I have a question regarding the usage of the ANTs composite transform file (.h5)
included in the fmriprep output.
I have calculated some statistical maps on the bold_space-MNI152NLin2009cAsym
that I want to transform to participant’s T1 space.
For that I am using this command:
antsApplyTransforms -d 4 --float 0 --verbose 1 \ -i dr_stage2_subject00000_Z.nii.gz \ -o dr_stage2_subject00000_Z_T1.nii.gz \ -r sub-01_T1w_preproc.nii.gz \ -t sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5 \ -n NearestNeighbor
This gives the output with the error:
Input scalar image: dr_stage2_subject00000_Z.nii.gz Reference image: sub-01_T1w_preproc.nii.gz Can't read initial transform sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
I am fairly new to ANTs that’s why I want to make sure that what I am doing here is
correct. Any ideas?
Note: I used the -d (dimension) flag with the value 4 here because the statistical maps I want to transform are the 4D melodic outputs with different independent components in each volume.
Can it be that that’s why the command is not working because the original registration is computed between two 3d images (MNI and T1) ?