Bug in mrregister outputting full warp


#1

Hello,

I have used mrregister to register a subjects native FOD image to a template FOD image and this works fine. However, when I use the full warp output by mrregister to warp an ROI into the template FOD it fails because it says a no linear transform can be found. mrregister is failing to output the full warp for the registration. Here are my commands and the resulting error.

mrregister sub1_FODs.nii.gz /crash-work/clint/FOD_template/average_FOD_mrtrix.nii.gz -mask1 new_brain_mask.nii.gz -mask2 /crash-work/clint/FOD_template/template_mask.nii.gz -transformed sub1_warped_mrtrix.nii.gz -nl_warp_full sub1_warp.nii.gz

mrtransform sub1_lesion_new.nii.gz -template /crash-work/clint/FOD_template/average_FOD_mrtrix.nii.gz -warp_full sub1_warp.nii.gz sub1_lesion_mrtix_template.nii.gz -interp nearest -force

mrtransform: [100%] uncompressing image “sub1_warp.nii.gz”
mrtransform: [100%] preloading data for “sub1_warp.nii.gz”
mrtransform: [100%] uncompressing image “sub1_lesion_new.nii.gz”
mrtransform: [100%] preloading data for “sub1_lesion_new.nii.gz”
mrtransform: [100%] compressing image “sub1_lesion_mrtix_template.nii.gz”
mrtransform: [ERROR] no linear transform found in initialisation syn warps image header

MRtrix 3.0_RC2-61-g068b1398


#2

Only .mif images are supported for the full warp, your nifti warp image is missing the linear transformation header entries. Since you don’t seem to have output linear transformation matrices either, you’ll have to repeat the subject to template registration.


#3

Thanks it’s working now