Apply registrations with ANTs and dHCP

Software Support
1

Hello,

This question will be probably be easily answered by @seanfitz. For the dHCP functional data, I am trying to apply the bold to template transforms with ANTs and the output image is empty. Thanks for pointing out what I am missing here. Trying to register the preproc functional images into 40wk template space:

antsApplyTransforms -d 3 -i sub-CC01236XX16_ses-155830_task-rest_desc-preproc_bold.nii.gz -r ../../../../atlases/anat_common_space/week40_T2w.nii.gz -t ../xfm/sub-CC01236XX16_ses-155830_from-bold_to-extdhcp40wk_mode-image.nii.gz -o test.nii.gz -n NearestNeighbor -v

Many thanks,
Alex

2

Hi,

The transformations were calculated with ANTs, but I think they are converted to FSL-like format. So your command should be:

applywarp -i sub-CC01236XX16_ses-155830_task-rest_desc-preproc_bold.nii.gz -o test.nii.gz -r ../../../../atlases/anat_common_space/week40_T2w.nii.gz -w ../xfm/sub-CC01236XX16_ses-155830_from-bold_to-extdhcp40wk_mode-image.nii.gz --interp=nn

I hope this helps.

Best regards,

Manuel