Description
What happened?
The T2* maps per run outputted by Nibabies for multi-echo data are not aligned with the 2mm NMI anatomicals (see screenshot)
@madisoth suggested that the BOLD-T1w transform step is missing
What command did you use?
singularity run --cleanenv \
-B /nibabies_test_binds/enh_single-anat/nibabies/nibabies/:/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies \
-B /bids_in/:/bids_dir \
-B /nibabies:/output_dir \
-B /derivatives:/derivatives \
-B /work/:/wd \
-B /license.txt:/opt/freesurfer/license.txt \
/nibabies_unstable_10052023a.sif /bids_dir /output_dir participant \
--project-goodvoxels \
--output-spaces MNI152NLin6Asym:res-2 \
--surface-recon-method mcribs \
--omp-nthreads 3 \
--derivatives /derivatives/bibsnet \
--cifti-output 91k \
-vv \
-w /wd \
--fd-radius 35 \
--skip-bids-validation \
--participant-label <>What version of NiBabies are you using?
unstable
Relevant log output
No response
Add any additional information or context about the problem here.
@madisoth provided an intermediate solution:
antsApplyTransforms --default-value 0 --float 1 --input /work/nibabies_23_2_wf/single_subject_01_wf/func_preproc_ses_01_task_restME_run_04_echo_1_wf/bold_t2smap_wf/t2smap_node/T2starmap.nii.gz --interpolation LanczosWindowedSinc --output /T2star/sub-_ses-01_task-restME_run-04_space-real-MNI152NLin6Asym_res-2_T2starmap.nii.gz --reference-image /any/anat/sub-_ses-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz --transform /work/nibabies_23_2_wf/single_subject__01_wf/infant_anat_wf/anat_norm_wf/_template_MNI152NLin6Asym/registration/ants_t1_to_mniComposite.h5 --transform /work/nibabies_23_2_wf/single_subject_ION0005_01_wf/func_preproc_ses_01_task_restME_run_04_echo_1_wf/bold_reg_wf/bbreg_wf/concat_xfm/out_fwd.tfm