant

    Hi neuropsyched,

    Try re-setting your axis. It may be that part of the image is just cutoff and that’s why it looks weird.

    You can get your axis limits by plotting all three slices in a separate figure and typing

    V = axis

    Go back to your 3D scene viewer and type this into the command window:

    resultfig = get(gcf);
    % Check that your current figure is correct
    if ~isempty(strfind(resultfig.Name,'Electrode-Scene'))
        axis(V) % re-set your axis
    end

    Hopefully that will fix it. Let me know if you have any problems.

    01/23/2017 at 8:31 PM #1949
    neuropsyched
    Participant

    Worked great! Thank you both very much.

    Native View

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