01/06/2017 at 12:32 AM #1877
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
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, Andy01/10/2017 at 10:01 PM #1899
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 here01/10/2017 at 10:06 PM #1902
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, Andy01/11/2017 at 3:46 AM #1904
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
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
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:
Best, Andy01/15/2017 at 8:50 AM #1915akappParticipant
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
Worked great! Thank you both very much.
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